Sharon R. Long

All Publications

• Symbiotic Performance of Sinorhizobium meliloti Lacking ppGpp Depends on the Medicago Host Species MOLECULAR PLANT-MICROBE INTERACTIONS Wippel, K., Long, S. R. 2019; 32 (6): 717?28

  View details for DOI 10.1094/MPMI-11-18-0306-R

  View details for Web of Science ID 000471600100007

• A high-throughput system to identify inhibitors of Candidatus Liberibacter asiaticus transcription regulators. Proceedings of the National Academy of Sciences of the United States of America Barnett, M. J., Solow-Cordero, D. E., Long, S. R. 2019

  Abstract

  Citrus greening disease, also known as huanglongbing (HLB), is the most devastating disease of Citrus worldwide. This incurable disease is caused primarily by the bacterium Candidatus Liberibacter asiaticus and spread by feeding of the Asian Citrus Psyllid, Diaphorina citriCa L. asiaticus cannot be cultured; its growth is restricted to citrus phloem and the psyllid insect. Management of infected trees includes use of broad-spectrum antibiotics, which have disadvantages. Recent work has sought to identify small molecules that inhibit Ca L. asiaticus transcription regulators, based on a premise that at least some regulators control expression of genes necessary for virulence. We describe a synthetic, high-throughput screening system to identify compounds that inhibit activity of Ca L. asiaticus transcription activators LdtR, RpoH, and VisNR. Our system uses the closely related model bacterium, Sinorhizobium meliloti, as a heterologous host for expression of a Ca L. asiaticus transcription activator, the activity of which is detected through expression of an enhanced green fluorescent protein (EGFP) gene fused to a target promoter. We used this system to screen more than 120,000 compounds for compounds that inhibited regulator activity, but not growth. Our screen identified several dozen compounds that inhibit regulator activity in our assay. This work shows that, in addition to providing a means of characterizing Ca L. asiaticus regulators, an S. meliloti host can be used for preliminary identification of candidate inhibitory molecules.

  View details for DOI 10.1073/pnas.1905149116

  View details for PubMedID 31427509

• Genome-wide identification of genes directly regulated by ChvI and a consensus sequence for ChvI binding in Sinorhizobium meliloti MOLECULAR MICROBIOLOGY Ratib, N. R., Sabio, E. Y., Mendoza, C., Barnett, M. J., Clover, S. B., Ortega, J. A., Dela Cruz, F. M., Balderas, D., White, H., Long, S. R., Chen, E. J. 2018; 110 (4): 596?615

  Abstract

  ExoS/ChvI two-component signaling in the nitrogen-fixing ?-proteobacterium Sinorhizobium meliloti is required for symbiosis and regulates exopolysaccharide production, motility, cell envelope integrity and nutrient utilization in free-living bacteria. However, identification of many ExoS/ChvI direct transcriptional target genes has remained elusive. Here, we performed chromatin immunoprecipitation followed by microarray analysis (chIP-chip) to globally identify DNA regions bound by ChvI protein in S. meliloti. We then performed qRT-PCR with chvI mutant strains to test ChvI-dependent expression of genes downstream of the ChvI-bound DNA regions. We identified 64 direct target genes of ChvI, including exoY, rem and chvI itself. We also identified ChvI direct target candidates, like exoR, that are likely controlled by additional regulators. Analysis of upstream sequences from the 64 ChvI direct target genes identified a 15 bp-long consensus sequence. Using electrophoretic mobility shift assays and transcriptional fusions with exoY, SMb21440, SMc00084, SMc01580, chvI, and ropB1, we demonstrated this consensus sequence is important for ChvI binding to DNA and transcription of ChvI direct target genes. Thus, we have comprehensively identified ChvI regulon genes and a 'ChvI box' bound by ChvI. Many ChvI direct target genes may influence the cell envelope, consistent with the critical role of ExoS/ChvI in growth and microbe-host interactions.

  View details for PubMedID 30192418

• Most Sinorhizobium meliloti Extracytoplasmic Function Sigma Factors Control Accessory Functions. mSphere Lang, C., Barnett, M. J., Fisher, R. F., Smith, L. S., Diodati, M. E., Long, S. R. 2018; 3 (5)

  Abstract

  Bacteria must sense alterations in their environment and respond with changes in function and/or structure in order to cope. Extracytoplasmic function sigma factors (ECF sigmas) modulate transcription in response to cellular and environmental signals. The symbiotic nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti carries genes for 11 ECF-like sigmas (RpoE1 to -E10 and FecI). We hypothesized that some of these play a role in mediating the interaction between the bacterium and its plant symbiotic partner. The bacterium senses changes in its immediate environment as it establishes contact with the plant root, initiates invasion of the plant as the root nodule is formed, traverses several root cell layers, and enters plant cortical cells via endocytosis. We used genetics, transcriptomics, and functionality to characterize the entire S. meliloti cohort of ECF sigmas. We discovered new targets for individual sigmas, confirmed others by overexpressing individual ECF sigmas, and identified or confirmed putative promoter motifs for nine of them. We constructed precise deletions of each ECF sigma gene and its demonstrated or putative anti-sigma gene and also a strain in which all 11 ECF sigma and anti-sigma genes were deleted. This all-ECF sigma deletion strain showed no major defects in free-living growth, in Biolog Phenotype MicroArray assays, or in response to multiple stresses. None of the ECF sigmas were required for symbiosis on the host plants Medicago sativa and Medicago truncatula: the strain deleted for all ECF sigma and anti-sigma genes was symbiotically normal.IMPORTANCE Fixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [sigmas]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress.

  View details for PubMedID 30305320

• Most Sinorhizobium meliloti Extracytoplasmic Function Sigma Factors Control Accessory Functions MSPHERE Lang, C., Barnett, M. J., Fisher, R. F., Smith, L. S., Diodati, M. E., Long, S. R. 2018; 3 (5)

  View details for DOI 10.1128/mSphereDirect.00454-18

  View details for Web of Science ID 000449522900038

• Characterization of Novel Plant Symbiosis Mutants Using a New Multiple Gene-Expression Reporter Sinorhizobium meliloti Strain (vol 9, 848, 2018) FRONTIERS IN PLANT SCIENCE Lang, C., Smith, L. S., Haney, C. H., Long, S. R. 2018; 9: 848

  Abstract

  [This corrects the article on p. 76 in vol. 9, PMID: 29467773.].

  View details for PubMedID 29930569

• OxyR-Dependent Transcription Response of Sinorhizobium meliloti to Oxidative Stress JOURNAL OF BACTERIOLOGY Lehman, A. P., Long, S. R. 2018; 200 (7)

  Abstract

  Reactive oxygen species such as peroxides play an important role in plant development, cell wall maturation, and defense responses. During nodulation with the host plant Medicago sativa, Sinorhizobium meliloti cells are exposed to H2O2 in infection threads and developing nodules (R. Santos, D. Hérouart, S. Sigaud, D. Touati, and A. Puppo, Mol Plant Microbe Interact 14:86-89, 2001, https://doi.org/10.1094/MPMI.2001.14.1.86). S. meliloti cells likely also experience oxidative stress, from both internal and external sources, during life in the soil. Here, we present microarray transcription data for S. meliloti wild-type cells compared to a mutant deficient in the key oxidative regulatory protein OxyR, each in response to H2O2 treatment. Several alternative sigma factor genes are upregulated in the response to H2O2; the stress sigma gene rpoE2 shows OxyR-dependent induction by H2O2, while rpoH1 expression is induced by H2O2 irrespective of the oxyR genotype. The activity of the RpoE2 sigma factor in turn causes increased expression of two more sigma factor genes, rpoE5 and rpoH2 Strains with deletions of rpoH1 showed improved survival in H2O2 as well as increased levels of oxyR and total catalase expression. These results imply that ?rpoH1 strains are primed to deal with oxidative stress. This work presents a global view of S. meliloti gene expression changes, and of regulation of those changes, in response to H2O2IMPORTANCE Like all aerobic organisms, the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti experiences oxidative stress throughout its complex life cycle. This report describes the global transcriptional changes that S. meliloti makes in response to H2O2 and the roles of the OxyR transcriptional regulator and the RpoH1 sigma factor in regulating those changes. By understanding the complex regulatory response of S. meliloti to oxidative stress, we may further understand the role that reactive oxygen species play as both stressors and potential signals during symbiosis.

  View details for PubMedID 29358497

  View details for PubMedCentralID PMC5847651

• Characterization of Novel Plant Symbiosis Mutants Using a New Multiple Gene-Expression Reporter Sinorhizobium meliloti Strain FRONTIERS IN PLANT SCIENCE Lang, C., Smith, L. S., Long, S. R. 2018; 9: 76

  Abstract

  The formation of nitrogen fixing root nodules by Medicago truncatula and Sinorhizobium meliloti requires communication between both organisms and coordinated differentiation of plant and bacterial cells. After an initial signal exchange, the bacteria invade the tissue of the growing nodule via plant-derived tubular structures, called infection threads. The bacteria are released from the infection threads into invasion-competent plant cells, where they differentiate into nitrogen-fixing bacteroids. Both organisms undergo dramatic transcriptional, metabolic and morphological changes during nodule development. To identify plant processes that are essential for the formation of nitrogen fixing nodules after nodule development has been initiated, large scale mutageneses have been conducted to discover underlying plant symbiosis genes. Such screens yield numerous uncharacterized plant lines with nitrogen fixation deficient nodules. In this study, we report construction of a S. meliloti strain carrying four distinct reporter constructs to reveal stages of root nodule development. The strain contains a constitutively expressed lacZ reporter construct; a PexoY-mTFP fusion that is expressed in infection threads but not in differentiated bacteroids; a PbacA-mcherry construct that is expressed in infection threads and during bacteroid differentiation; and a PnifH-uidA construct that is expressed during nitrogen fixation. We used this strain together with fluorescence microscopy to study nodule development over time in wild type nodules and to characterize eight plant mutants from a fast neutron bombardment screen. Based on the signal intensity and the localization patterns of the reporter genes, we grouped mutants with similar phenotypes and placed them in a developmental context.

  View details for PubMedID 29467773

• Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides in Sinorhizobium meliloti JOURNAL OF BACTERIOLOGY Barnett, M. J., Long, S. R. 2018; 200 (3)

  View details for DOI 10.1128/JB.00501-17

  View details for Web of Science ID 000419731400003

• Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides in Sinorhizobium meliloti. Journal of bacteriology Barnett, M. J., Long, S. R. 2018; 200 (3)

  Abstract

  Sinorhizobium meliloti is a soil-dwelling alphaproteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important both for adapting to stresses in the soil and for the development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides I (EPS-I; succinoglycan) and II (EPS-II; galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots. Previous genetic screens discovered mutants with impaired EPS production, allowing the delineation of EPS biosynthetic pathways. Here we report on a genetic screen to isolate mutants with mucoid colonial morphologies that suggest EPS overproduction. Screening with Tn5-110, which allows the recovery of both null and upregulation mutants, yielded 47 mucoid mutants, most of which overproduce EPS-I; among the 30 unique genes and intergenic regions identified, 14 have not been associated with EPS production previously. We identified a new protein-coding gene, emmD, which may be involved in the regulation of EPS-I production as part of the EmmABC three-component regulatory circuit. We also identified a mutant defective in EPS-I production, motility, and symbiosis, where Tn5-110 was not responsible for the mutant phenotypes; these phenotypes result from a missense mutation in rpoA corresponding to the domain of the RNA polymerase alpha subunit known to interact with transcription regulators.IMPORTANCE The alphaproteobacterium Sinorhizobium meliloti converts dinitrogen to ammonium while inhabiting specialized plant organs termed root nodules. The transformation of S. meliloti from a free-living soil bacterium to a nitrogen-fixing plant symbiont is a complex developmental process requiring close interaction between the two partners. As the interface between the bacterium and its environment, the S. meliloti cell surface plays a critical role in adaptation to varied soil environments and in interaction with plant hosts. We isolated and characterized S. meliloti mutants with increased production of exopolysaccharides, key cell surface components. Our diverse set of mutants suggests roles for exopolysaccharide production in growth, metabolism, cell division, envelope homeostasis, biofilm formation, stress response, motility, and symbiosis.

  View details for PubMedID 29158240

• LDSS-P: an advanced algorithm to extract functional short motifs associated with coordinated gene expression NUCLEIC ACIDS RESEARCH Ichida, H., Long, S. R. 2016; 44 (11): 5045-5053

  Abstract

  Identifying functional elements in promoter sequences is a major goal in computational and experimental genome biology. Here, we describe an algorithm, Local Distribution of Short Sequences for Prokaryotes (LDSS-P), to identify conserved short motifs located at specific positions in the promoters of co-expressed prokaryotic genes. As a test case, we applied this algorithm to a symbiotic nitrogen-fixing bacterium, Sinorhizobium meliloti The LDSS-P profiles that overlap with the 5' section of the extracytoplasmic function RNA polymerase sigma factor RpoE2 consensus sequences displayed a sharp peak between -34 and -32 from TSS positions. The corresponding genes overlap significantly with RpoE2 targets identified from previous experiments. We further identified several groups of genes that are co-regulated with characterized marker genes. Our data indicate that in S. meliloti, and possibly in other Rhizobiaceae species, the master cell cycle regulator CtrA may recognize an expanded motif (AACCAT), which is positionally shifted from the previously reported CtrA consensus sequence in Caulobacter crescentus Bacterial one-hybrid experiments showed that base substitution in the expanded motif either increase or decrease the binding by CtrA. These results show the effectiveness of LDSS-P as a method to delineate functional promoter elements.

  View details for DOI 10.1093/nar/gkw435

  View details for Web of Science ID 000379753100017

  View details for PubMedID 27190233

  View details for PubMedCentralID PMC4914127

• Contributions of Sinorhizobium meliloti Transcriptional Regulator DksA to Bacterial Growth and Efficient Symbiosis with Medicago sativa. Journal of bacteriology Wippel, K., Long, S. R. 2016; 198 (9): 1374-1383

  Abstract

  The stringent response, mediated by the (p)ppGpp synthetase RelA and the RNA polymerase-binding protein DksA, is triggered by limiting nutrient conditions. For some bacteria, it is involved in regulation of virulence. We investigated the role of two DksA-like proteins from the Gram-negative nitrogen-fixing symbiontSinorhizobium melilotiin free-living culture and in interaction with its host plantMedicago sativa The two paralogs, encoded by the genesSMc00469andSMc00049, differ in the constitution of two major domains required for function in canonical DksA: the DXXDXA motif at the tip of a coiled-coil domain and a zinc finger domain. Using mutant analyses of single, double, and triple deletions forSMc00469(designateddksA),SMc00049, andrelA, we found that the ?dksAmutant but not the ?SMc00049mutant showed impaired growth on minimal medium, reduced nodulation on the host plant, and lower nitrogen fixation activity in early nodules, while itsnodgene expression was normal. The ?relAmutant showed severe pleiotropic phenotypes under all conditions tested. OnlyS. melilotidksAcomplemented the metabolic defects of anEscherichia coli dksAmutant. Modifications of the DXXDXA motif in SMc00049 failed to establish DksA function. Our results imply a role for transcriptional regulator DksA in theS. meliloti-M. sativasymbiosis.The stringent response is a bacterial transcription regulation process triggered upon nutritional stress.Sinorhizobium meliloti, a soil bacterium establishing agriculturally important root nodule symbioses with legume plants, undergoes constant molecular adjustment during host interaction. Analyzing the components of the stringent response in this alphaproteobacterium helps understand molecular control regarding the development of plant interaction. Using mutant analyses, we describe how the lack of DksA influences symbiosis withMedicago sativaand show that a second paralogousS. melilotiprotein cannot substitute for this missing function. This work contributes to the field by showing the similarities and differences ofS. melilotiDksA-like proteins to orthologs from other species, adding information to the diversity of the stringent response regulatory system.

  View details for DOI 10.1128/JB.00013-16

  View details for PubMedID 26883825

  View details for PubMedCentralID PMC4836237

• SnapShot: Signaling in Symbiosis. Cell Long, S. R. 2016; 167 (2): 582?82.e1

  Abstract

  The nitrogen-fixing Rhizobium-legume partnership is presently the best understood of all host-microbe symbioses. Bacterial and plant partners signal across developmental time and space.

  View details for PubMedID 27716511

• Transcriptomic Analysis of Sinorhizobium meliloti and Medicago truncatula Symbiosis Using Nitrogen Fixation-Deficient Nodules MOLECULAR PLANT-MICROBE INTERACTIONS Lang, C., Long, S. R. 2015; 28 (8): 856-868

  Abstract

  The bacterium Sinorhizobium meliloti interacts symbiotically with legume plant hosts such as Medicago truncatula to form nitrogen-fixing root nodules. During symbiosis, plant and bacterial cells differentiate in a coordinated manner, resulting in specialized plant cells that contain nitrogen-fixing bacteroids. Both plant and bacterial genes are required at each developmental stage of symbiosis. We analyzed gene expression in nodules formed by wild-type bacteria on six plant mutants with defects in nitrogen fixation. We observed differential expression of 482 S. meliloti genes with functions in cell envelope homeostasis, cell division, stress response, energy metabolism, and nitrogen fixation. We simultaneously analyzed gene expression in M. truncatula and observed differential regulation of host processes that may trigger bacteroid differentiation and control bacterial infection. Our analyses of developmentally arrested plant mutants indicate that plants use distinct means to control bacterial infection during early and late symbiotic stages.

  View details for DOI 10.1094/MPMI-12-14-0407-R

  View details for Web of Science ID 000359434700002

  View details for PubMedID 25844838

• The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3. Journal of bacteriology Barnett, M. J., Long, S. R. 2015; 197 (10): 1792-1806

  Abstract

  In Sinorhizobium meliloti, three NodD transcriptional regulators activate bacterial nodulation (nod) gene expression. NodD1 and NodD2 require plant compounds to activate nod genes. The NodD3 protein does not require exogenous compounds to activate nod gene expression; instead, another transcriptional regulator, SyrM, activates nodD3 expression. In addition, NodD3 can activate syrM expression. SyrM also activates expression of another gene, syrA, which when overexpressed causes a dramatic increase in exopolysaccharide production. In a previous study, we identified more than 200 genes with altered expression in a strain overexpressing nodD3. In this work, we define the transcriptomes of strains overexpressing syrM or syrA. The syrM, nodD3, and syrA overexpression transcriptomes share similar gene expression changes; analyses imply that nodD3 and syrA are the only targets directly activated by SyrM. We propose that most of the gene expression changes observed when nodD3 is overexpressed are due to NodD3 activation of syrM expression, which in turn stimulates SyrM activation of syrA expression. The subsequent increase in SyrA abundance results in broad changes in gene expression, most likely mediated by the ChvI-ExoS-ExoR regulatory circuit.Symbioses with bacteria are prevalent across the animal and plant kingdoms. Our system of study, the rhizobium-legume symbiosis (Sinorhizobium meliloti and Medicago spp.), involves specific host-microbe signaling, differentiation in both partners, and metabolic exchange of bacterial fixed nitrogen for host photosynthate. During this complex developmental process, both bacteria and plants undergo profound changes in gene expression. The S. meliloti SyrM-NodD3-SyrA and ChvI-ExoS-ExoR regulatory circuits affect gene expression and are important for optimal symbiosis. In this study, we defined the transcriptomes of S. meliloti overexpressing SyrM or SyrA. In addition to identifying new targets of the SyrM-NodD3-SyrA regulatory circuit, our work further suggests how it is linked to the ChvI-ExoS-ExoR regulatory circuit.

  View details for DOI 10.1128/JB.02626-14

  View details for PubMedID 25777671

• Symbiosis: Receptive to infection. Nature Long, S. R. 2015; 523 (7560): 298?99

  View details for PubMedID 26153862

• Exopolysaccharides from Sinorhizobium meliloti Can Protect against H2O2-Dependent Damage JOURNAL OF BACTERIOLOGY Lehman, A. P., Long, S. R. 2013; 195 (23): 5362-5369

  Abstract

  Sinorhizobium meliloti requires exopolysaccharides in order to form a successful nitrogen-fixing symbiosis with Medicago species. Additionally, during early stages of symbiosis, S. meliloti is presented with an oxidative burst that must be overcome. Levels of production of the exopolysaccharides succinoglycan (EPS-I) and galactoglucan (EPS-II) were found to correlate positively with survival in hydrogen peroxide (H2O2). H2O2 damage is dependent on the presence of iron and is mitigated when EPS-I and EPS-II mutants are cocultured with cells expressing either exopolysaccharide. Purified EPS-I is able to decrease in vitro levels of H2O2, and this activity is specific to the symbiotically active low-molecular-weight form of EPS-I. This suggests a potential protective function of exopolysaccharides against H2O2 during early symbiosis.

  View details for DOI 10.1128/JB.00681-13

  View details for Web of Science ID 000327545600014

  View details for PubMedID 24078609

  View details for PubMedCentralID PMC3837946

• Isolation and Characterization of Mutant Sinorhizobium meliloti NodD1 Proteins with Altered Responses to Luteolin JOURNAL OF BACTERIOLOGY Peck, M. C., Fisher, R. F., Bliss, R., Long, S. R. 2013; 195 (16): 3714-3723

  Abstract

  NodD1, a member of the NodD family of LysR-type transcriptional regulators (LTTRs), mediates nodulation (nod) gene expression in the soil bacterium Sinorhizobium meliloti in response to the plant-secreted flavonoid luteolin. We used genetic screens and targeted approaches to identify NodD1 residues that show altered responses to luteolin during the activation of nod gene transcription. Here we report four types of NodD1 mutants. Type I (NodD1 L69F, S104L, D134N, and M193I mutants) displays reduced or no activation of nod gene expression. Type II (NodD1 K205N) is constitutively active but repressed by luteolin. Type III (NodD1 L280F) demonstrates enhanced activity with luteolin compared to that of wild-type NodD1. Type IV (NodD1 D284N) shows moderate constitutive activity yet can still be induced by luteolin. In the absence of luteolin, many mutants display a low binding affinity for nod gene promoter DNA in vitro. Several mutants also show, as does wild-type NodD1, increased affinity for nod gene promoters with added luteolin. All of the NodD1 mutant proteins can homodimerize and heterodimerize with wild-type NodD1. Based on these data and the crystal structures of several LTTRs, we present a structural model of wild-type NodD1, identifying residues important for inducer binding, protein multimerization, and interaction with RNA polymerase at nod gene promoters.

  View details for DOI 10.1128/JB.00309-13

  View details for Web of Science ID 000322226100023

  View details for PubMedID 23772067

  View details for PubMedCentralID PMC3754574

• Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021 BMC GENOMICS Schlueter, J., Reinkensmeier, J., Barnett, M. J., Lang, C., Krol, E., Giegerich, R., Long, S. R., Becker, A. 2013; 14

  Abstract

  Sinorhizobium meliloti is a soil-dwelling ?-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important model organism, global characterization of genetic regulatory circuits has been hampered by a lack of information about transcription and promoters.Using an RNAseq approach and RNA populations representing 16 different growth and stress conditions, we comprehensively mapped S. meliloti transcription start sites (TSS). Our work identified 17,001 TSS that we grouped into six categories based on the genomic context of their transcripts: mRNA (4,430 TSS assigned to 2,657 protein-coding genes), leaderless mRNAs (171), putative mRNAs (425), internal sense transcripts (7,650), antisense RNA (3,720), and trans-encoded sRNAs (605). We used this TSS information to identify transcription factor binding sites and putative promoter sequences recognized by seven of the 15 known S. meliloti ? factors ?70, ?54, ?H1, ?H2, ?E1, ?E2, and ?E9). Altogether, we predicted 2,770 new promoter sequences, including 1,302 located upstream of protein coding genes and 722 located upstream of antisense RNA or trans-encoded sRNA genes. To validate promoter predictions for targets of the general stress response ? factor, RpoE2 (?E2), we identified rpoE2-dependent genes using microarrays and confirmed TSS for a subset of these by 5' RACE mapping.By identifying TSS and promoters on a global scale, our work provides a firm foundation for the continued study of S. meliloti gene expression with relation to gene organization, ? factors and other transcription factors, and regulatory RNAs.

  View details for DOI 10.1186/1471-2164-14-156

  View details for Web of Science ID 000317412400001

  View details for PubMedID 23497287

• Development of Tools for the Biochemical Characterization of the Symbiotic Receptor-Like Kinase DMI2 MOLECULAR PLANT-MICROBE INTERACTIONS Riely, B. K., Larrainzar, E., Haney, C. H., Mun, J., Gil-Quintana, E., Gonzalez, E. M., Yu, H., Tricoli, D., Ehrhardt, D. W., Long, S. R., Cook, D. R. 2013; 26 (2): 216-226

  Abstract

  The Medicago truncatula DMI2 gene encodes a leucine-rich repeat receptor-like kinase that is essential for symbiosis with nitrogen-fixing rhizobia. While phenotypic analyses have provided a description for the host's responses mediated by DMI2, a lack of tools for in vivo biochemical analysis has hampered efforts to elucidate the mechanisms by which DMI2 mediates symbiotic signal transduction. Here, we report stably transformed M. truncatula lines that express a genomic DMI2 construct that is fused to a dual-affinity tag containing three copies of the hemagglutinin epitope and a single StrepII tag (gDMI2:HAST). gDMI2: HAST complements the dmi2-1 mutation, and transgenic plants expressing this construct behave similarly to wild-type plants. We show that the expression patterns of gDMI2:HAST recapitulate those of endogenous DMI2 and that we can detect and purify DMI2:HAST from microsomal root and nodule extracts. Using this line, we show that DMI2 resides in a high-molecular weight complex, which is consistent with our observation that DMI2:GFP localizes to plasma membrane-associated puncta and cytoplasmic vesicles. We further demonstrate that Nod factor (NF) perception increases the abundance of DMI2 vesicles. These tools should be a valuable resource for the Medicago community to dissect the biochemical function of DMI2.

  View details for DOI 10.1094/MPMI-10-11-0276

  View details for Web of Science ID 000314003000007

  View details for PubMedID 23013436

• Dual RpoH Sigma Factors and Transcriptional Plasticity in a Symbiotic Bacterium JOURNAL OF BACTERIOLOGY Barnett, M. J., Bittner, A. N., Toman, C. J., Oke, V., Long, S. R. 2012; 194 (18): 4983-4994

  Abstract

  Sinorhizobium meliloti can live as a soil saprophyte and can engage in a nitrogen-fixing symbiosis with plant roots. To succeed in such diverse environments, the bacteria must continually adjust gene expression. Transcriptional plasticity in eubacteria is often mediated by alternative sigma (?) factors interacting with core RNA polymerase. The S. meliloti genome encodes 14 of these alternative ? factors, including two putative RpoH ("heat shock") ? factors. We used custom Affymetrix symbiosis chips to characterize the global transcriptional response of S. meliloti rpoH1, rpoH2, and rpoH1 rpoH2 mutants during heat shock and stationary-phase growth. Under these conditions, expression of over 300 genes is dependent on rpoH1 and rpoH2. We mapped transcript start sites of 69 rpoH-dependent genes using 5' RACE (5' rapid amplification of cDNA ends), which allowed us to determine putative RpoH1-dependent, RpoH2-dependent, and dual-promoter (RpoH1- and RpoH2-dependent) consensus sequences that were each used to search the genome for other potential direct targets of RpoH. The inferred S. meliloti RpoH promoter consensus sequences share features of Escherichia coli RpoH promoters but lack extended -10 motifs.

  View details for DOI 10.1128/JB.00449-12

  View details for Web of Science ID 000308446100023

  View details for PubMedID 22773790

  View details for PubMedCentralID PMC3430346

• Rhizobial Plasmids That Cause Impaired Symbiotic Nitrogen Fixation and Enhanced Host Invasion MOLECULAR PLANT-MICROBE INTERACTIONS Crook, M. B., Lindsay, D. P., Biggs, M. B., Bentley, J. S., Price, J. C., Clement, S. C., Clement, M. J., Long, S. R., Griffitts, J. S. 2012; 25 (8): 1026-1033

  Abstract

  The genetic rules that dictate legume-rhizobium compatibility have been investigated for decades, but the causes of incompatibility occurring at late stages of the nodulation process are not well understood. An evaluation of naturally diverse legume (genus Medicago) and rhizobium (genus Sinorhizobium) isolates has revealed numerous instances in which Sinorhizobium strains induce and occupy nodules that are only minimally beneficial to certain Medicago hosts. Using these ineffective strain-host pairs, we identified gain-of-compatibility (GOC) rhizobial variants. We show that GOC variants arise by loss of specific large accessory plasmids, which we call HR plasmids due to their effect on symbiotic host range. Transfer of HR plasmids to a symbiotically effective rhizobium strain can convert it to incompatibility, indicating that HR plasmids can act autonomously in diverse strain backgrounds. We provide evidence that HR plasmids may encode machinery for their horizontal transfer. On hosts in which HR plasmids impair N fixation, the plasmids also enhance competitiveness for nodule occupancy, showing that naturally occurring, transferrable accessory genes can convert beneficial rhizobia to a more exploitative lifestyle. This observation raises important questions about agricultural management, the ecological stability of mutualisms, and the genetic factors that distinguish beneficial symbionts from parasites.

  View details for DOI 10.1094/MPMI-02-12-0052-R

  View details for Web of Science ID 000306116300002

  View details for PubMedID 22746823

• The conserved polarity factor PodJ1 impacts multiple cell envelope-associated functions in Sinorhizobium meliloti MOLECULAR MICROBIOLOGY Fields, A. T., Navarrete, C. S., Zare, A. Z., Huang, Z., Mostafavi, M., Lewis, J. C., Rezaeihaghighi, Y., Brezler, B. J., Ray, S., Rizzacasa, A. L., Barnett, M. J., Long, S. R., Chen, E. J., Chen, J. C. 2012; 84 (5): 892-920

  Abstract

  Although diminutive in size, bacteria possess highly diverse and spatially confined cellular structures. Two related alphaproteobacteria, Sinorhizobium meliloti and Caulobacter crescentus, serve as models for investigating the genetic basis of morphological variations. S. meliloti, a symbiont of leguminous plants, synthesizes multiple flagella and no prosthecae, whereas C. crescentus, a freshwater bacterium, has a single polar flagellum and stalk. The podJ gene, originally identified in C. crescentus for its role in polar organelle development, is split into two adjacent open reading frames, podJ1 and podJ2, in S. meliloti. Deletion of podJ1 interferes with flagellar motility, exopolysaccharide production, cell envelope integrity, cell division and normal morphology, but not symbiosis. As in C. crescentus, the S. meliloti PodJ1 protein appears to act as a polarity beacon and localizes to the newer cell pole. Microarray analysis indicates that podJ1 affects the expression of at least 129 genes, the majority of which correspond to observed mutant phenotypes. Together, phenotypic characterization, microarray analysis and suppressor identification suggest that PodJ1 controls a core set of conserved elements, including flagellar and pili genes, the signalling proteins PleC and DivK, and the transcriptional activator TacA, while alternative downstream targets have evolved to suit the distinct lifestyles of individual species.

  View details for DOI 10.1111/j.1365-2958.2012.08064.x

  View details for Web of Science ID 000304301500008

  View details for PubMedID 22553970

  View details for PubMedCentralID PMC3359409

• Pseudonodule Formation by Wild-Type and Symbiotic Mutant Medicago truncatula in Response to Auxin Transport Inhibitors MOLECULAR PLANT-MICROBE INTERACTIONS Rightmyer, A. P., Long, S. R. 2011; 24 (11): 1372-1384

  Abstract

  Rhizobium and allied bacteria form symbiotic nitrogen-fixing nodules on legume roots. Plant hormones play key roles in nodule formation. We treated Medicago truncatula roots with auxin transport inhibitors (ATI) N-(1-naphthyl)phthalamic acid (NPA) and 2,3,5-triiodobenzoic acid (TIBA) to induce the formation of pseudonodules. M. truncatula mutants defective for rhizobial Nod factor signal transduction still formed pseudonodules in response to ATI. However, a M. truncatula ethylene-insensitive supernodulator, sickle 1-1, did not form pseudonodules in response to TIBA, suggesting that the ethylene response pathway is involved in ATI-induced pseudonodule formation. We compared the transcriptional responses of M. truncatula roots treated with ATI to roots inoculated with Sinorhizobium meliloti. Some genes showed consistently parallel expression in ATI-induced and Rhizobium-induced nodules. For other genes, the transcriptional response of M. truncatula roots 1 and 7 days after ATI treatment was in the opposite direction to roots treated with S. meliloti; then, by 21 days, the transcriptional patterns for the two conditions became similar. We silenced 17 genes that were upregulated in both ATI and S. meliloti treatments to determine their effect on nodule formation. Some gene-silenced roots showed a decrease in nodulation efficiency, suggesting a role in nodule formation but not in later nodule functions.

  View details for DOI 10.1094/MPMI-04-11-0103

  View details for Web of Science ID 000296035000013

  View details for PubMedID 21809981

• The ROOT DETERMINED NODULATION1 Gene Regulates Nodule Number in Roots of Medicago truncatula and Defines a Highly Conserved, Uncharacterized Plant Gene Family PLANT PHYSIOLOGY Schnabel, E. L., Kassaw, T. K., Smith, L. S., Marsh, J. F., Oldroyd, G. E., Long, S. R., Frugoli, J. A. 2011; 157 (1): 328-340

  Abstract

  The formation of nitrogen-fixing nodules in legumes is tightly controlled by a long-distance signaling system in which nodulating roots signal to shoot tissues to suppress further nodulation. A screen for supernodulating Medicago truncatula mutants defective in this regulatory behavior yielded loss-of-function alleles of a gene designated ROOT DETERMINED NODULATION1 (RDN1). Grafting experiments demonstrated that RDN1 regulatory function occurs in the roots, not the shoots, and is essential for normal nodule number regulation. The RDN1 gene, Medtr5g089520, was identified by genetic mapping, transcript profiling, and phenotypic rescue by expression of the wild-type gene in rdn1 mutants. A mutation in a putative RDN1 ortholog was also identified in the supernodulating nod3 mutant of pea (Pisum sativum). RDN1 is predicted to encode a 357-amino acid protein of unknown function. The RDN1 promoter drives expression in the vascular cylinder, suggesting RDN1 may be involved in initiating, responding to, or transporting vascular signals. RDN1 is a member of a small, uncharacterized, highly conserved gene family unique to green plants, including algae, that we have named the RDN family.

  View details for DOI 10.1104/pp.111.178756

  View details for Web of Science ID 000294491800026

  View details for PubMedID 21742814

• Symbiotic Rhizobia Bacteria Trigger a Change in Localization and Dynamics of the Medicago truncatula Receptor Kinase LYK3 PLANT CELL Haney, C. H., Riely, B. K., Tricoli, D. M., Cook, D. R., Ehrhardt, D. W., Long, S. R. 2011; 23 (7): 2774-2787

  Abstract

  To form nitrogen-fixing symbioses, legume plants recognize a bacterial signal, Nod Factor (NF). The legume Medicago truncatula has two predicted NF receptors that direct separate downstream responses to its symbiont Sinorhizobium meliloti. NOD FACTOR PERCEPTION encodes a putative low-stringency receptor that is responsible for calcium spiking and transcriptional responses. LYSIN MOTIF RECEPTOR-LIKE KINASE3 (LYK3) encodes a putative high-stringency receptor that mediates bacterial infection. We localized green fluorescent protein (GFP)-tagged LYK3 in M. truncatula and found that it has a punctate distribution at the cell periphery consistent with a plasma membrane or membrane-tethered vesicle localization. In buffer-treated control roots, LYK3:GFP puncta are dynamic. After inoculation with compatible S. meliloti, LYK3:GFP puncta are relatively stable. We show that increased LYK3:GFP stability depends on bacterial NF and NF structure but that NF is not sufficient for the change in LYK3:GFP dynamics. In uninoculated root hairs, LYK3:GFP has little codistribution with mCherry-tagged FLOTILLIN4 (FLOT4), another punctate plasma membrane-associated protein required for infection. In inoculated root hairs, we observed an increase in FLOT4:mCherry and LYK3:GFP colocalization; both proteins localize to positionally stable puncta. We also demonstrate that the localization of tagged FLOT4 is altered in plants carrying a mutation that inactivates the kinase domain of LYK3. Our work indicates that LYK3 protein localization and dynamics are altered in response to symbiotic bacteria.

  View details for DOI 10.1105/tpc.111.086389

  View details for Web of Science ID 000294164300027

  View details for PubMedID 21742993

  View details for PubMedCentralID PMC3226205

• Employing Site-Specific Recombination for Conditional Genetic Analysis in Sinorhizobium meliloti APPLIED AND ENVIRONMENTAL MICROBIOLOGY Harrison, C. L., Crook, M. B., Peco, G., Long, S. R., Griffitts, J. S. 2011; 77 (12): 3916-3922

  Abstract

  The ability to remove a genetic function from an organism with good temporal resolution is crucial for characterizing essential genes or genes that act in complex developmental programs. The rhizobium-legume symbiosis involves an elaborate two-organism interaction requiring multiple levels of signal exchange. As an important step toward probing rhizobium genetic functions with temporal resolution, we present the development of a conditional gene deletion system in Sinorhizobium meliloti that employs Cre/loxP site-specific recombination. This system enables chemically inducible and irreversible gene deletion or gene upregulation. Recombinase-mediated excision events can be positively or negatively selected or monitored by a colorimetric assay. The system may be adaptable to various bacterial species, in which recombinase activity may be placed under the control of diverse user-defined promoters. This system also shows promise for uses in promoter trapping and biosensing applications.

  View details for DOI 10.1128/AEM.00544-11

  View details for Web of Science ID 000291341800002

  View details for PubMedID 21515717

• COMPETENCIES IN PREMEDICAL AND MEDICAL EDUCATION the AAMC-HHMI Report PERSPECTIVES IN BIOLOGY AND MEDICINE Alpern, R. J., Belitsky, R., Long, S. 2011; 54 (1): 30-35

  Abstract

  One hundred years ago, Flexner emphasized the importance of science in medicine and medical education. Over the subsequent years, science education in the premedical and medical curricula has changed little, in spite of the vast changes in the biomedical sciences. The National Research Council, in their report Bio 2010, noted that the premedical curriculum caused many students to lose interest in medicine and in the biological sciences in general. Many medical students and physicians have come to view the premedical curriculum as of limited relevance to medicine and designed more as a screening mechanism for medical school admission. To address this, the Association of American Medical Colleges and the Howard Hughes Medical Institute formed a committee to evaluate the premedical and medical school science curricula. The committee made a number of recommendations that are summarized in this essay. Most important were that competencies replace course requirements and that the physical sciences and mathematics be better integrated with the biological sciences and medicine. The goal is that all physicians possess a strong scientific knowledge base and come to appreciate the importance of this to the practice of medicine. While science education needs to evolve, Flexner's vision is as relevant today as it was 100 years ago.

  View details for Web of Science ID 000286695400006

  View details for PubMedID 21399381

• Transcript profiling in M. truncatula lss and sunn-1 mutants reveals different expression profiles despite disrupted SUNN gene function in both mutants. Plant signaling & behavior Schnabel, E., Smith, L., Long, S., Frugoli, J. 2010; 5 (12): 1657-1659

  Abstract

  A novel autoregulation of nodulation locus in Medicago truncatula, lss, silences the SUNN gene thorough a cis-acting mechanism. Microarray analysis was performed on the Affymetrix Gene Chip® Medicago Genome Array with cDNA isolated from seven-day-old seedlings of wild type, sunn-1 and lss plants. The results suggest that in lss plants expression of only a few dozen genes differs significantly from wild type while in sunn-1 plants expression of several hundred genes represented by over 800 probe sets is altered. These results suggest that the kinase domain modification caused by the sunn-1 mutation alters the receptor's influence on gene expression and that these differences are present even in the absence of nodulation.

  View details for PubMedID 21150299

• Conservation in Function of a SCAR/WAVE Component During Infection Thread and Root Hair Growth in Medicago truncatula MOLECULAR PLANT-MICROBE INTERACTIONS Miyahara, A., Richens, J., Starker, C., Morieri, G., Smith, L., Long, S., Downie, J. A., Oldroyd, G. E. 2010; 23 (12): 1553-1562

  Abstract

  Nitrogen-fixing symbioses of plants are often associated with bacterially infected nodules where nitrogen fixation occurs. The plant host facilitates bacterial infection with the formation of infection threads, unique structures associated with these symbioses, which are invaginations of the host cell with the capability of traversing cellular junctions. Here, we show that the infection thread shares mechanistic similarities to polar-growing cells, because the required for infection thread (RIT) locus of Medicago truncatula has roles in root-hair, trichome, and infection-thread growth. We show that RIT encodes the M. truncatula ortholog of NAP1, a component of the SCAR/WAVE (suppressor of cAMP receptor/WASP-family verprolin homologous protein) complex that regulates actin polymerization, through the activation of ARP2/3. NAP1 of Arabidopsis thaliana functions equivalently to the M. truncatula gene, indicating that the mode of action of NAP1 is functionally conserved across species and that legumes have not evolved a unique functionality for NAP1 during rhizobial colonization. This work highlights the surprising commonality between polar-growing cells and a polar-growing cellular intrusion and reveals important insights into the formation and maintenance of infection-thread development.

  View details for DOI 10.1094/MPMI-06-10-0144

  View details for Web of Science ID 000284304200004

  View details for PubMedID 20731530

• The lss Supernodulation Mutant of Medicago truncatula Reduces Expression of the SUNN Gene PLANT PHYSIOLOGY Schnabel, E., Mukherjee, A., Smith, L., Kassaw, T., Long, S., Frugoli, J. 2010; 154 (3): 1390-1402

  Abstract

  The number of nodules that form in a legume when interacting with compatible rhizobia is regulated by the plant. We report the identification of a mutant in nodule regulation in Medicago truncatula, like sunn supernodulator (lss), which displays shoot-controlled supernodulation and short roots, similar to sunn mutants. In contrast with the sunn-1 mutant, nodulation in the lss mutant is more extensive and is less sensitive to nitrate and ethylene, resembling the sunn-4 presumed null allele phenotype. Although the lss locus maps to the SUNN region of linkage group 4 and sunn and lss do not complement each other, there is no mutation in the genomic copy of the SUNN gene or in the 15-kb surrounding region in the lss mutant. However, expression of the SUNN gene in the shoots of lss plants is greatly reduced compared with wild-type plants. Analysis of cDNA from plants heterozygous for lss indicates that lss is a cis-acting factor affecting the expression of SUNN, and documented reversion events show it to be unstable, suggesting a possible reversible DNA rearrangement or an epigenetic change in the lss mutant. Assessment of the SUNN promoter revealed low levels of cytosine methylation in the 700-bp region proximal to the predicted transcription start site in both wild-type and lss plants, indicating that promoter hypermethylation is not responsible for the suppression of SUNN expression in lss. Thus, lss represents either a distal novel locus within the mapped region affecting SUNN expression or an uncharacterized epigenetic modification at the SUNN locus.

  View details for DOI 10.1104/pp.110.164889

  View details for Web of Science ID 000283710300032

  View details for PubMedID 20861425

• Role of the Sinorhizobium meliloti Global Regulator Hfp in Gene Regulation and Symbiosis MOLECULAR PLANT-MICROBE INTERACTIONS Gao, M., Barnett, M. J., Long, S. R., Teplitski, M. 2010; 23 (4): 355-365

  Abstract

  The RNA-binding protein Hfq is a global regulator which controls diverse cellular processes in bacteria. To begin understanding the role of Hfq in the Sinorhizobium meliloti-Medicago truncatula nitrogen-fixing symbiosis, we defined free-living and symbiotic phenotypes of an hfq mutant. Over 500 transcripts were differentially accumulated in the hfq mutant of S. meliloti Rm1021 when grown in a shaking culture. Consistent with transcriptome-wide changes, the hfq mutant displayed dramatic alterations in metabolism of nitrogen-containing compounds, even though its carbon source utilization profiles were nearly identical to the wild type. The hfq mutant had reduced motility and was impaired for growth at alkaline pH. A deletion of hfq resulted in a reduced symbiotic efficiency, although the mutant was still able to initiate nodule development and differentiate into bacteroids.

  View details for DOI 10.1094/MPMI-23-4-0355

  View details for Web of Science ID 000275712000001

  View details for PubMedID 20192823

• A Nodule-Specific Protein Secretory Pathway Required for Nitrogen-Fixing Symbiosis SCIENCE Wang, D., Griffitts, J., Starker, C., Fedorova, E., Limpens, E., Ivanov, S., Bisseling, T., Long, S. 2010; 327 (5969): 1126-1129

  Abstract

  The nitrogen-fixing symbiosis between Sinorhizobium meliloti and its leguminous host plant Medicago truncatula occurs in a specialized root organ called the nodule. Bacteria that are released into plant cells are surrounded by a unique plant membrane compartment termed a symbiosome. We found that in the symbiosis-defective dnf1 mutant of M. truncatula, bacteroid and symbiosome development are blocked. We identified the DNF1 gene as encoding a subunit of a signal peptidase complex that is highly expressed in nodules. By analyzing data from whole-genome expression analysis, we propose that correct symbiosome development in M. truncatula requires the orderly secretion of protein constituents through coordinated up-regulation of a nodule-specific pathway exemplified by DNF1.

  View details for DOI 10.1126/science.1184096

  View details for Web of Science ID 000274901100035

  View details for PubMedID 20185723

• Striking a balance EMBO REPORTS Breithaupt, H., Caddick, S., Long, S. R. 2010; 11 (2): 82-85

  View details for DOI 10.1038/embor.2009.285

  View details for Web of Science ID 000274196600006

• Plant flotillins are required for infection by nitrogen-fixing bacteria PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Haney, C. H., Long, S. R. 2010; 107 (1): 478-483

  Abstract

  To establish compatible rhizobial-legume symbioses, plant roots support bacterial infection via host-derived infection threads (ITs). Here, we report the requirement of plant flotillin-like genes (FLOTs) in Sinorhizobium meliloti infection of its host legume Medicago truncatula. Flotillins in other organisms have roles in viral pathogenesis, endocytosis, and membrane shaping. We identified seven FLOT genes in the M. truncatula genome and show that two, FLOT2 and FLOT4, are strongly up-regulated during early symbiotic events. This up-regulation depends on bacterial Nod Factor and the plant's ability to perceive Nod Factor. Microscopy data suggest that M. truncatula FLOT2 and FLOT4 localize to membrane microdomains. Upon rhizobial inoculation, FLOT4 uniquely becomes localized to the tips of elongating root hairs. Silencing FLOT2 and FLOT4 gene expression reveals a nonredundant requirement for both genes in IT initiation and nodule formation. FLOT4 is uniquely required for IT elongation, and FLOT4 localizes to IT membranes. This work reveals a critical role for plant flotillins in symbiotic bacterial infection.

  View details for DOI 10.1073/pnas.0910081107

  View details for Web of Science ID 000273559200083

  View details for PubMedID 20018678

  View details for PubMedCentralID PMC2806772

• Medical Report's Static Charge Sparks Shock Response SCIENCE Alpern, R., Long, S. 2009; 326 (5959): 1481-1482

  View details for Web of Science ID 000272623600018

• Identification of Direct Transcriptional Target Genes of ExoS/ChvI Two- Component Signaling in Sinorhizobium meliloti JOURNAL OF BACTERIOLOGY Chen, E. J., Fisher, R. F., Perovich, V. M., Sabio, E. A., Long, S. R. 2009; 191 (22): 6833-6842

  Abstract

  The Sinorhizobium meliloti ExoS/ChvI two-component signaling pathway is required for the development of a nitrogen-fixing symbiosis between S. meliloti and its plant hosts. ExoS/ChvI also has important roles in regulating succinoglycan production, biofilm formation, motility, nutrient utilization, and the viability of free-living bacteria. Previous microarray experiments with an exoS96::Tn5 mutant indicated that ExoS/ChvI influences the expression of a few hundred genes, complicating the investigation of which downstream genes respond directly or indirectly to ExoS/ChvI regulation. To focus our study of ExoS/ChvI transcriptional target genes, we performed transcriptional profiling with chvI gain-of-function and reduced-function strains. The chvI gain-of-function strain that we used contains a dominant gain-of-function chvI allele in addition to wild-type chvI. We identified genes that, relative to their expression level in the wild type, are both upregulated in the chvI gain-of-function strain and downregulated in the reduced-function strain or vice versa. Guided by this focused set of genes, we performed gel mobility shift assays and demonstrated that ChvI directly binds the intergenic regions upstream of ropB1, SMb21440, and SMc01580. Furthermore, DNase I footprint analysis of the region upstream of SMc01580 identified a specific DNA sequence bound by ChvI and allowed the discovery of a possible motif for ChvI binding. Our results provide insight into the mechanism of how ExoS/ChvI regulates its downstream targets and lay a foundation for studying this conserved pathway with critical roles in free-living and symbiotic bacteria.

  View details for DOI 10.1128/JB.00734-09

  View details for Web of Science ID 000271195300009

  View details for PubMedID 19749054

  View details for PubMedCentralID PMC2772461

• Science for Future Physicians SCIENCE Long, S., Alpern, R. 2009; 324 (5932): 1241-1241

  View details for DOI 10.1126/science.1176994

  View details for Web of Science ID 000266635100001

  View details for PubMedID 19498132

• A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data JOURNAL OF BIOTECHNOLOGY Becker, A., Barnett, M. J., Capela, D., Dondrup, M., Kamp, P., Krol, E., Linke, B., Rueberg, S., Runte, K., Schroeder, B. K., Weidner, S., Yurgel, S. N., Batut, J., Long, S. R., Puehler, A., Goesmann, A. 2009; 140 (1-2): 45-50

  Abstract

  Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Like other rhizobia, S. meliloti induces nitrogen-fixing root nodules on leguminous plants. This is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. The S. meliloti-Medicago truncatula (barrel medic) association is an important symbiosis model. The S. meliloti genome was published in 2001, and the M. truncatula genome currently is being sequenced. Many new resources and data have been made available since the original S. meliloti genome annotation and an update was needed. In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new web-based portal RhizoGATE. About 1000 annotation updates were made; these included assigning functions to 313 putative proteins, assigning EC numbers to 431 proteins, and identifying 86 new putative genes. RhizoGATE incorporates the new annotion with the S. meliloti GenDB project, a platform that allows annotation updates in real time. Locations of transposon insertions, plasmid integrations, and array probe sequences are available in the GenDB project. RhizoGATE employs the EMMA platform for management and analysis of transcriptome data and the IGetDB data warehouse to integrate a variety of heterogeneous external data sources.

  View details for DOI 10.1016/j.jbiotec.2008.11.006

  View details for Web of Science ID 000265007100007

  View details for PubMedID 19103235

• The periplasmic regulator ExoR inhibits ExoS/ChvI two-component signalling in Sinorhizobium meliloti MOLECULAR MICROBIOLOGY Chen, E. J., Sabio, E. A., Long, S. R. 2008; 69 (5): 1290-1303

  Abstract

  Sinorhizobium meliloti requires ExoS/ChvI two-component signalling to establish a nitrogen-fixing symbiosis with legume hosts. The importance of ExoS/ChvI signalling in microbe-host interactions is underscored by the requirement of ExoS/ChvI orthologues for virulence of the related alpha-proteobacteria Agrobacterium tumefaciens and Brucella abortus. In S. meliloti, ExoS/ChvI is a key regulator of gene expression for exopolysaccharide synthesis, biofilm formation, motility, nutrient utilization and free-living viability. Previously, we showed that the novel conserved regulator ExoR interacts genetically with both ExoS and ChvI, and localizes to the periplasm of S. meliloti. Here, we show that ExoR physically associates with ExoS and that this association is important for regulating ExoS/ChvI signalling. We have identified point mutations in the Sel1-like repeat region of ExoR that disrupt binding to ExoS and cause a dramatic increase in ExoS/ChvI-dependent gene expression. Furthermore, we have found that physical interaction with ExoS stabilizes the ExoR protein. Together, our results indicate that ExoR binds to ExoS in the periplasm of S. meliloti to inhibit ExoS/ChvI activity, and that ExoR represents a novel periplasmic inhibitor of two-component signalling.

  View details for DOI 10.1111/j.1365-2958.2008.06362.x

  View details for Web of Science ID 000258222700017

  View details for PubMedID 18631237

• The Medicago truncatula ortholog of Arabidopsis EIN2, sickle, is a negative regulator of symbiotic and pathogenic microbial associations PLANT JOURNAL Penmetsa, R. V., Uribe, P., Anderson, J., Lichtenzveig, J., Gish, J., Nam, Y. W., Engstrom, E., Xu, K., Sckisel, G., Pereira, M., Baek, J. M., Lopez-Meyer, M., Long, S. R., Harrison, M. J., Singh, K. B., Kiss, G. B., Cook, D. R. 2008; 55 (4): 580-595

  Abstract

  The plant hormone ethylene negatively regulates bacterial infection and nodule formation in legumes in response to symbiotic rhizobia, but the molecular mechanism(s) of ethylene action in symbiosis remain obscure. We have identified and characterized multiple mutant alleles of the MtSkl1 gene, which controls both ethylene sensitivity and nodule numbers. We show that this locus encodes the Medicago truncatula ortholog of the Arabidopsis ethylene signaling protein EIN2. In addition to the well-characterized role of MtSkl1 in rhizobial symbiosis, we show that MtSkl1 is involved in regulating early phases of the symbiotic interaction with mycorrhizal fungi, and in mediating root responses to cytokinin. MtSkl1 also functions in the defense against Rhizoctonia solani and Phytophthora medicaginis, with the latter interaction likely to involve positive feedback amplification of ethylene biosynthesis. Overexpression of the C-terminal domain of MtEIN2 is sufficient to block nodulation responses, consistent with previous reports in Arabidopsis on the activation of ethylene signaling. This same C-terminal region is uniquely conserved throughout the EIN2 homologs of angiosperms, which is consistent with its role as a higher plant-specific innovation essential to EIN2 function.

  View details for DOI 10.1111/j.1365-313X.2008.03531.x

  View details for Web of Science ID 000258287700004

  View details for PubMedID 18435823

• A Sinorhizobium meliloti osmosensory two-component system required for cyclic glucan export and symbiosis MOLECULAR MICROBIOLOGY Griffitts, J. S., Carlyon, R. E., Erickson, J. H., Moulton, J. L., Barnett, M. J., Toman, C. J., Long, S. R. 2008; 69 (2): 479-490

  Abstract

  screen for novel symbiotic mutants of the nitrogen-fixing legume symbiont Sinorhizobium meliloti uncovered a crucial role for the putative response regulator FeuP in the symbiotic infection process. Transcriptome analysis shows that FeuP controls the transcription of at least 16 genes, including ndvA, which encodes an ATP-dependent exporter of cyclic beta glucans. Loss of feuP function gives rise to traits associated with cyclic beta glucan biosynthetic defects, including poor growth and motility under hypoosmotic conditions, and the inability to invade plant tissue during the early stages of symbiotic infection. Analysis of cyclic glucans indicates that the feuP mutant is able to synthesize intracellular cyclic beta glucans, but is unable to export them. Cyclic beta glucan export can be restored to feuP mutant cells by constitutive expression of ndvA; likewise, the symbiotic phenotype of a feuP mutant is rescued by ectopic ndvA expression. We further show that the linked sensor kinase gene, feuQ, is also important for modulating ndvA transcription, and that signalling through the FeuP/FeuQ pathway is responsive to extracellular osmotic conditions, with low osmolarity stimulating ndvA expression.

  View details for DOI 10.1111/j.1365-2958.2008.06304.x

  View details for Web of Science ID 000257569200015

  View details for PubMedID 18630344

• A symbiotic mutant of Sinorhizobium meliloti reveals a novel genetic pathway involving succinoglycan biosynthetic functions MOLECULAR MICROBIOLOGY Griffitts, J. S., Long, S. R. 2008; 67 (6): 1292-1306

  Abstract

  A large-scale screen for symbiotic mutants was carried out using the model root nodulating bacterium Sinorhizobium meliloti. Several mutations in the previously uncharacterized gene msbA2 were isolated. msbA2 encodes a member of the ATP-binding cassette exporter family. This protein family is known to export a wide variety of compounds from bacterial cells. S. meliloti MsbA2 is required for the invasion of nodule tissue, with msbA2 mutant cells stimulating nodule primordium morphogenesis, but failing to invade plant tissue beyond the epidermal cell layer. msbA2 mutants do not exhibit any of the free-living traits often found to correlate with symbiotic defects, suggesting that MsbA2 may take part in a specifically symbiotic function. In strains that overproduce the symbiotic signalling polysaccharide succinoglycan, loss of MsbA2 function is extremely deleterious. This synthetic lethal phenotype can be suppressed by disrupting the succinoglycan biosynthetic genes exoY or exoA. It can also be suppressed by disrupting putative glycosyltransferase-encoding genes found upstream of msbA2. Finally, the symbiotic phenotype of a msbA2 null mutant is suppressed by secondary mutations in these upstream transferase genes, indicating that the msbA2 mutant phenotype may be caused by an inhibitory accumulation of a novel polysaccharide that is synthesized from succinoglycan precursors.

  View details for DOI 10.1111/j.1365-2958.2008.06123.x

  View details for Web of Science ID 000253633000009

  View details for PubMedID 18284576

• ExoR is genetically coupled to the ExoS-Chvl two-component system and located in the periplasm of Sinorhizobium meliloti MOLECULAR MICROBIOLOGY Wells, D. H., Chen, E. J., Fisher, R. F., Long, S. R. 2007; 64 (3): 647-664

  Abstract

  Sinorhizobium meliloti enters into a symbiotic relationship with legume host plants, providing fixed nitrogen in exchange for carbon and amino acids. In S. meliloti, exoR and the exoS-chvI two-component system regulate the biosynthesis of succinoglycan, an exopolysaccharide important for host invasion. It was previously reported that a loss-of-function mutation in exoR and a gain-of-function mutation in exoS cause overproduction of succinoglycan and loss of motility, indicating that ExoR negatively regulates and ExoS-ChvI positively regulates downstream genes. However, a relationship between exoR and exoS-chvI has never been clearly established. By identification and detailed characterization of suppressor strains, we provide genetic evidence that exoR and exoS-chvI control many similar phenotypes. These include succinoglycan production, symbiosis, motility, and previously uncharacterized prototrophy and biofilm formation, all of which are co-ordinately restored by suppressors. We further demonstrate that ExoR is located in the periplasm, suggesting that it functions to regulate downstream genes in a novel manner. In pathogenic bacteria closely related to S. meliloti, exoS-chvI homologues are required for virulence and the regulation of cell envelope composition. Our data suggest that periplasmically localized ExoR and ExoS-ChvI function together in a unique and critical regulatory system associated with both free-living and symbiotic states of S. meliloti.

  View details for DOI 10.1111/j.1365-2958.2007.05680.x

  View details for Web of Science ID 000245991000007

  View details for PubMedID 17462014

• The symbiosis regulator CbrA modulates a complex regulatory network affecting the flagellar apparatus and cell envelope proteins JOURNAL OF BACTERIOLOGY Gibson, K. E., Barnett, M. J., Toman, C. J., Long, S. R., Walker, G. C. 2007; 189 (9): 3591-3602

  Abstract

  Sinorhizobium meliloti participates in a nitrogen-fixing symbiosis with legume plant host species of the genera Medicago, Melilotus, and Trigonella. We recently identified an S. meliloti two-component sensory histidine kinase, CbrA, which is absolutely required to establish a successful symbiosis with Medicago sativa (K. E. Gibson, G. R. Campbell, J. Lloret, and G. C. Walker, J. Bacteriol. 188:4508-4521, 2006). In addition to having a symbiotic defect, the cbrA::Tn5 mutant also has free-living phenotypes that suggest a cell envelope perturbation. Because the bases for these phenotypes are not well understood, we undertook an identification of CbrA-regulated genes. We performed a microarray analysis and compared the transcriptome of the cbrA::Tn5 mutant to that of the wild type. Our global analysis of gene expression identified 162 genes that are differentially expressed in the cbrA::Tn5 mutant, including those encoding proteins involved in motility and chemotaxis, metabolism, and cell envelope function. With regard to those genes with a known role in symbiosis, we observed increased expression of nine genes with overlapping functions in bacterial invasion of its host, which suggests that the mutant could be competent for invasion. Since these CbrA-repressed genes are vital to the invasion process, it appears that down-regulation of CbrA activity is important at this stage of nodule development. In contrast, our previous work showed that CbrA is required for bacteria to establish themselves within the host as nitrogen-fixing symbionts. Therefore, we propose a model in which CbrA functions as a developmental switch during symbiosis.

  View details for DOI 10.1128/JB.01834-06

  View details for Web of Science ID 000246028400028

  View details for PubMedID 17237174

• Medicago truncatula NIN is essential for rhizobial-independent nodule organogenesis induced by autoactive calcium/calmodulin-dependent protein kinase PLANT PHYSIOLOGY Marsh, J. F., Rakocevic, A., Mitra, R. M., Brocard, L., Sun, J., Eschstruth, A., Long, S. R., Schultze, M., Ratet, P., Oldroyd, G. E. 2007; 144 (1): 324-335

  Abstract

  The symbiotic association between legumes and nitrogen-fixing bacteria collectively known as rhizobia results in the formation of a unique plant root organ called the nodule. This process is initiated following the perception of rhizobial nodulation factors by the host plant. Nod factor (NF)-stimulated plant responses, including nodulation-specific gene expression, is mediated by the NF signaling pathway. Plant mutants in this pathway are unable to nodulate. We describe here the cloning and characterization of two mutant alleles of the Medicago truncatula ortholog of the Lotus japonicus and pea (Pisum sativum) NIN gene. The Mtnin mutants undergo excessive root hair curling but are impaired in infection and fail to form nodules following inoculation with Sinorhizobium meliloti. Our investigation of early NF-induced gene expression using the reporter fusion ENOD11::GUS in the Mtnin-1 mutant demonstrates that MtNIN is not essential for early NF signaling but may negatively regulate the spatial pattern of ENOD11 expression. It was recently shown that an autoactive form of a nodulation-specific calcium/calmodulin-dependent protein kinase is sufficient to induce nodule organogenesis in the absence of rhizobia. We show here that MtNIN is essential for autoactive calcium/calmodulin-dependent protein kinase-induced nodule organogenesis. The non-nodulating hcl mutant has a similar phenotype to Mtnin, but we demonstrate that HCL is not required in this process. Based on our data, we suggest that MtNIN functions downstream of the early NF signaling pathway to coordinate and regulate the correct temporal and spatial formation of root nodules.

  View details for DOI 10.1104/pp.106.093021

  View details for Web of Science ID 000246356300027

  View details for PubMedID 17369436

• An ERF transcription factor in Medicago truncatula that is essential for nod factor signal transduction PLANT CELL Middleton, P. H., Jakab, J., Penmetsa, R. V., Starker, C. G., Doll, J., Kalo, P., Prabhu, R., Marsh, J. F., Mitra, R. M., Kereszt, A., Dudas, B., VandenBosch, K., Long, S. R., Cook, D. R., Kiss, G. B., Oldroyd, G. E. 2007; 19 (4): 1221-1234

  Abstract

  Rhizobial bacteria activate the formation of nodules on the appropriate host legume plant, and this requires the bacterial signaling molecule Nod factor. Perception of Nod factor in the plant leads to the activation of a number of rhizobial-induced genes. Putative transcriptional regulators in the GRAS family are known to function in Nod factor signaling, but these proteins have not been shown to be capable of direct DNA binding. Here, we identify an ERF transcription factor, ERF Required for Nodulation (ERN), which contains a highly conserved AP2 DNA binding domain, that is necessary for nodulation. Mutations in this gene block the initiation and development of rhizobial invasion structures, termed infection threads, and thus block nodule invasion by the bacteria. We show that ERN is necessary for Nod factor-induced gene expression and for spontaneous nodulation activated by the calcium- and calmodulin-dependent protein kinase, DMI3, which is a component of the Nod factor signaling pathway. We propose that ERN is a component of the Nod factor signal transduction pathway and functions downstream of DMI3 to activate nodulation gene expression.

  View details for DOI 10.1105/tpc.106.048264

  View details for Web of Science ID 000246802200010

  View details for PubMedID 17449807

• Diverse flavonoids stimulate NodD1 binding to nod gene promoters in Sinorhizobium meliloti JOURNAL OF BACTERIOLOGY Peck, M. C., Fisher, R. F., Long, S. R. 2006; 188 (15): 5417-5427

  Abstract

  NodD1 is a member of the NodD family of LysR-type transcriptional regulators that mediates the expression of nodulation (nod) genes in the soil bacterium Sinorhizobium meliloti. Each species of rhizobia establishes a symbiosis with a limited set of leguminous plants. This host specificity results in part from a NodD-dependent upregulation of nod genes in response to a cocktail of flavonoids in the host plant's root exudates. To demonstrate that NodD is a key determinant of host specificity, we expressed nodD genes from different species of rhizobia in a strain of S. meliloti lacking endogenous NodD activity. We observed that nod gene expression was initiated in response to distinct sets of flavonoid inducers depending on the source of NodD. To better understand the effects of flavonoids on NodD, we assayed the DNA binding activity of S. meliloti NodD1 treated with the flavonoid inducer luteolin. In the presence of luteolin, NodD1 exhibited increased binding to nod gene promoters compared to binding in the absence of luteolin. Surprisingly, although they do not stimulate nod gene expression in S. meliloti, the flavonoids naringenin, eriodictyol, and daidzein also stimulated an increase in the DNA binding affinity of NodD1 to nod gene promoters. In vivo competition assays demonstrate that noninducing flavonoids act as competitive inhibitors of luteolin, suggesting that both inducing and noninducing flavonoids are able to directly bind to NodD1 and mediate conformational changes at nod gene promoters but that only luteolin is capable of promoting the downstream changes necessary for nod gene induction.

  View details for DOI 10.1128/JB.00376-06

  View details for PubMedID 16855231

• Nitrogen fixation mutants of Medicago truncatula fail to support plant and bacterial symbiotic gene expression PLANT PHYSIOLOGY Starker, C. G., Parra-Colmenares, A. L., Smith, L., Mitra, R. M., Long, S. R. 2006; 140 (2): 671-680

  Abstract

  The Rhizobium-legume symbiosis culminates in the exchange of nutrients in the root nodule. Bacteria within the nodule reduce molecular nitrogen for plant use and plants provide bacteria with carbon-containing compounds. Following the initial signaling events that lead to plant infection, little is known about the plant requirements for establishment and maintenance of the symbiosis. We screened 44,000 M2 plants from fast neutron-irradiated Medicago truncatula seeds and isolated eight independent mutant lines that are defective in nitrogen fixation. The eight mutants are monogenic and represent seven complementation groups. To monitor bacterial status in mutant nodules, we assayed Sinorhizobium meliloti symbiosis gene promoters (nodF, exoY, bacA, and nifH) in the defective in nitrogen fixation mutants. Additionally, we used an Affymetrix oligonucleotide microarray to monitor gene expression changes in wild-type and three mutant plants during the nodulation process. These analyses suggest the mutants can be separated into three classes: one class that supports little to no nitrogen fixation and minimal bacterial expression of nifH; another class that supports no nitrogen fixation and minimal bacterial expression of nodF, bacA, and nifH; and a final class that supports low levels of both nitrogen fixation and bacterial nifH expression.

  View details for DOI 10.1104/pp.105.072132

  View details for Web of Science ID 000235215000023

  View details for PubMedID 16407449

  View details for PubMedCentralID PMC1361333

• An anisotropic-viscoplastic model of plant cell morphogenesis by tip growth INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY Dumais, J., Shaw, S. L., Steele, C. R., Long, S. R., Ray, P. M. 2006; 50 (2-3): 209-222

  Abstract

  Plant cell morphogenesis depends critically on two processes: the deposition of new wall material at the cell surface and the mechanical deformation of this material by the stresses resulting from the cell's turgor pressure. We developed a model of plant cell morphogenesis that is a first attempt at integrating these two processes. The model is based on the theories of thin shells and anisotropic viscoplasticity. It includes three sets of equations that give the connection between wall stresses, wall strains and cell geometry. We present an algorithm to solve these equations numerically. Application of this simulation approach to the morphogenesis of tip-growing cells illustrates how the viscoplastic properties of the cell wall affect the shape of the cell at steady state. The same simulation approach was also used to reproduce morphogenetic transients such as the initiation of tip growth and other non-steady changes in cell shape. Finally, we show that the mechanical anisotropy built into the model is required to account for observed patterns of wall expansion in plant cells.

  View details for DOI 10.1387/ijdb.052066jd

  View details for Web of Science ID 000236977200014

  View details for PubMedID 16479489

• Reducing Candida infections during neonatal intensive care: Management choices, infection control, and fluconazole prophylaxis JOURNAL OF PEDIATRICS Long, S. S., Stevenson, D. K. 2005; 147 (2): 135-141

  View details for DOI 10.1016/j.jpeds.2005.04.033

  View details for Web of Science ID 000231785000002

  View details for PubMedID 16126036

• Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators SCIENCE Kalo, P., Gleason, C., Edwards, A., Marsh, J., Mitra, R. M., Hirsch, S., Jakab, J., Sims, S., Long, S. R., Rogers, J., Kiss, G. B., Downie, J. A., Oldroyd, G. E. 2005; 308 (5729): 1786-1789

  Abstract

  Rhizobial bacteria enter a symbiotic interaction with legumes, activating diverse responses in roots through the lipochito oligosaccharide signaling molecule Nod factor. Here, we show that NSP2 from Medicago truncatula encodes a GRAS protein essential for Nod-factor signaling. NSP2 functions downstream of Nod-factor-induced calcium spiking and a calcium/calmodulin-dependent protein kinase. We show that NSP2-GFP expressed from a constitutive promoter is localized to the endoplasmic reticulum/nuclear envelope and relocalizes to the nucleus after Nod-factor elicitation. This work provides evidence that a GRAS protein transduces calcium signals in plants and provides a possible regulator of Nod-factor-inducible gene expression.

  View details for DOI 10.1126/science.1110951

  View details for Web of Science ID 000229926800054

  View details for PubMedID 15961668

• Genetic and molecular analysis of Nod factor signalling in Medicago truncatula 14th International Nitrogen Fixation Congress Debelle, F., Bres, C., Levy, J., Ben Amor, B., Arrighi, J. F., Maillet, F., Ane, J. M., Rosenberg, C., Denarie, J., Shaw, S., Oldroyd, G., Long, S., Penmetsa, R., Cook, D., Geurts, R., Bisseling, T., Duc, G., Gough, C. SPRINGER. 2005: 165?168

  View details for Web of Science ID 000233543700057

• Activation and perception of calcium oscillations during Nod factor signalling 14th International Nitrogen Fixation Congress Gleason, C., Mitra, R., Kalo, P., Galera, C., Gough, C., Denarie, J., Long, S. R., Oldroyd, G. E. SPRINGER. 2005: 169?172

  View details for Web of Science ID 000233543700058

• A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Barnett, M. J., Tolman, C. J., Fisher, R. F., Long, S. R. 2004; 101 (47): 16636-16641

  Abstract

  The soil-dwelling alpha-proteobacterium Sinorhizobium meliloti engages in a symbiosis with legumes: S. meliloti elicits the formation of plant root nodules where it converts dinitrogen to ammonia for use by the plant in exchange for plant photosynthate. To study the coordinate differentiation of S. meliloti and its legume partner during nodule development, we designed a custom Affymetrix GeneChip with the complete S. meliloti genome and approximately 10,000 probe sets for the plant host, Medicago truncatula. Expression profiling of free-living S. meliloti grown with the plant signal molecule luteolin in defined minimal and rich media or of strains altered in the expression of key regulatory proteins (NodD1, NodD3, and RpoN) confirms previous data and identifies previously undescribed regulatory targets. Analyses of root nodules show that this Symbiosis Chip allows the study of gene expression in both partners simultaneously. Our studies detail nearly 5,000 transcriptome changes in symbiosis and document complex transcriptional profiles of S. meliloti in different environments.

  View details for DOI 10.1073/pnas.0407269101

  View details for PubMedID 15542588

• The mechanics of surf ace expansion anisotropy in Medicago truncatula root hairs PLANT PHYSIOLOGY Dumais, J., Long, S. R., Shaw, S. L. 2004; 136 (2): 3266-3275

  Abstract

  Wall expansion in tip-growing cells shows variations according to position and direction. In Medicago truncatula root hairs, wall expansion exhibits a strong meridional gradient with a maximum near the pole of the cell. Root hair cells also show a striking expansion anisotropy, i.e. over most of the dome surface the rate of circumferential wall expansion exceeds the rate of meridional expansion. Concomitant measurements of expansion rates and wall stresses reveal that the extensibility of the cell wall must vary abruptly along the meridian of the cell to maintain the gradient of wall expansion. To determine the mechanical basis of expansion anisotropy, we compared measurements of wall expansion with expansion patterns predicted from wall structural models that were either fully isotropic, transversely isotropic, or fully anisotropic. Our results indicate that a model based on a transversely isotropic wall structure can provide a good fit of the data although a fully anisotropic model offers the best fit overall. We discuss how such mechanical properties could be controlled at the microstructural level.

  View details for DOI 10.1104/pp.104.043752

  View details for Web of Science ID 000224497000034

  View details for PubMedID 15448192

• Six nonnodulating plant mutants defective for Nod factor-induced transcriptional changes associated with the legume-rhizobia symbiosis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Mitra, R. M., Shaw, S. L., Long, S. R. 2004; 101 (27): 10217-10222

  Abstract

  As the legume-rhizobia symbiosis is established, the plant recognizes bacterial-signaling molecules, Nod factors (NFs), and initiates transcriptional and developmental changes within the root to allow bacterial invasion and the construction of a novel organ, the nodule. Plant mutants defective in nodule initiation (Nod(-)) are thought to have defects in NF-signal transduction. However, it is unknown whether WT plants respond to NF-independent bacterial-derived signals or whether Nod(-) plant mutants show defects in global symbiosis-associated gene expression. To characterize plant gene expression in the establishment of the symbiosis, we used an Affymetrix oligonucleotide microarray representing 9,935 Medicago truncatula expressed sequences. We identified 46 sequences that are differentially expressed in plants exposed for 24 h to WT Sinorhizobium meliloti or to the invasion defective S. meliloti mutant, exoA. Eight of these genes encode nucleolar proteins, which are implicated in ribosome biogenesis. We also identified differentially expressed transcription factors, signaling components, defense response proteins, stress response proteins, and several previously uncharacterized genes. NF appears both necessary and sufficient to induce most changes. Six of seven Nod(-) M. truncatula mutants (nfp, dmi1, dmi2, dmi3, nsp1, and nsp2) showed no transcriptional response to S. meliloti, suggesting that the encoded proteins are required for initiating new transcription. The Nod(-) mutant hcl, however, exhibits a reduced transcriptional response to S. meliloti, indicating that the machinery responsible for initiating new transcription is at least partially functional in this mutant.

  View details for DOI 10.1073/pnas.0402186101

  View details for Web of Science ID 000222534200050

  View details for PubMedID 15220482

  View details for PubMedCentralID PMC454190

• A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Mitra, R. M., Gleason, C. A., Edwards, A., Hadfield, J., Downie, J. A., Oldroyd, G. E., Long, S. R. 2004; 101 (13): 4701-4705

  Abstract

  In the establishment of the legume-rhizobial symbiosis, bacterial lipochitooligosaccharide signaling molecules termed Nod factors activate the formation of a novel root organ, the nodule. Nod factors elicit several responses in plant root hair cells, including oscillations in cytoplasmic calcium levels (termed calcium spiking) and alterations in root hair growth. A number of plant mutants with defects in the Nod factor signaling pathway have been identified. One such Medicago truncatula mutant, dmi3, exhibits calcium spiking and root hair swelling in response to Nod factor, but fails to initiate symbiotic gene expression or cell divisions for nodule formation. On the basis of these data, it is thought that the dmi3 mutant perceives Nod factor but fails to transduce the signal downstream of calcium spiking. Additionally, the dmi3 mutant is defective in the symbiosis with mycorrhizal fungi, indicating the importance of the encoded protein in multiple symbioses. We report the identification of the DMI3 gene, using a gene cloning method based on transcript abundance. We show that transcript-based cloning is a valid approach for cloning genes in barley, indicating the value of this technology in crop plants. DMI3 encodes a calcium/calmodulin-dependent protein kinase. Mutants in pea sym9 have phenotypes similar to dmi3 and have alterations in this gene. The DMI3 class of proteins is well conserved among plants that interact with mycorrhizal fungi, but it is less conserved in Arabidopsis thaliana, which does not participate in the mycorrhizal symbiosis.

  View details for DOI 10.1073/pnas.0400595101

  View details for Web of Science ID 000220648700067

  View details for PubMedID 15070781

  View details for PubMedCentralID PMC384810

• Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes SCIENCE Ane, J. M., Kiss, G. B., Riely, B. K., Penmetsa, R. V., Oldroyd, G. E., Ayax, C., Levy, J., Debelle, F., Baek, J. M., Kalo, P., Rosenberg, C., Roe, B. A., Long, S. R., Denarie, J., Cook, D. R. 2004; 303 (5662): 1364-1367

  Abstract

  Legumes form symbiotic associations with both mycorrhizal fungi and nitrogen-fixing soil bacteria called rhizobia. Several of the plant genes required for transduction of rhizobial signals, the Nod factors, are also necessary for mycorrhizal symbiosis. Here, we describe the cloning and characterization of one such gene from the legume Medicago truncatula. The DMI1 (does not make infections) gene encodes a novel protein with low global similarity to a ligand-gated cation channel domain of archaea. The protein is highly conserved in angiosperms and ancestral to land plants. We suggest that DMI1 represents an ancient plant-specific innovation, potentially enabling mycorrhizal associations.

  View details for DOI 10.1126/science.1092986

  View details for Web of Science ID 000189238600050

  View details for PubMedID 14963334

• Plant and bacterial symbiotic mutants define three transcriptionally distinct stages in the development of the Medicago truncatula/Sinorhizobium meliloti symbiosis PLANT PHYSIOLOGY Mitra, R. M., Long, S. R. 2004; 134 (2): 595-604

  Abstract

  In the Medicago truncatula/Sinorhizobium meliloti symbiosis, the plant undergoes a series of developmental changes simultaneously, creating a root nodule and allowing bacterial entry and differentiation. Our studies of plant genes reveal novel transcriptional regulation during the establishment of the symbiosis and identify molecular markers that distinguish classes of plant and bacterial symbiotic mutants. We have identified three symbiotically regulated plant genes encoding a beta,1-3 endoglucanase (MtBGLU1), a lectin (MtLEC4), and a cysteine-containing protein (MtN31). MtBGLU1 is down-regulated in the plant 24 h after exposure to the bacterial signal, Nod factor. The non-nodulating plant mutant dmi1 is defective in the ability to down-regulate MtBGLU1. MtLEC4 and MtN31 are induced 1 and 2 weeks after bacterial inoculation, respectively. We examined the regulation of these two genes and three previously identified genes (MtCAM1, ENOD2, and MtLB1) in plant symbiotic mutants and wild-type plants inoculated with bacterial symbiotic mutants. Plant (bit1, rit1, and Mtsym1) and bacterial (exoA and exoH) mutants with defects in the initial stages of invasion are unable to induce MtLEC4, MtN31, MtCAM1, ENOD2, and MtLB1. Bacterial mutants (fixJ and nifD) and a subset of plant mutants (dnf2, dnf3, dnf4, dnf6, and dnf7) defective for nitrogen fixation induce the above genes. The bacA bacterial mutant, which senesces upon deposition into plant cells, and two plant mutants with defects in nitrogen fixation (dnf1 and dnf5) induce MtLEC4 and ENOD2 but not MtN31, MtCAM1, or MtLB1. These data suggest the presence of at least three transcriptionally distinct developmental stages during invasion of M. truncatula by S. meliloti.

  View details for DOI 10.1104/pp.103.031518

  View details for Web of Science ID 000189108100006

  View details for PubMedID 14739349

  View details for PubMedCentralID PMC344536

• Mutations in rpo-BC suppress the defects of a Sinorhizobium meliloti relA mutant JOURNAL OF BACTERIOLOGY Wells, D. H., Long, S. R. 2003; 185 (18): 5602-5610

  Abstract

  The nitrogen-fixing symbiosis between Sinorhizobium meliloti and Medicago sativa requires complex physiological adaptation by both partners. One method by which bacteria coordinately control physiological adaptation is the stringent response, which is triggered by the presence of the nucleotide guanosine tetraphosphate (ppGpp). ppGpp, produced by the RelA enzyme, is thought to bind to and alter the ability of RNA polymerase (RNAP) to initiate and elongate transcription and affect the affinity of the core enzyme for various sigma factors. An S. meliloti relA mutant which cannot produce ppGpp was previously shown to be defective in the ability to form nodules. This mutant also overproduces a symbiotically necessary exopolysaccharide called succinoglycan. The work presented here encompasses the analysis of suppressor mutants, isolated from host plants, that suppress the symbiotic defects of the relA mutant. All suppressor mutations are extragenic and map to either rpoB or rpoC, which encode the beta and beta' subunits of RNAP. Phenotypic, structural, and gene expression analyses reveal that suppressor mutants can be divided into two classes; one is specific in its effect on stringent response-regulated genes and shares striking similarity with suppressor mutants of Escherichia coli strains that lack ppGpp, and another reduces transcription of all genes tested in comparison to that in the relA parent strain. Our findings indicate that the ability to successfully establish symbiosis is tightly coupled with the bacteria's ability to undergo global physiological adjustment via the stringent response.

  View details for DOI 10.1128/JB.185.18.5602-5610.2003

  View details for Web of Science ID 000185181500030

  View details for PubMedID 12949113

  View details for PubMedCentralID PMC193748

• Nod factor inhibition of reactive oxygen efflux in a host legume PLANT PHYSIOLOGY Shaw, S. L., Long, S. R. 2003; 132 (4): 2196-2204

  Abstract

  Hydrogen peroxide (H(2)O(2)) efflux was measured from Medicago truncatula root segments exposed to purified Nod factor and to poly-GalUA (PGA) heptamers. Nod factor, at concentrations > 100 pM, reduced H(2)O(2) efflux rates to 60% of baseline levels beginning 20 to 30 min after exposure, whereas the PGA elicitor, at > 75 nM, caused a rapid increase in H(2)O(2) efflux to >200% of baseline rates. Pretreatment of plants with Nod factor alters the effect of PGA by limiting the maximum H(2)O(2) efflux rate to 125% of that observed for untreated plants. Two Nod factor-related compounds showed no ability to modulate peroxide efflux, and tomato (Lycopersicon esculentum), a nonlegume, showed no response to 1 nM Nod factor. Seven M. truncatula mutants, lacking the ability to make nodules, were tested for Nod factor effects on H(2)O(2) efflux. The nfp mutant was blocked for suppression of peroxide efflux, whereas the dmi1 and dmi2 mutants, previously shown to be blocked for early Nod factor responses, showed a wild-type peroxide efflux modulation. These data demonstrate that exposure to Nod factor suppresses the activity of the reactive oxygen-generating system used for plant defense responses.

  View details for DOI 10.1104/pp.103.021113

  View details for PubMedID 12913174

  View details for PubMedCentralID PMC181303

• The NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation PLANT JOURNAL Ben Amor, B., Shaw, S. L., Oldroyd, G. E., Maillet, F., Penmetsa, R. V., Cook, D., Long, S. R., Denarie, J., Gough, C. 2003; 34 (4): 495-506

  Abstract

  Establishment of the Rhizobium-legume symbiosis depends on a molecular dialogue, in which rhizobial nodulation (Nod) factors act as symbiotic signals, playing a key role in the control of specificity of infection and nodule formation. Using nodulation-defective (Nod-) mutants of Medicago truncatula to study the mechanisms controlling Nod factor perception and signalling, we have previously identified five genes that control components of a Nod factor-activated signal transduction pathway. Characterisation of a new M. truncatula Nod- mutant led to the identification of the Nod Factor Perception (NFP) locus. The nfp mutant has a novel phenotype among Nod- mutants of M. truncatula, as it does not respond to Nod factors by any of the responses tested. The nfp mutant thus shows no rapid calcium flux, the earliest detectable Nod factor response of wild-type plants, and no root hair deformation. The nfp mutant is also deficient in Nod factor-induced calcium spiking and early nodulin gene expression. While certain genes controlling Nod factor signal transduction also control the establishment of an arbuscular mycorrhizal symbiosis, the nfp mutant shows a wild-type mycorrhizal phenotype. These data indicate that the NFP locus controls an early step of Nod factor signal transduction, upstream of previously identified genes and specific to nodulation.

  View details for Web of Science ID 000182785300009

  View details for PubMedID 12753588

• Rhizobium-induced calcium spiking in Lotus japonicus MOLECULAR PLANT-MICROBE INTERACTIONS Harris, J. M., Wais, R., Long, S. R. 2003; 16 (4): 335-341

  Abstract

  Legumes and rhizobium bacteria form a symbiosis that results in the development of nitrogen-fixing nodules on the root of the host plant. The earliest plant developmental changes are triggered by bacterially produced nodulation (Nod) factors. Within minutes of exposure to Nod factors, sharp oscillations in cytoplasmic calcium levels (calcium spiking) occur in epidermal cells of several closely related legumes. We found that Lotus japonicus, a legume that follows an alternate developmental pathway, responds to both its bacterial partner and to the purified bacterial signal with calcium spiking. Thus, calcium spiking is not restricted to a particular pathway of nodule development and may be a general component of the response of host legumes to their bacterial partner. Using Nod factor-induced calcium spiking as a tool to identify mutants blocked early in the response to Nod factor, we show that the L. japonicus Ljsym22-1 mutant but not the Ljsym30 mutant fails to respond to Nod factor with calcium spiking.

  View details for Web of Science ID 000181728400008

  View details for PubMedID 12744462

• Identification and characterization of nodulation-signaling pathway 2, a gene of Medicago truncatula involved in Nod factor signaling PLANT PHYSIOLOGY Oldroyd, G. E., Long, S. R. 2003; 131 (3): 1027-1032

  Abstract

  Bacterially derived Nod factor is critical in the establishment of the legume/rhizobia symbiosis. Understanding the mechanisms of Nod factor perception and signal transduction in the plant will greatly advance our understanding of this complex interaction. Here, we describe the identification of a new locus, nodulation-signaling pathway 2 (NSP2), of Medicago truncatula that is involved in Nod factor signaling. Mutants at this locus are blocked for Nod factor-induced gene expression and show a reduced root hair deformation response. nsp2 plants also show a complete absence of infection and cortical cell division following Sinorhizobium meliloti inoculation. Nod factor-induced calcium spiking, one of the earliest responses tested, is still functional in these mutant plants. We conclude that the gene NSP2 is a component of the Nod factor signal transduction pathway that lies downstream of the calcium-spiking response.

  View details for DOI 10.1104/pp.102.010710

  View details for Web of Science ID 000185076100020

  View details for PubMedID 12644655

  View details for PubMedCentralID PMC166868

• Nod factor elicits two separable calcium responses in Medicago truncatula root hair cells PLANT PHYSIOLOGY Shaw, S. L., Long, S. R. 2003; 131 (3): 976-984

  Abstract

  Modulation of intracellular calcium levels plays a key role in the transduction of many biological signals. Here, we characterize early calcium responses of wild-type and mutant Medicago truncatula plants to nodulation factors produced by the bacterial symbiont Sinorhizobium meliloti using a dual-dye ratiometric imaging technique. When presented with 1 nM Nod factor, root hair cells exhibited only the previously described calcium spiking response initiating 10 min after application. Nod factor (10 nM) elicited an immediate increase in calcium levels that was temporally earlier and spatially distinct from calcium spikes occurring later in the same cell. Nod factor analogs that were structurally related, applied at 10 nM, failed to initiate this calcium flux response. Cells induced to spike with low Nod factor concentrations show a calcium flux response when Nod factor is raised from 1 to 10 nM. Plant mutants previously shown to be deficient for the calcium spiking response (dmi1 and dmi2) exhibited an immediate, truncated calcium flux with 10 nM Nod factor, demonstrating a competence to respond to Nod factor but an impaired ability to generate a full biphasic response. These results demonstrate that the legume root hair cell exhibits two independent calcium responses to Nod factor triggered at different agonist concentrations and suggests an early branch point in the Nod factor signal transduction pathway.

  View details for DOI 10.1104/pp.005546

  View details for Web of Science ID 000185076100015

  View details for PubMedID 12644650

  View details for PubMedCentralID PMC166863

• Dual genetic pathways controlling nodule number in Medicago truncatula PLANT PHYSIOLOGY Penmetsa, R. V., Frugoli, J. A., Smith, L. S., Long, S. R., Cook, D. R. 2003; 131 (3): 998-1008

  Abstract

  We report the isolation and characterization of a new Medicago truncatula hyper-nodulation mutant, designated sunn (super numeric nodules). Similar to the previously described ethylene-insensitive mutant sickle, sunn exhibits a 10-fold increase in the number of nodules within the primary nodulation zone. Despite this general similarity, these two mutants are readily distinguished based on anatomical, genetic, physiological, and molecular criteria. In contrast to sickle, where insensitivity to ethylene is thought to be causal to the hyper-nodulation phenotype (R.V. Penmetsa, D.R. Cook [1997] Science 275: 527-530), nodulation in sunn is normally sensitive to ethylene. Nevertheless, sunn exhibits seedling root growth that is insensitive to ethylene, although other aspects of the ethylene triple response are normal; these observations suggest that hormonal responses might condition the sunn phenotype in a manner distinct from sickle. The two mutants also differ in the anatomy of the nodulation zone: Successful infection and nodule development in sunn occur predominantly opposite xylem poles, similar to wild type. In sickle, however, both infection and nodulation occur randomly throughout the circumference of the developing root. Genetic analysis indicates that sunn and sickle correspond to separate and unlinked loci, whereas the sunn/skl double mutant exhibits a novel and additive super-nodulation phenotype. Taken together, these results suggest a working hypothesis wherein sunn and sickle define distinct genetic pathways, with skl regulating the number and distribution of successful infection events, and sunn regulating nodule organogenesis.

  View details for DOI 10.1104/pp.015677

  View details for Web of Science ID 000185076100017

  View details for PubMedID 12644652

  View details for PubMedCentralID PMC166865

• A Sinorhizobium meliloti lipopolysaccharide mutant altered in cell surface sulfation JOURNAL OF BACTERIOLOGY Keating, D. H., Willits, M. G., Long, S. R. 2002; 184 (23): 6681-6689

  Abstract

  The Rhizobium-legume symbiosis involves the formation of a novel plant organ, the nodule, in which intracellular bacteria reduce molecular dinitrogen in exchange for plant photosynthates. Nodule development requires a bacterial signal referred to as Nod factor, which in Sinorhizobium meliloti is a beta-(1,4)-linked tetramer of N-acetylglucosamine containing N-acyl and O-acetyl modifications at the nonreducing end and a critical 6-O-sulfate at the reducing end. This sulfate modification requires the action of three gene products: nodH, which catalyzes the sulfonyl transfer, and nodPQ, which produce the activated form of sulfate, 3'-phosphoadenosine-5'-phosphosulfate. It was previously reported that S. meliloti cell surface polysaccharides are also covalently modified by sulfate in a reaction dependent on NodPQ. We have further characterized this unique form of bacterial carbohydrate modification. Our studies have determined that one of the nodPQ mutant strains used in the initial study of sulfation of cell surface harbored a second unlinked mutation. We cloned the gene affected by this mutation (referred to as lps-212) and found it to be an allele of lpsL, a gene previously predicted to encode a UDP-glucuronic acid epimerase. We demonstrated that lpsL encoded a UDP-glucuronic acid epimerase activity that was reduced in the lps-212 mutant. The lps-212 mutation resulted in an altered lipopolysaccharide structure that was reduced in sulfate modification in vitro and in vivo. Finally, we determined that the lps-212 mutation resulted in a reduced ability to elicit the formation of plant nodules and by altered infection thread structures that aborted prematurely.

  View details for DOI 10.1128/JB.184.23.6681-6689.2002

  View details for Web of Science ID 000179242600033

  View details for PubMedID 12426356

  View details for PubMedCentralID PMC135449

• Analysis of differences between Sinorhizobium meliloti 1021 and 2011 strains using the host calcium spiking response MOLECULAR PLANT-MICROBE INTERACTIONS Wais, R. J., Wells, D. H., Long, S. R. 2002; 15 (12): 1245-1252

  Abstract

  In the Rhizobium-legume symbiosis, compatible partners recognize each other through an exchange of signals. Plant inducers act together with bacterial transcriptional activators, the NodD proteins, to regulate the expression of bacterial biosynthetic nodulation (nod) genes. These genes direct the synthesis of a lipochito-oligosaccharide signal called Nod factor (NF). NFs elicit an early host response, root hair calcium spiking, that is initiated in root hair cells within 15 min of NF or live Rhizobium inoculation. We used calcium spiking as an assay to compare two closely related strains of Sinorhizobium meliloti, Rm1021 and Rm2011, derived from the same field isolate. We found that the two strains show a kinetic difference in the calcium spiking assay: Rm1021 elicits calcium spiking in host root hairs as rapidly as purified NF, whereas Rm2011 shows a significant delay. This difference can be overcome by raising expression levels of either the NodD transcriptional activators or GroEL, a molecular chaperone that affects expression of the biosynthetic nod genes. We further demonstrate that the delay in triggering calcium spiking exhibited by Rm2011 is correlated with a reduced amount of nod gene expression compared with Rm1021. Therefore, calcium spiking is a useful tool in detecting subtle differences in bacterial gene expression that affect the early stages of the Rhizobium-legume symbiosis.

  View details for Web of Science ID 000179413300007

  View details for PubMedID 12481997

• The RNA polymerase a subunit from Sinorhizobium meliloti can assemble with RNA polymerase subunits from Escherichia coli and function in basal and activated transcription both in vivo and in vitro JOURNAL OF BACTERIOLOGY Peck, M. C., Gaal, T., Fisher, R. F., Gourse, R. L., Long, S. R. 2002; 184 (14): 3808-3814

  Abstract

  Sinorhizobium meliloti, a gram-negative soil bacterium, forms a nitrogen-fixing symbiotic relationship with members of the legume family. To facilitate our studies of transcription in S. meliloti, we cloned and characterized the gene for the alpha subunit of RNA polymerase (RNAP). S. meliloti rpoA encodes a 336-amino-acid, 37-kDa protein. Sequence analysis of the region surrounding rpoA identified six open reading frames that are found in the conserved gene order secY (SecY)-adk (Adk)-rpsM (S13)-rpsK (S11)-rpoA (alpha)-rplQ (L17) found in the alpha-proteobacteria. In vivo, S. meliloti rpoA expressed in Escherichia coli complemented a temperature sensitive mutation in E. coli rpoA, demonstrating that S. meliloti alpha supports RNAP assembly, sequence-specific DNA binding, and interaction with transcriptional activators in the context of E. coli. In vitro, we reconstituted RNAP holoenzyme from S. meliloti alpha and E. coli beta, beta', and sigma subunits. Similar to E. coli RNAP, the hybrid RNAP supported transcription from an E. coli core promoter and responded to both upstream (UP) element- and Fis-dependent transcription activation. We obtained similar results using purified RNAP from S. meliloti. Our results demonstrate that S. meliloti alpha functions are conserved in heterologous host E. coli even though the two alpha subunits are only 51% identical. The ability to utilize E. coli as a heterologous system in which to study the regulation of S. meliloti genes could provide an important tool for our understanding and manipulation of these processes.

  View details for DOI 10.1128/JB.184.14.3808-3814.2002

  View details for PubMedID 12081950

• Activity of Sinorhizobium meliloti NodAB and NodH enzymes on thiochitooligosaccharides JOURNAL OF BACTERIOLOGY Southwick, A. M., Wang, L. X., Long, S. R., Lee, Y. C. 2002; 184 (14): 4039-4043

  Abstract

  Rhizobium bacteria synthesize signal molecules called Nod factors that elicit responses in the legume root during nodulation. Nod factors, modified N-acylated beta-(1,4)-N-acetylglucosamine, are synthesized by the nodulation (nod) gene products. We tested the ability of three Sinorhizobium meliloti nod gene products to modify Nod factor analogs with thio linkages instead of O-glycosidic bonds in the oligosaccharide backbone.

  View details for DOI 10.1128/JB.184.14.4039-4043.2002

  View details for Web of Science ID 000176582200033

  View details for PubMedID 12081977

  View details for PubMedCentralID PMC135183

• Structure-function analysis of nod factor-induced root hair calcium spiking in rhizobium-legume symbiosis PLANT PHYSIOLOGY Wais, R. J., Keating, D. H., Long, S. R. 2002; 129 (1): 211-224

  Abstract

  In the Rhizobium-legume symbiosis, compatible bacteria and host plants interact through an exchange of signals: Host compounds promote the expression of bacterial biosynthetic nod (nodulation) genes leading to the production of a lipochito-oligosaccharide signal, the Nod factor (NF). The particular array of nod genes carried by a given species of Rhizobium determines the NF structure synthesized and defines the range of legume hosts by which the bacterium is recognized. Purified NF can induce early host responses even in the absence of live Rhizobium One of the earliest known host responses to NF is an oscillatory behavior of cytoplasmic calcium, or calcium spiking, in root hair cells, initially observed in Medicago spp. and subsequently characterized in four other genera (D.W. Ehrhardt, R. Wais, S.R. Long [1996] Cell 85: 673-681; S.A. Walker, V. Viprey, J.A. Downie [2000] Proc Natl Acad Sci USA 97: 13413-13418; D.W. Ehrhardt, J.A. Downie, J. Harris, R.J. Wais, and S.R. Long, unpublished data). We sought to determine whether live Rhizobium trigger a rapid calcium spiking response and whether this response is NF dependent. We show that, in the Sinorhizobium meliloti-Medicago truncatula interaction, bacteria elicit a calcium spiking response that is indistinguishable from the response to purified NF. We determine that calcium spiking is a nod gene-dependent host response. Studies of calcium spiking in M. truncatula and alfalfa (Medicago sativa) also uncovered the possibility of differences in early NF signal transduction. We further demonstrate the sufficiency of the nod genes for inducing calcium spiking by using Escherichia coli BL21 (DE3) engineered to express 11 S. meliloti nod genes.

  View details for DOI 10.1104/pp.010690

  View details for Web of Science ID 000175762000023

  View details for PubMedID 12011352

  View details for PubMedCentralID PMC155885

• Nodulation in legumes (Book Review) NATURE Book Review Authored by: Long, S. R. 2002; 416 (6880): 478-478

  View details for Web of Science ID 000174756500018

• Pharmacological analysis of nod factor-induced calcium spiking in Medicago truncatula. Evidence for the requirement of type IIA calcium pumps and phosphoinositide signaling PLANT PHYSIOLOGY Engstrom, E. M., Ehrhardt, D. W., Mitra, R. M., Long, S. R. 2002; 128 (4): 1390-1401

  Abstract

  Bacterial Nod factors trigger a number of cellular responses in root hairs of compatible legume hosts, which include periodic, transient increases in cytosolic calcium levels, termed calcium spiking. We screened 13 pharmaceutical modulators of eukaryotic signal transduction for effects on Nod factor-induced calcium spiking. The purpose of this screening was 2-fold: to implicate enzymes required for Nod factor-induced calcium spiking in Medicago sp., and to identify inhibitors of calcium spiking suitable for correlating calcium spiking to other Nod factor responses to begin to understand the function of calcium spiking in Nod factor signal transduction. 2-Aminoethoxydiphenylborate, caffeine, cyclopiazonic acid (CPA), 2,5-di-(t-butyl)-1,4-hydroquinone, and U-73122 inhibit Nod factor-induced calcium spiking. CPA and U-73122 are inhibitors of plant type IIA calcium pumps and phospholipase C, respectively, and implicate the requirement for these enzymes in Nod factor-induced calcium spiking. CPA and U-73122 inhibit Nod factor-induced calcium spiking robustly at concentrations with no apparent toxicity to root hairs, making CPA and U-73122 suitable for testing whether calcium spiking is causal to subsequent Nod factor responses.

  View details for DOI 10.1104/pp.010691

  View details for Web of Science ID 000175209900025

  View details for PubMedID 11950987

  View details for PubMedCentralID PMC154266

• The Sinorhizobium meliloti stringent response affects multiple aspects of symbiosis MOLECULAR MICROBIOLOGY Wells, D. H., Long, S. R. 2002; 43 (5): 1115-1127

  Abstract

  Sinorhizobium meliloti and host legumes enter into a nitrogen-fixing, symbiotic relationship triggered by an exchange of signals between bacteria and plant. S. meliloti produces Nod factor, which elicits the formation of nodules on plant roots, and succinoglycan, an exopolysaccharide that allows for bacterial invasion and colonization of the host. The biosynthesis of these molecules is well defined, but the specific regulation of these compounds is not completely understood. Bacteria control complex regulatory networks by the production of ppGpp, the effector molecule of the stringent response, which induces physiological change in response to adverse growth conditions and can also control bacterial development and virulence. Through detailed analysis of an S. meliloti mutant incapable of producing ppGpp, we show that the stringent response is required for nodule formation and regulates the production of succinoglycan. Although it remains unknown whether these phenotypes are connected, we have isolated suppressor strains that restore both defects and potentially identify key downstream regulatory genes. These results indicate that the S. meliloti stringent response has roles in both succinoglycan production and nodule formation and, more importantly, that control of bacterial physiology in response to the plant and surrounding environment is critical to the establishment of a successful symbiosis.

  View details for Web of Science ID 000174774100005

  View details for PubMedID 11918800

• Heterologous expression to assay for plant lectins or receptors PLANT MOLECULAR BIOLOGY REPORTER Southwick, A. M., Long, S. R. 2002; 20 (1): 27-41

  View details for Web of Science ID 000175308000003

• Luteolin and GroESL modulate in vitro activity of NodD JOURNAL OF BACTERIOLOGY Yeh, K. C., Peck, M. C., Long, S. R. 2002; 184 (2): 525-530

  Abstract

  In the early stages of symbiosis between the soil bacterium Sinorhizobium meliloti and its leguminous host plant, alfalfa, bacterial nodulation (nod) genes are controlled by NodD1, NodD2, and NodD3, members of the LysR family of transcriptional regulators, in response to flavonoid and other inducers released by alfalfa. To gain an understanding of the biochemical aspects of this action, epitope-tagged recombinant NodD1 and NodD3 were overexpressed in Escherichia coli. The DNA binding properties of the purified recombinant NodD proteins were indistinguishable from those of NodD isolated from S. meliloti. In addition, the E. coli GroEL chaperonin copurified with the recombinant NodD proteins. In this study, we showed that NodD proteins are in vitro substrates of the GroESL chaperonin system and that their DNA binding activity is modulated by GroESL. This confirmed the earlier genetic implication that the GroESL chaperonin system is essential for the function of these regulators. Increased DNA binding activity by NodD1 in the presence of luteolin confirmed that NodD1 is involved in recognizing the plant signal during the early stages of symbiosis.

  View details for Web of Science ID 000173009700023

  View details for PubMedID 11751831

• Evidence for structurally specific negative feedback in the Nod factor signal transduction pathway PLANT JOURNAL Oldroyd, G. E., Mitra, R. M., Wais, R. J., Long, S. R. 2001; 28 (2): 191-199

  Abstract

  Nod factor is a critical signalling molecule in the establishment of the legume/rhizobial symbiosis. The Nod factor of Sinorhizobium meliloti carries O-sulphate, O-acetate and C16:2 N-acyl attachments that define its activity and host specificity. Here we assess the relative importance of these modifications for the induction of calcium spiking in Medicago truncatula. We find that Nod factor structures lacking the O-sulphate, structures lacking the O-acetate and N-acyl groups, and structures lacking the O-acetate combined with a C18:1 N-acyl group all show calcium spiking when applied at high concentrations. These calcium responses are blocked in dmi1 and dmi2 mutants, suggesting that they function through the Nod factor signal transduction pathway. The dmi3 mutant, which is proposed to function in the Nod factor signal transduction pathway downstream of calcium spiking, shows increased sensitivity to Nod factor. This increased sensitivity is only active with wild-type Nod factor and was not present when the plants were treated with mutant Nod factor structures. We propose that the Nod factor signal transduction pathway is under negative feedback regulation that is activated at or downstream of DMI3 and requires structural components of the Nod factor molecule for activity.

  View details for Web of Science ID 000172099500007

  View details for PubMedID 11722762

• Identification of the heat-shock sigma factor RpoH and a second RpoH-like protein in Sinorhizobium meliloti MICROBIOLOGY-SGM Oke, V., Rushing, B. G., Fisher, E. J., Moghadam-Tabrizi, M., Long, S. R. 2001; 147: 2399-2408

  Abstract

  Hybridization to a PCR product derived from conserved sigma-factor sequences led to the identification of two Sinorhizobium meliloti DNA segments that display significant sequence similarity to the family of rpoH genes encoding the sigma(32) (RpoH) heat-shock transcription factors. The first gene, rpoH1, complements an Escherichia coli rpoH mutation. Cells containing an rpoH1 mutation are impaired in growth at 37 degrees C under free-living conditions and are defective in nitrogen fixation during symbiosis with alfalfa. A plasmid-borne rpoH1-gusA fusion increases in expression upon entry of the culture into the stationary phase of growth. The second gene, designated rpoH2, is 42% identical to the S. meliloti rpoH1 gene. Cells containing an rpoH2 mutation have no apparent phenotype under free-living conditions or during symbiosis with the host plant alfalfa. An rpoH2-gusA fusion increases in expression during the stationary phase of growth. The presence of two rpoH-like sequences in S. meliloti is reminiscent of the situation in Bradyrhizobium japonicum, which has three rpoH genes.

  View details for Web of Science ID 000170946600002

  View details for PubMedID 11535780

• Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Barnett, M. J., Fisher, R. F., Jones, T., Komp, C., Abola, A. P., Barloy-Hubler, F., Bowser, L., Capela, D., Galibert, F., Gouzy, J., Gurjal, M., Hong, A., Huizar, L., Hyman, R. W., Kahn, D., Kahn, M. L., Kalman, S., Keating, D. H., Palm, C., Peck, M. C., Surzycki, R., Wells, D. H., Yeh, K. C., Davis, R. W., Federspiel, N. A., Long, S. R. 2001; 98 (17): 9883-9888

  Abstract

  The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be specifically involved in symbiosis, pSymA contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.

  View details for Web of Science ID 000170539600076

  View details for PubMedID 11481432

  View details for PubMedCentralID PMC55547

• Ethylene inhibits the nod factor signal transduction pathway of Medicago truncatula PLANT CELL Oldroyd, G. E., Engstrom, E. M., Long, S. R. 2001; 13 (8): 1835-1849

  Abstract

  Legumes form a mutualistic symbiosis with bacteria collectively referred to as rhizobia. The bacteria induce the formation of nodules on the roots of the appropriate host plant, and this process requires the bacterial signaling molecule Nod factor. Although the interaction is beneficial to the plant, the number of nodules is tightly regulated. The gaseous plant hormone ethylene has been shown to be involved in the regulation of nodule number. The mechanism of the ethylene inhibition on nodulation is unclear, and the position at which ethylene acts in this complex developmental process is unknown. Here, we used direct and indirect ethylene application and inhibition of ethylene biosynthesis, together with comparison of wild-type plants and an ethylene-insensitive supernodulating mutant, to assess the effect of ethylene at multiple stages of this interaction in the model legume Medicago truncatula. We show that ethylene inhibited all of the early plant responses tested, including the initiation of calcium spiking. This finding suggests that ethylene acts upstream or at the point of calcium spiking in the Nod factor signal transduction pathway, either directly or through feedback from ethylene effects on downstream events. Furthermore, ethylene appears to regulate the frequency of calcium spiking, suggesting that it can modulate both the degree and the nature of Nod factor pathway activation.

  View details for Web of Science ID 000170538900010

  View details for PubMedID 11487696

• The composite genome of the legume symbiont Sinorhizobium meliloti SCIENCE Galibert, F., Finan, T. M., Long, S. R., Puhler, A., Abola, P., Ampe, F., Barloy-Hubler, F., Barnett, M. J., Becker, A., Boistard, P., Bothe, G., Boutry, M., Bowser, L., Buhrmester, J., Cadieu, E., Capela, D., Chain, P., Cowie, A., Davis, R. W., Dreano, S., Federspiel, N. A., Fisher, R. F., Gloux, S., Godrie, T., Goffeau, A., Golding, B., Gouzy, J., Gurjal, M., Hernandez-Lucas, I., Hong, A., Huizar, L., Hyman, R. W., Jones, T., Kahn, D., Kahn, M. L., Kalman, S., Keating, D. H., Kiss, E., Komp, C., Lalaure, V., Masuy, D., Palm, C., Peck, M. C., Pohl, T. M., Portetelle, D., Purnelle, B., Ramsperger, U., Surzycki, R., Thebault, P., Vandenbol, M., Vorholter, F. J., Weidner, S., Wells, D. H., Wong, K., Yeh, K. C., Batut, J. 2001; 293 (5530): 668-672

  Abstract

  The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.

  View details for Web of Science ID 000170204600047

  View details for PubMedID 11474104

• A homolog of the CtrA cell cycle regulator is present and essential in Sinorhizobium meliloti JOURNAL OF BACTERIOLOGY Barnett, M. J., Hung, D. Y., Reisenauer, A., Shapiro, L., Long, S. R. 2001; 183 (10): 3204-3210

  Abstract

  During development of the symbiotic soil bacterium Sinorhizobium meliloti into nitrogen-fixing bacteroids, DNA replication and cell division cease and the cells undergo profound metabolic and morphological changes. Regulatory genes controlling the early stages of this process have not been identified. As a first step in the search for regulators of these events, we report the isolation and characterization of a ctrA gene from S. meliloti. We show that the S. meliloti CtrA belongs to the CtrA-like family of response regulators found in several alpha-proteobacteria. In Caulobacter crescentus, CtrA is essential and is a global regulator of multiple cell cycle functions. ctrA is also an essential gene in S. meliloti, and it is expressed similarly to the autoregulated C. crescentus ctrA in that both genes have complex promoter regions which bind phosphorylated CtrA.

  View details for Web of Science ID 000168535000028

  View details for PubMedID 11325950

  View details for PubMedCentralID PMC95222

• Genes and signals in the Rhizobium-legume symbiosis PLANT PHYSIOLOGY Long, S. R. 2001; 125 (1): 69-72

  View details for Web of Science ID 000167544600017

  View details for PubMedID 11154299

• Genetic analysis of calcium spiking responses in nodulation mutants of Medicago truncatula PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wais, R. J., Galera, C., Oldroyd, G., Catoira, R., Penmetsa, R. V., Cook, D., Gough, C., Denarie, J., Long, S. R. 2000; 97 (24): 13407-13412

  Abstract

  The symbiotic interaction between Medicago truncatula and Sinorhizobium meliloti results in the formation of nitrogen-fixing nodules on the roots of the host plant. The early stages of nodule formation are induced by bacteria via lipochitooligosaccharide signals known as Nod factors (NFs). These NFs are structurally specific for bacterium-host pairs and are sufficient to cause a range of early responses involved in the host developmental program. Early events in the signal transduction of NFs are not well defined. We have previously reported that Medicago sativa root hairs exposed to NF display sharp oscillations of cytoplasmic calcium ion concentration (calcium spiking). To assess the possible role of calcium spiking in the nodulation response, we analyzed M. truncatula mutants in five complementation groups. Each of the plant mutants is completely Nod- and is blocked at early stages of the symbiosis. We defined two genes, DMI1 and DMI2, required in common for early steps of infection and nodulation and for calcium spiking. Another mutant, altered in the DMI3 gene, has a similar mutant phenotype to dmi1 and dmi2 mutants but displays normal calcium spiking. The calcium behavior thus implies that the DMI3 gene acts either downstream of calcium spiking or downstream of a common branch point for the calcium response and the later nodulation responses. Two additional mutants, altered in the NSP and HCL genes, which show root hair branching in response to NF, are normal for calcium spiking. This system provides an opportunity to use genetics to study ligand-stimulated calcium spiking as a signal transduction event.

  View details for Web of Science ID 000165476300091

  View details for PubMedID 11078514

• Cell surface expansion in polarly growing root hairs of Medicago truncatula PLANT PHYSIOLOGY Shaw, S. L., Dumais, J., Long, S. R. 2000; 124 (3): 959-969

  Abstract

  Fluorescent microspheres were used as material markers to investigate the relative rates of cell surface expansion at the growing tips of Medicago truncatula root hairs. From the analysis of tip shape and microsphere movements, we propose three characteristic zones of expansion in growing root hairs. The center of the apical dome is an area of 1- to 2- microm diameter with relatively constant curvature and high growth rate. Distal to the apex is a more rapidly expanding region 1 to 2 microm in width exhibiting constant surges of off-axis growth. This middle region forms an annulus of maximum growth rate and is visible as an area of accentuated curvature in the tip profile. The remainder of the apical dome is characterized by strong radial expansion anisotropy where the meridional rate of expansion falls below the radial expansion rate. Data also suggest possible meridional contraction at the juncture between the apical dome and the cell body. The cell cylinder distal to the tip expands slightly over time, but only around the circumference. These data for surface expansion in the legume root hair provide new insight into the mechanism of tip growth and the morphogenesis of the root hair.

  View details for Web of Science ID 000165365800006

  View details for PubMedID 11080274

• New genetic tools for use in the Rhizobiaceae and other bacteria BIOTECHNIQUES Barnett, R. J., OKE, V., Long, S. R. 2000; 29 (2): 240-?

  View details for Web of Science ID 000088679400016

  View details for PubMedID 10948423

• High-resolution physical map of the Sinorhizobium meliloti 1021 pSyma megaplasmid JOURNAL OF BACTERIOLOGY Barloy-Hubler, F., Capela, D., Barnett, M. J., Kalman, S., Federspiel, N. A., Long, S. R., Galibert, F. 2000; 182 (4): 1185-1189

  Abstract

  To facilitate sequencing of the Sinorhizobium meliloti 1021 pSyma megaplasmid, a high-resolution map was constructed by ordering 113 overlapping bacterial artificial chromosome clones with 192 markers. The 157 anonymous sequence tagged site markers (81,072 bases) reveal hypothetical functions encoded by the replicon.

  View details for Web of Science ID 000085033800045

  View details for PubMedID 10648551

• Bacteroid formation in the Rhizobium-legume symbiosis CURRENT OPINION IN MICROBIOLOGY OKE, V., Long, S. R. 1999; 2 (6): 641-646

  Abstract

  During the Rhizobium-legume symbiosis, bacteria enter the cells of host plants and differentiate into nitrogen-fixing bacteroids. Recent mutant screens and expression studies have revealed bacterial genes involved in the developmental pathway and demonstrate how the genetic requirements can vary from one host-microbe system to another. Whether bacteroids are terminally differentiated cells is an ongoing debate and new experimental systems are required to address this issue.

  View details for Web of Science ID 000083999700012

  View details for PubMedID 10607628

• Expression of the pea (Pisum sativum L.) alpha-tubulin gene TubA1 is correlated with cell division activity PLANT MOLECULAR BIOLOGY Stotz, H. U., Long, S. R. 1999; 41 (5): 601-614

  Abstract

  Microtubules are thought to be major determinants of plant morphogenesis, through effects on planes of cell division and on directions of differential cell expansion. In differentiation and redifferentiation processes, tubulin expression may prove a useful early indicator of cell activity. We examined the expression and localization of the pea alpha-tubulin gene TubA1 in situ and in transgenic alfalfa (Medicago sativa) to explore its use as a probe for plant development, and as a test case for correct developmental expression between two legume species commonly compared for studies of symbiosis with Rhizobium. The TubA1 mRNA was more abundant in root tips and immature leaves than in other tissues of pea. The promoter of TubA1 was fused to beta-glucuronidase (GUS) to analyze alpha-tubulin expression in transgenic alfalfa. Transient assays indicated that the TubA1 gene is transcribed at moderate levels compared to the cauliflower mosaic virus (CaMV) 35S promoter. Histochemical staining for GUS activity confirmed a correlation between TubA1 expression and cell division in nodules, roots and leaves. TubA1 promoter activity was first detected in the inner cortex of the root between 18 h and 24 h after spot inoculation with Rhizobium meliloti. Expression of a c-myc epitope fused to the carboxy-terminus of TubA1 resulted in an incorporation into the microtubular cytoskeleton, demonstrating the effectiveness of at least one epitope tag in creating functional tubulin fusions.

  View details for Web of Science ID 000084856200003

  View details for PubMedID 10645720

• Reduction of adenosine-5 '-phosphosulfate instead of 3 '-phosphoadenosine-5 '-phosphosulfate in cysteine biosynthesis by Rhizobium meliloti and other members of the family Rhizobiaceae JOURNAL OF BACTERIOLOGY Abola, A. P., Willits, M. G., Wang, R. C., Long, S. R. 1999; 181 (17): 5280-5287

  Abstract

  We have cloned and sequenced three genes from Rhizobium meliloti (Sinorhizobium meliloti) that are involved in sulfate activation for cysteine biosynthesis. Two of the genes display homology to the Escherichia coli cysDN genes, which code for an ATP sulfurylase (EC 2.7.7.4). The third gene has homology to the E. coli cysH gene, a 3'-phosphoadenosine-5'-phosphosulfate (PAPS) reductase (EC 1.8.99.4), but has greater homology to a set of genes found in Arabidopsis thaliana that encode an adenosine-5'-phosphosulfate (APS) reductase. In order to determine the specificity of the R. meliloti reductase, the R. meliloti cysH homolog was histidine tagged and purified, and its specificity was assayed in vitro. Like the A. thaliana reductases, the histidine-tagged R. meliloti cysH gene product appears to favor APS over PAPS as a substrate, with a Km for APS of 3 to 4 microM but a Km for PAPS of >100 microM. In order to determine whether this preference for APS is unique to R. meliloti among members of the family Rhizobiaceae or is more widespread, cell extracts from R. leguminosarum, Rhizobium sp. strain NGR234, Rhizobium fredii (Sinorhizobium fredii), and Agrobacterium tumefaciens were assayed for APS or PAPS reductase activity. Cell extracts from all four species also preferentially reduce APS over PAPS.

  View details for Web of Science ID 000082318000019

  View details for PubMedID 10464198

• Bacterial genes induced within the nodule during the Rhizobium-legume symbiosis MOLECULAR MICROBIOLOGY OKE, V., Long, S. R. 1999; 32 (4): 837-849

  Abstract

  During the symbiosis between the bacterium Rhizobium meliloti and plants such as alfalfa, the bacteria elicit the formation of nodules on the roots of host plants. The bacteria infect the nodule, enter the cytoplasm of plant cells and differentiate into a distinct cell type called a bacteroid, which is capable of fixing atmospheric nitrogen. To discover bacterial genes involved in the infection and differentiation stages of symbiosis, we obtained genes expressed at the appropriate time and place in the nodule by identifying promoters that are able to direct expression of the bacA gene, which is required for bacteroid differentiation. We identified 230 fusions that are expressed predominantly in the nodule. Analysis of 23 sequences indicated that only three encode proteins known to be involved in the Rhizobium-legume symbiosis, six encode proteins with homology to proteins not previously associated with symbiosis, and 14 have no significant similarity to proteins of known function. Disruption of a locus that encodes a protein with homology to a cell adhesion molecule led to a defect in the formation of nitrogen-fixing nodules, resulting in an increased number of nitrogen-starved plants. Our isolation of a large number of nodule-expressed genes will help to open the intermediate stages of nodulation to molecular analysis.

  View details for Web of Science ID 000080721400015

  View details for PubMedID 10361286

• alpha-galactoside uptake in Rhizobium meliloti: Isolation and characterization of agpA, a gene encoding a periplasmic binding protein required for melibiose and raffinose utilization JOURNAL OF BACTERIOLOGY Gage, D. J., Long, S. R. 1998; 180 (21): 5739-5748

  Abstract

  Rhizobium meliloti can occupy at least two distinct ecological niches; it is found in the soil as a free-living saprophyte, and it also lives as a nitrogen-fixing intracellular symbiont in root nodules of alfalfa and related legumes. One approach to understanding how R. meliloti alters its physiology in order to become an integral part of a developing nodule is to identify and characterize genes that are differentially expressed by bacteria living inside nodules. We used a screen to identify genes under the control of the R. meliloti regulatory protein NodD3, SyrM, or SyrA. These regulatory proteins are expressed by bacteria growing inside the root nodule. One gene isolated in this screen was mapped to pSymB and displayed complex regulation. The gene was downregulated by the syrA gene product and also by glucose and succinate. This gene, referred to as agpA, encodes a periplasmic binding protein that is most similar to proteins from the periplasmic oligopeptide binding protein family. It is likely that AgpA binds alpha-galactosides, because alpha-galactosides induce the expression of agpA, and agpA mutants cannot utilize or transport these sugars. Activity of an agpA::TnphoA fusion was downregulated by SyrA. Because syrA is known to be expressed at high levels in intracellular symbiotic R. meliloti and at low levels in the free-living bacteria, we propose that AgpA may belong to the class of gene products whose expression decreases when R. meliloti becomes an intracellular symbiont.

  View details for Web of Science ID 000076758900032

  View details for PubMedID 9791127

• Requirements for syrM and nodD genes in the nodulation of Medicago truncatula by Rhizobium meliloti 1021 MOLECULAR PLANT-MICROBE INTERACTIONS Smith, L. S., Long, S. R. 1998; 11 (9): 937-940

  View details for Web of Science ID 000075484400012

• Expressed sequence tags from a root-hair-enriched Medicago truncatula cDNA library PLANT PHYSIOLOGY Covitz, P. A., Smith, L. S., Long, S. R. 1998; 117 (4): 1325-1332

  View details for Web of Science ID 000075485800021

• Multiple genetic controls on Rhizobium meliloti syrA, a regulator of exopolysaccharide abundance GENETICS Barnett, M. J., Swanson, J. A., Long, S. R. 1998; 148 (1): 19-32

  Abstract

  Exopolysaccharides (EPS) are produced by a wide assortment of bacteria including plant pathogens and rhizobial symbionts. Rhizobium meliloti mutants defective in EPS production fail to invade alfalfa nodules. Production of EPS in R. meliloti is likely controlled at several levels. We have characterized a new gene of this regulatory circuit. syrA was identified by its ability to confer mucoid colony morphology and by its ability to suppress the colonial phenotype of an exoD mutant. Here we show that syrA encodes a 9-kD hydrophobic protein that has sequence similarity to two other EPS regulatory proteins: ExoX of Rhizobium NGR234 and R. meliloti, and Psi of R. leguminosarum bv. phaseoli. The syrA transcription start site lies 522 nucleotides upstream of a non-canonical TTG start codon. The syrA promoter region is similar to the promoter region of the nodulation regulatory protein, nodD3. We found that in free-living bacteria, syrA expression is activated by the regulatory locus, syrM, but not by nodD3. In planta, syrM is not required for expression of syrA. Instead, expression of the nitrogen fixation (nifHDKE) genes upstream of syrA plays a role. Specific and distinct sets of genetic controls may operate at different times during nodule invasion.

  View details for Web of Science ID 000071494000005

  View details for PubMedID 9475718

• Identification and characterization of a gene on Rhizobium meliloti pSyma, syrB, that negatively affects syrM expression MOLECULAR PLANT-MICROBE INTERACTIONS Barnett, M. J., Long, S. R. 1997; 10 (5): 550-559

  Abstract

  The Rhizobium meliloti SyrM protein activates transcription of nodD3 and syrA. Regulation of syrM is complex and may involve as yet undiscovered genes. Here we report the isolation of insertion mutants showing increased expression of a syrM-gusA gene fusion. Characterization of one mutant strain, designated SYR-B, revealed a mutation consisting of a transposon insertion linked to a large deletion. The corresponding wild-type DNA was cloned as a 5.3-kb BamHI fragment. Genetic and physical analysis of this DNA demonstrated that an open reading frame (ORF) near one end of the fragment, encoding the 16.5-kDa SyrB protein, is responsible for the repression of syrM activity. Results of complementation experiments with the 5.3-kb BamHI DNA led us to hypothesize that other genes within this DNA fragment interfere with the expression or activity of SyrB. Our analysis showed that the region upstream of syrB contains three ORFs. One ORF is similar to the Ros repressor of Agrobacterium tumefaciens and the MucR repressor of R. meliloti.

  View details for Web of Science ID A1997XF37200003

  View details for PubMedID 9204561

• Use of green fluorescent protein to visualize the early events of symbiosis between Rhizobium meliloti and alfalfa (Medicago sativa) JOURNAL OF BACTERIOLOGY Gage, D. J., Bobo, T., Long, S. R. 1996; 178 (24): 7159-7166

  Abstract

  A gene encoding a variant of green fluorescent protein (GFP) of Aequorea victoria was put under the control of a promoter which is constitutive in Rhizobium meliloti. The heterologous GFP gene was expressed at high levels during all stages of symbiosis, allowing R. meliloti cells to be visualized as they grew in the rhizosphere, on the root surface, and inside infection threads. In addition, nodules that were infected with bacteria which were synthesizing GFP fluoresced when illuminated with blue light. GFP-tagged bacteria could be seen inside infection threads, providing the opportunity to measure the growth rate and determine the patterns of growth of R. meliloti residing inside its host plant.

  View details for Web of Science ID A1996VX46500018

  View details for PubMedID 8955397

• Deletion analysis of the 5' untranslated region of the Rhizobium meliloti nodF gene MOLECULAR PLANT-MICROBE INTERACTIONS KALINOWSKI, G., Long, S. R. 1996; 9 (9): 869-873

  Abstract

  Efficient establishment of the symbiosis between rhizobia and their host plants requires precise regulation of bacterial nod genes. The nod gene transcripts in Rhizobium meliloti have approximately 200 nucleotides of untranslated sequence 5' of the start codon (5' UTR). We measured the significance of this region by constructing fusions between deletion derivatives of nodF and the reporter beta-glucuronidase (GUS). Flavonoid-inducible expression of the fusions in R. meliloti was evident when extra copies of the positive transcriptional activators NodD1, NodD3, or SyrM were present. The fusions responded normally over a range of inducer concentrations in Rhizobium leguminosarum bv. trifolii. GUS assays in planta showed no significant difference between the deletion constructs and a wild-type fusion. We conclude that the 5' UTRs of the nod gene transcripts are unlikely to have a significant regulatory role.

  View details for Web of Science ID A1996VX33800016

  View details for PubMedID 8969536

• Rhizobium symbiosis: Nod factors in perspective PLANT CELL Long, S. R. 1996; 8 (10): 1885-1898

  View details for Web of Science ID A1996VQ89400018

  View details for PubMedID 8914326

• Calcium spiking in alfalfa root hairs responding to Rhizobium meliloti nodulation signals Ehrhardt, D., Wais, R., Long, S. R. AMER SOC PLANT BIOLOGISTS. 1996: 61002?

  View details for Web of Science ID A1996UR53400039

• Calcium spiking in plant root hairs responding to Rhizobium nodulation signals CELL Ehrhardt, D. W., Wais, R., Long, S. R. 1996; 85 (5): 673-681

  Abstract

  Rhizobium lipochitooligosaccharide signal molecules stimulate multiple responses in legume host plants, including changes in host gene expression, cell growth, and mitoses leading to root nodule development. The basis for signal transduction in the plant is not known. We examined cytoplasmic free calcium in host root hairs using calcium-sensitive reporter dyes. Image analysis of injected dyes revealed localized periodic spikes in cytoplasmic calcium levels that ensued after a characteristic lag following signal application. Structural features of the signal molecules required to cause nodulation responses in alfalfa are also essential for stimulating calcium spiking. A nonnodulating alfalfa mutant is defective in calcium spiking, consistent with the possibility that this mutant is blocked in an early stage of nodulation signal perception.

  View details for Web of Science ID A1996UP34400008

  View details for PubMedID 8646776

• Transcription start sites for syrM and nodD3 flank an insertion sequence relic in Rhizobium meliloti JOURNAL OF BACTERIOLOGY Barnett, M. J., Rushing, B. G., Fisher, R. F., Long, S. R. 1996; 178 (7): 1782-1787

  Abstract

  In Rhizobium meliloti the syrM regulatory gene positively controls nod D3 and syrA, and nodD3 positively controls syrM and nod regulon genes such as nodABC, syrM and nodD3 are divergently transcribed and are separated by approximately 2.8 kb of DNA. The 885-bp SphI DNA fragment between syrM and nodD3 was subcloned and sequenced. Analysis of this intergenic region showed two open reading frames similar to those found in insertion elements of the IS3 family. We determined transcription initiation sites for both syrM and nodD3 using primer extension. The syrM transcription initiation site is 499 bp upstream of the syrM protein-coding region and downstream of a nod box which shows several differences from the R. meliloti nod box consensus sequence. We demonstrated binding of NodD3 to DNA containing the syrM nod box. The nodD3 start site maps 659 bp upstream of the nodD3 translation initiation site. A putative SyrM binding site was identified upstream of the nodD3 start site on the basis of sequence similarity to the upstream region of syrA, another locus regulated by SyrM.

  View details for Web of Science ID A1996UD48400002

  View details for PubMedID 8606148

  View details for PubMedCentralID PMC177869

• CLONING AND CHARACTERIZATION OF THE SIGA GENE ENCODING THE MAJOR SIGMA-SUBUNIT OF RHIZOBIUM-MELILOTI JOURNAL OF BACTERIOLOGY Rushing, B. G., Long, S. R. 1995; 177 (23): 6952-6957

  Abstract

  Using PCR to create a probe based on conserved region 2 of sigma factors, we have cloned the sigA gene coding for the major sigma factor of Rhizobium meliloti. The 684-residue protein encoded by the sigA gene was expressed in vitro in coupled transcription-translation experiments with R. meliloti extracts and migrated aberrantly in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Its deduced amino acid sequence is similar to that of RpoD of Escherichia coli and is nearly identical to that of SigA of the closely related bacterium Agrobacterium tumefaciens. Through Southern analysis, we located the gene on the R. meliloti main chromosome rather than on one of the megaplasmids. The sigA locus does not appear to be part of a macromolecular synthesis operon (MMS), as in many other bacterial species, but rather lies downstream of a partial open reading frame showing similarity to the threonine dehydrogenase gene (tdh) of E. coli.

  View details for Web of Science ID A1995TG22400035

  View details for PubMedID 7592490

• IN-VITRO SULFOTRANSFERASE ACTIVITY OF NODH, A NODULATION PROTEIN OF RHIZOBIUM-MELILOTI REQUIRED FOR HOST-SPECIFIC NODULATION JOURNAL OF BACTERIOLOGY Ehrhardt, D. W., Atkinson, E. M., Faull, K. F., Freedberg, D. I., Sutherlin, D. P., Armstrong, R., Long, S. R. 1995; 177 (21): 6237-6245

  Abstract

  Early stages of nodulation involve the exchange of signals between the bacterium and the host plant. Bacterial nodulation (nod) genes are required for Rhizobium spp. to synthesize lipooligosaccharide morphogens, termed Nod factors. The common nod genes encode enzymes that synthesize the factor core structure, which is modified by host-specific gene products. Here we show direct in vitro evidence that Rhizobium meliloti NodH, a host-specific nodulation gene, catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to the terminal 6-O position of Nod factors, and we show substrate requirements for the reaction. Our results indicate that polymerization of the chitooligosaccharide backbone likely precedes sulfation and that sulfation is not absolutely dependent on the presence or the particular structure of the N-acyl modification. NodH sulfation provides a tool for the enzymatic in vitro synthesis of novel Nod factors, or putative Nod factors intermediates, with high specific activity.

  View details for Web of Science ID A1995TC11400028

  View details for PubMedID 7592390

• SIGNALS AND CELL RESPONSES IN RHIZOBIUM SYMBIOSIS Long, S. R. ACADEMIC PRESS INC ELSEVIER SCIENCE. 1995: 742?42

  View details for Web of Science ID A1995RQ08400074

• PLANT PHYSIOLOGY - 3 YEARS INTO A NEW ERA PLANT PHYSIOLOGY Long, S. 1995; 108 (3): 883-884

  View details for Web of Science ID A1995RJ23500001

• IMPROVING SCIENCE LITERACY AND SCIENCE-EDUCATION AT THE UNIVERSITY-LEVEL Long, S. R. AMER SOC PLANT BIOLOGISTS. 1995: 16?16

  View details for Web of Science ID A1995RE28900037

• THE DNAA GENE OF RHIZOBIUM-MELILOTI LIES WITHIN AN UNUSUAL GENE ARRANGEMENT JOURNAL OF BACTERIOLOGY Margolin, W., Bramhill, D., Long, S. R. 1995; 177 (10): 2892-2900

  Abstract

  Rhizobium meliloti exists either as a free-living soil organism or as a differentiated endosymbiont bacteroid form within the nodules of its host plant, alfalfa (Medicago sativa), where it fixes atmospheric N2. Differentiation is accompanied by major changes in DNA replication and cell division. In addition, R. meliloti harbors three unique large circular chromosome-like elements whose replication coordination may be complex. As part of a study of DNA replication control in R. meliloti, we isolated a dnaA homolog. The deduced open reading frame predicts a protein of 57 kDa that is 36% identical to the DnaA protein of Escherichia coli, and the predicted protein was confirmed by immunoblot analysis. In a comparison with the other known DnaA proteins, this protein showed the highest similarity to that of Caulobacter crescentus and was divergent in some domains that are highly conserved in other unrelated species. The dnaA genes of a diverse group of bacteria are adjacent to a common set of genes. Surprisingly, analysis of the DNA sequence flanking dnaA revealed none of these genes, except for an rpsT homolog, also found upstream of dnaA in C. crescentus. Instead, upstream of rpsT lie homologs of fpg, encoding a DNA glycosylase, and fadB1, encoding an enoyl-coenzyme A hydratase with a strikingly high (53 to 55%) level of predicted amino acid identity to two mammalian mitochondrial homologs. Downstream of dnaA, there are two open reading frames that are probably expressed but are not highly similar to any genes in the databases. These results show that R. meliloti dnaA is located within a novel gene arrangement.

  View details for Web of Science ID A1995QX75200037

  View details for PubMedID 7751302

• THE RHIZOBIUM-MELILOTI GROELC LOCUS IS REQUIRED FOR REGULATION OF EARLY NOD GENES BY THE TRANSCRIPTION ACTIVATOR NODD GENES & DEVELOPMENT Ogawa, J., Long, S. R. 1995; 9 (6): 714-729

  Abstract

  The molecular chaperones related to GroEL (hsp60, cpn60) interact with partially folded proteins and appear to assist them to attain active and correctly folded conformation. They are required for cell viability but are probably more important for some processes than for others. Through a random genetic search to find loci that are required for expression of the Rhizobium meliloti nod (nodulation) genes, we isolated a mutant (B4) defective in luteolin-dependent activation of nod gene expression, and found it carries a Tn5 insertion within a chromosomal groEL gene (groELc) located just downstream of a groESc gene. The groELc mutation affected activity of three related LysR-type activator proteins NodD1, NodD3, and SyrM; on plants, the mutants formed nodules late, and the nodules were Fix-. Hybridization and protein expression analysis show that a similar groESL locus (groESLa) maps to the Rm1021 megaplasmid pSyma. Southern blot analysis revealed additional, but less closely related sequences hybridizing to groELc and groESc probes elsewhere in the R. meliloti genome. Clones of groESLc and groESLa can each restore robust phage lambda growth on an Escherichia coli groE mutant. Likewise each clone can complement all of the phenotypes observed for B4 mutants; thus, the two appear to be functionally equivalent if expression is controlled. We determined that groELc is required for normal DNA binding of the NodD target sequence in R. meliloti. GroEL coimmunopurifies with NodD1 from R. meliloti, which suggests a direct physical association between these proteins. GroEL is thus probably involved in the folding or assembly of transcriptionally active NodD.

  View details for Web of Science ID A1995QT07800007

  View details for PubMedID 7729688

• EXPRESSION AND BIOCHEMICAL FUNCTION OF NODPQ1 AND NODPQ2 IN RHIZOBIUM-MELILOTI Willits, M. G., Long, S. R. WILEY-BLACKWELL. 1995: 492?492

  View details for Web of Science ID A1995QT86401780

• THE PISUM-SATIVUM TUBA1 GENE, A MEMBER OF A SMALL FAMILY OF ALPHA-TUBULIN SEQUENCES PLANT MOLECULAR BIOLOGY BRIERLEY, H. L., Webster, P., Long, S. R. 1995; 27 (4): 715-727

  Abstract

  alpha- and beta-tubulin proteins are subunits of microtubules, which as primary elements of the plant cytoskeleton play major roles in plant cell division and cell morphogenesis. Several higher-plant alpha- and beta-tubulin gene families have been reported to have at least six to nine members each. Using genomic Southern hybridizations and polymerase chain reaction (PCR) experiments, we have found that the Pisum sativum (garden pea) genome has only four copies of alpha-tubulin sequences and a similar number of beta-tubulin sequences. We have characterized the pea alpha-tubulin gene TubA1. Its nucleotide sequence predicts a 452 amino acid product which is 89-98% identical to those predicted for other plant alpha-tubulins. By S1 nuclease analysis we have located the transcript start site at 102 bases upstream of the ATG. We have also shown that the TubA1 gene is expressed by northern hybridization with a gene-specific probe.

  View details for Web of Science ID A1995QU43800007

  View details for PubMedID 7727749

• DIFFERENTIATION OF RHIZOBIUM DURING NODULATION OF ALFALFA OKE, V., RUSHING, B., Willits, M., Long, S. WILEY-BLACKWELL. 1995: 341?341

  View details for Web of Science ID A1995QQ99701181

• THE DNAA GENE OF RHIZOBIUM-MELILOTI LIES WITHIN AN UNUSUAL GENE ARRANGEMENT Margolin, W., Long, S. R. WILEY-BLACKWELL. 1995: 113?113

  View details for Web of Science ID A1995QQ99700419

• PLANT-CELL RESPONSES TO RHIZOBIUM DURING SYMBIOSIS Long, S. R., Ehrhardt, D. W., Southwick, A., Allen, N. S., COVITZ, P., STOTZ, H. WILEY-BLACKWELL. 1995: 126?126

  View details for Web of Science ID A1995QQ99700463

• RHIZOBIUM-MELILOTI NODP AND NODQ FORM A MULTIFUNCTIONAL SULFATE-ACTIVATING COMPLEX REQUIRING GTP FOR ACTIVITY JOURNAL OF BACTERIOLOGY SCHWEDOCK, J. S., Liu, C. X., Leyh, T. S., Long, S. R. 1994; 176 (22): 7055-7064

  Abstract

  The nodulation genes nodP and nodQ are required for production of Rhizobium meliloti nodulation (Nod) factors. These sulfated oligosaccharides act as morphogenic signals to alfalfa, the symbiotic host of R. meliloti. In previous work, we have shown that nodP and nodQ encode ATP sulfurylase, which catalyzes the formation of APS (adenosine 5'-phosphosulfate) and PPi. In the subsequent metabolic reaction, APS is converted to PAPS (3'-phosphoadenosine 5'-phosphosulfate) by APS kinase. In Escherichia coli, cysD and cysN encode ATP sulfurylase; cysC encodes APS kinase. Here, we present genetic, enzymatic, and sequence similarity data demonstrating that nodP and nodQ encode both ATP sulfurylase and APS kinase activities and that these enzymes associate into a multifunctional protein complex which we designate the sulfate activation complex. We have previously described the presence of a putative GTP-binding site in the nodQ sequence. The present report also demonstrates that GTP enhances the rate of PAPS synthesis from ATP and sulfate (SO4(2-)) by NodP and NodQ expressed in E. coli. Thus, GTP is implicated as a metabolic requirement for synthesis of the R. meliloti Nod factors.

  View details for Web of Science ID A1994PQ98400037

  View details for PubMedID 7961471

• BIOSYNTHESIS OF RHIZOBIUM-MELILOTI LIPOOLIGOSACCHARIDE NOD FACTORS - NODA IS REQUIRED FOR AN N-ACYLTRANSFERASE ACTIVITY PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Atkinson, E. M., Palcic, M. M., Hindsgaul, O., Long, S. R. 1994; 91 (18): 8418-8422

  Abstract

  Rhizobium bacteria synthesize N-acylated beta-1,4-N-acetylglucosamine lipooligosaccharides, called Nod factors, which act as morphogenic signal molecules to legume roots during development of nitrogen-fixing nodules. The biosynthesis of Nod factors is genetically dependent upon the nodulation (nod) genes, including the common nod genes nodABC. We used the Rhizobium meliloti NodH sulfotransferase to prepare 35S-labeled oligosaccharides which served as metabolic tracers for Nod enzyme activities. This approach provides a general method for following chitooligosaccharide modifications. We found nodAB-dependent conversion of N-acetylchitotetraose (chitotetraose) monosulfate into hydrophobic compounds which by chromatographic and chemical tests were equivalent to acylated Nod factors. Sequential incubation of labeled intermediates with Escherichia coli containing either NodA or NodB showed that NodB was required before NodA during Nod factor biosynthesis. The acylation activity was sensitive to oligosaccharide chain length, with chitotetraose serving as a better substrate than chitobiose or chitotriose. We constructed a putative Nod factor intermediate, GlcN-beta 1,4-(GlcNAc)3, by enzymatic synthesis and labeled it by NodH-mediated sulfation to create a specific metabolic probe. Acylation of this oligosaccharide required only NodA. These results confirm previous reports that NodB is an N-deacetylase and suggest that NodA is an N-acyltransferase.

  View details for Web of Science ID A1994PE38800023

  View details for PubMedID 8078897

• RHIZOBIUM-MELILOTI CONTAINS A NOVEL 2ND-HOMOLOG OF THE CELL-DIVISION GENE FTSZ JOURNAL OF BACTERIOLOGY Margolin, W., Long, S. R. 1994; 176 (7): 2033-2043

  Abstract

  We have identified a second homolog of the cell division gene, ftsZ, in the endosymbiont Rhizobium meliloti. The ftsZ2 gene was cloned by screening a genomic lambda library with a probe derived from PCR amplification of a highly conserved domain. It encodes a 36-kDa protein which shares a high level of sequence similarity with the FtsZ proteins of Escherichia coli and Bacillus subtilis and FtsZ1 (Z1) of R. meliloti but lacks the carboxy-terminal region conserved in other FtsZ proteins. The identity of the ftsZ2 gene product was confirmed both by in vitro transcription-translation in an R. meliloti S-30 extract and by overproduction in R. meliloti cells. As with Z1, the overproduction of FtsZ2 in E. coli inhibited cell division and induced filamentation, although to a lesser extent than with Z1. However, the expression of ftsZ2 in E. coli under certain conditions caused some cells to coil dramatically, a phenotype not observed during Z1 overproduction. Although several Tn3-GUS (glucuronidase) insertions in a plasmid-borne ftsZ2 gene failed to cross into the chromosome, one interruption in the chromosomal ftsZ2 gene was isolated, suggesting that ftsZ2 is nonessential for viability. The two ftsZ genes were genetically mapped to the R. meliloti main chromosome, approximately 100 kb apart.

  View details for Web of Science ID A1994ND18300029

  View details for PubMedID 8144471

• WOMEN IN BIOMEDICINE - ENCOURAGEMENT SCIENCE Long, S. R., ZAKIAN, V., Allen, N. S., Arvin, A. M., Bakken, A., BEEMON, K., Belfort, M., Bennett, K. L., Bissell, M. J., Blackburn, E., Blau, H., Carlson, M., Chandler, V., CHILTON, M. D., Clarke, A. E., Coleman, M. S., Coruzzi, G., Craig, E. A., Davis, T. N., Dutcher, S. K., Eckhardt, L. A., Elgin, S. C., Enrietto, P. J., Esposito, R. E., Flint, J., Fuller, M. T., Galloway, D., Goodenough, U., Graves, B., Greenwald, I., Gross, C. A., Hanson, M. R., Henry, S. A., Huang, A. S., Kimble, J., Klinman, J. P., Lidstrom, M. E., Lindquist, S., Linial, M., WONGSTAAL, F., Martin, N. C., Olmsted, J. B., Prakash, L., Prives, C., Pukkila, P. J., Raikhel, N., Robinson, H. L., Rosenberg, N., ROTHMANDENES, L. B., Rowley, J. D., Rudner, R., Schaal, B. A., Schupbach, T., Shapiro, L., Sibley, C. H., Singer, M. F., SKALKA, A. M., SOLLNERWEBB, B., Spector, D. H., Steitz, J. A., Strome, S., Tilghman, S. M., Tobin, E. M., Wall, J. D., Wessler, S., Hopper, A. K. 1994; 263 (5152): 1357-1358

  View details for Web of Science ID A1994MZ92700002

  View details for PubMedID 8128213

• MORPHOGENETIC RESCUE OF RHIZOBIUM-MELILOTI NODULATION MUTANTS BY TRANS-ZEATIN SECRETION PLANT CELL Cooper, J. B., Long, S. R. 1994; 6 (2): 215-225

  View details for Web of Science ID A1994MZ40000006

• Effects of Nod factors on alfalfa root hair Ca++ and H+ currents and on cytoskeletal behavior 7th International Symposium on Molecular Plant-Microbe Interactions Allen, N. S., BENNETT, M. N., Cox, D. N., Shipley, A., Ehrhardt, D. W., Long, S. R. KLUWER ACADEMIC PUBL. 1994: 107?113

  View details for Web of Science ID A1994BD49V00016

• Nodulation gene expression in Rhizobium meliloti 7th International Symposium on Molecular Plant-Microbe Interactions Fisher, R. F., RUSHING, B., Ogawa, J., Barnett, M., Long, S. R. KLUWER ACADEMIC PUBL. 1994: 99?102

  View details for Web of Science ID A1994BD49V00014

• AN OPEN READING FRAME DOWNSTREAM OF RHIZOBIUM-MELILOTI NODQ1 SHOWS NUCLEOTIDE-SEQUENCE SIMILARITY TO AN AGROBACTERIUM-TUMEFACIENS INSERTION-SEQUENCE MOLECULAR PLANT-MICROBE INTERACTIONS Schwedock, J., Long, S. R. 1994; 7 (1): 151-153

  Abstract

  We sequenced a small uncharacterized region in the Rhizobium meliloti nod gene cluster downstream of nodQ1. We found the beginning of a large open reading frame (260 amino acids) in this fragment. The sequence reported here has striking similarity to IS66 (Y. Machida, M. Sakurai, S. Kiyokawa, A. Ubasawa, and S. Yasushiro, 1984, Proc. Natl. Acad. Sci. USA 81:7495-7499), an insertion element found in an Agrobacterium tumefaciens mutant.

  View details for Web of Science ID A1994NF82700017

  View details for PubMedID 8167368

• Morphogenetic Rescue of Rhizobium meliloti Nodulation Mutants by trans-Zeatin Secretion. The Plant cell Cooper, J. B., Long, S. R. 1994; 6 (2): 215?25

  Abstract

  The development of nitrogen-fixing nodules is induced on the roots of legume host plants by Rhizobium bacteria. We employed a novel strategy to probe the underlying mechanism of nodule morphogenesis in alfalfa roots using pTZS, a broad host range plasmid carrying a constitutive trans-zeatin secretion (tzs) gene from Agrobacterium tumefaciens T37. This plasmid suppressed the Nod- phenotype of Rhizobium nodulation mutants such that mutants harboring pTZS stimulated the formation of nodulelike structures. Alfalfa roots formed more or fewer of these nodules according to both the nitrogen content of the environment and the position along the root at which the pTZS+ bacteria were applied, which parallels the physiological and developmental regulation of true Rhizobium nodule formation. This plasmid also conferred on Escherichia coli cells the ability to induce root cortical cell mitoses. Both the pattern of induced cell divisions and the spatially restricted expression of an alfalfa nodule-specific marker gene (MsENOD2) in pTZS-induced nodules support the conclusion that localized cytokinin production produces a phenocopy of nodule morphogenesis.

  View details for DOI 10.1105/tpc.6.2.215

  View details for PubMedID 12244237

• INTERACTIONS OF NODD AT THE NOD BOX - NODD BINDS TO 2 DISTINCT SITES ON THE SAME FACE OF THE HELIX AND INDUCES A BEND IN THE DNA JOURNAL OF MOLECULAR BIOLOGY Fisher, R. F., Long, S. R. 1993; 233 (3): 336-348

  Abstract

  The Rhizobium meliloti nodD gene products are positive transcriptional activators of genes required for early stages of nodule morphogenesis in the R. meliloti-alfalfa symbiosis (nod genes). The regulatory activity of NodD, a member of the LysR family of activator proteins, is mediated in part through its binding to conserved DNA sequences termed nod boxes which lie upstream of the inducible nod genes. Here we use interference footprinting to identify two NodD binding sites in the nodA, nodF and nodH nod boxes. These two binding sites are located on the same face of the DNA helix and can be separated by an additional 10 bp with retention of activity. By systematic alteration of the phasing of the two binding sites on the DNA helix, we showed that only constructs which contain both sites on the same side of the helix are recognized by NodD as determined by migration retardation assay and by in vivo activation of nod box-lacZ fusions. Moreover, NodD apparently induces a bend in the DNA upon binding at the nod box as shown by migration retardation behavior of circularly permuted nod box fragments.

  View details for Web of Science ID A1993MA02800002

  View details for PubMedID 8411148

• ISOLATION AND CHARACTERIZATION OF A DNA-REPLICATION ORIGIN FROM THE 1,700-KILOBASE-PAIR SYMBIOTIC MEGAPLASMID PSYM-B OF RHIZOBIUM-MELILOTI JOURNAL OF BACTERIOLOGY Margolin, W., Long, S. R. 1993; 175 (20): 6553-6561

  Abstract

  A 4-kb fragment active as an autonomously replicating sequence (ARS) from the Rhizobium meliloti symbiotic megaplasmid pSym-b was isolated by selecting for sequences that allowed a normally nonreplicative pBR322 derivative to replicate in R. meliloti. The resulting Escherichia coli-R. meliloti shuttle plasmid (mini-pSym-b) containing the ARS also replicated in the closely related Agrobacterium tumefaciens, but only in strains carrying pSym-b, suggesting that a megaplasmid-encoded trans-acting factor is required. The copy number of mini-pSym-b was approximately the same as that of the resident megaplasmid, and mini-pSym-b was unstable in the absence of antibiotic selection. An 0.8-kb DNA subfragment was sufficient for replication in both R. meliloti and A. tumefaciens. The minimal ARS exhibited several sequence motifs common to other replication origins, such as an AT-rich region, three potential DnA binding sites, a potential 13-mer sequence, and several groups of short direct repeats. Hybridization experiments indicated that there may be a related ARS on the other megaplasmid, pSym-a. The pSym-b ARS was mapped near exoA, within a region nonessential for pSym-b replication. These results suggest that the R. meliloti megaplasmids share conserved replication origins and that pSym-b contains multiple replication origins. Since the mini-pSym-b shuttle vector can coexist with IncP-1 broad-host-range plasmids, it is also now possible to use two compatible plasmids for cloning and genetic manipulation in R. meliloti.

  View details for Web of Science ID A1993MC02300023

  View details for PubMedID 8407832

• PROKARYOTIC PLANT PARASITES CELL Long, S. R., Staskawicz, B. J. 1993; 73 (5): 921-935

  View details for Web of Science ID A1993LF06100009

  View details for PubMedID 8500181

• REGULATION OF SYRM AND NODD3 IN RHIZOBIUM-MELILOTI GENETICS Swanson, J. A., Mulligan, J. T., Long, S. R. 1993; 134 (2): 435-444

  Abstract

  The early steps of symbiotic nodule formation by Rhizobium on plants require coordinate expression of several nod gene operons, which is accomplished by the activating protein NodD. Three different NodD proteins are encoded by Sym plasmid genes in Rhizobium meliloti, the alfalfa symbiont. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to host plant inducers. The third, NodD3, is an inducer-independent activator of nod operons. We previously observed that nodD3 carried on a multicopy plasmid required another closely linked gene, syrM, for constitutive nod operon expression. Here, we show that syrM activates expression of the nodD3 gene, and that nodD3 activates expression of syrM. The two genes constitute a self-amplifying positive regulatory circuit in both cultured Rhizobium and cells within the symbiotic nodule. We find little effect of plant inducers on the circuit or on expression of nodD3 carried on pSyma. This regulatory circuit may be important for regulation of nod genes within the developing nodule.

  View details for Web of Science ID A1993LE03800005

  View details for PubMedID 8325480

• EARLY IONIC RESPONSES OF ALFALFA ROOT HAIRS TO NODULATION FACTORS - A VIBRATING PROBE ANALYSIS Cox, D. N., Shipley, A., Ehrhardt, D. W., Long, S. R., Allen, N. S. AMER SOC PLANT BIOLOGISTS. 1993: 110?10

  View details for Web of Science ID A1993LD89000620

• RHIZOBIUM-MELILOTI GENES INVOLVED IN SULFATE ACTIVATION - THE 2 COPIES OF NODPQ AND A NEW LOCUS, SAA GENETICS SCHWEDOCK, J. S., Long, S. R. 1992; 132 (4): 899-909

  Abstract

  The nitrogen-fixing symbiont Rhizobium meliloti establishes nodules on leguminous host plants. Nodulation (nod) genes used for this process are located in a cluster on the pSym-a megaplasmid of R. meliloti. These genes include nodP and nodQ (here termed nodPQ), which encode ATP sulfurylase and APS kinase, enzymes that catalyze the conversion of ATP and SO(4)2- into the activated sulfate form 3'-phosphoadenosine 5'-phosphosulfate (PAPS), an intermediate in cysteine synthesis. In Rhizobium, PAPS is also a precursor for sulfated and N-acylated oligosaccharide Nod-factor signals that cause symbiotic responses on specific host plants such as alfalfa. We previously found a highly conserved second copy of nodPQ in R. meliloti. We report here the mapping and cloning of this second copy, and its location on the second megaplasmid, pSym-b. The function of nodP2Q2 is equivalent to that of nodP1Q1 in complementation tests of R. meliloti and Escherichia coli mutants in ATP sulfurylase and adenosine 5'-phosphosulfate (APS) kinase. Mutations in nodP2Q2 do not have as severe an effect on symbiosis or plant host range as do those in nodP1Q1, however, possibly reflecting differences in expression and/or channeling of metabolites to specific enzymes involved in sulfate transfer. Strains mutated or deleted for both copies of nodQ are severely defective in symbiotic phenotypes, but remain prototrophic. This suggests the existence in R. meliloti of a third locus for ATP sulfurylase and APS kinase activities. We have found a new locus saa (sulfur amino acid), which may also encode these activities.

  View details for Web of Science ID A1992JZ83200005

  View details for PubMedID 1459442

• HOMOLOGY OF RHIZOBIUM-MELILOTI NODC TO POLYSACCHARIDE POLYMERIZING ENZYMES MOLECULAR PLANT-MICROBE INTERACTIONS Atkinson, E. M., Long, S. R. 1992; 5 (5): 439-442

  Abstract

  Rhizobium bacteria form nitrogen-fixing nodules on legume roots. As part of the nodulation process, they secrete Nod factors that are beta-1,4-linked oligomers of N-acetylglucosamine. These factors depend on nodulation (nod) genes, but most aspects of factor synthesis are not yet known. We show here that one gene, nodC, shows striking similarity to genes encoding proteins known to be involved in polysaccharide synthesis in yeast and bacteria, specifically chitin and cellulose synthases, as well as a protein with unknown function in Xenopus embryos, DG42. This similarity is consistent with a role for the NodC protein in the formation of the beta-1,4-linkage in Nod factors.

  View details for Web of Science ID A1992KR49400013

  View details for PubMedID 1472720

• RHIZOBIUM - PLANT SIGNAL EXCHANGE NATURE Fisher, R. F., Long, S. R. 1992; 357 (6380): 655-660

  Abstract

  Initial stages in the Rhizobium-legume symbiosis can be thought of as a reciprocal molecular conversation: transmission of a gene inducer from legume host to bacterium, with ensuing bacterial synthesis of a morphogen that is transmitted to the plant, switching the developmental fate of the legume root. These signal molecules have a key role in determining bacterium-host specificity and the purified Nod factor compounds provide useful new tools to probe plant cell function.

  View details for Web of Science ID A1992JA43000059

  View details for PubMedID 1614514

• DEPOLARIZATION OF ALFALFA ROOT HAIR MEMBRANE-POTENTIAL BY RHIZOBIUM-MELILOTI NOD FACTORS SCIENCE Ehrhardt, D. W., Atkinson, E. M., Long, S. R. 1992; 256 (5059): 998-1000

  Abstract

  Although much is known about the bacterial genetics of early nodulation, little is known about the plant cell response. Alfalfa root hair cells were impaled with intracellular microelectrodes to measure a membrane potential depolarizing activity in Rhizobium meliloti cell-free filtrates, a plant response dependent on the bacterial nodulation genes. The depolarization was desensitized by repeated exposure to factors and was not observed in a representative nonlegume. A purified extracellular Nod factor, NodRm-IV(S), caused membrane potential depolarization at nanomolar concentrations. This rapid single-cell assay provides a tool for dissecting the mechanisms of host cell response in early nodulation.

  View details for Web of Science ID A1992HU22400030

  View details for PubMedID 10744524

• CLONING AND CHARACTERIZATION OF A RHIZOBIUM-MELILOTI HOMOLOG OF THE ESCHERICHIA-COLI CELL-DIVISION GENE FTSZ JOURNAL OF BACTERIOLOGY Margolin, W., Corbo, J. C., Long, S. R. 1991; 173 (18): 5822-5830

  Abstract

  The ftsZ gene is essential for initiation of cell division in Escherichia coli and Bacillus subtilis. To begin our studies of division arrest during differentiation of Rhizobium meliloti bacteroids, we isolated a R. meliloti ftsZ homolog, ftsZRm. Degenerate primers directed towards a conserved region of ftsZ were used to amplify a segment of R. meliloti DNA by polymerase chain reaction, and the product of this reaction was then used to isolate positive clones from a bacteriophage library. The DNA sequence of an open reading frame containing the region of homology indicated that the R. meliloti FtsZ protein (FtsZRm) is 50% homologous to the known E. coli and B. subtilis FtsZ proteins, but at 590 amino acids (63 kDa), it is predicted to be nearly 50% larger. Strong expression of an approximately 70-kDa labeled protein in a coupled in vitro transcription-translation system supports this prediction. The additional 200 amino acids appear to fall in a single internal domain highly enriched for proline and glutamine residues. When we regulated R. meliloti ftsZ (ftsZRm) expression on a high-copy-number plasmid in E. coli with Plac and laclq, cells were smaller than normal in the presence of low FtsZRm levels (with no isopropyl-beta-D-thiogalactopyranoside [IPTG]) and filamentous when FtsZRm was overproduced (with IPTG). These results suggest that low levels of FtsZRm stimulate E. coli cell division, while high levels may be inhibitory.

  View details for Web of Science ID A1991GF09800030

  View details for PubMedID 1653222

• ANALYSIS OF RHIZOBIUM-MELILOTI NODULATION MUTANT WL131 - NOVEL INSERTION-SEQUENCE ISRM3 IN NODG AND ALTERED NODH PROTEIN PRODUCT JOURNAL OF BACTERIOLOGY Ogawa, J., BRIERLEY, H. L., Long, S. R. 1991; 173 (10): 3060-3065

  Abstract

  Nodulation (nod) genes are required for invasion of legumes by Rhizobium bacteria. Mutant WL131 is a derivative of 102F51 that has a severe Nod- phenotype on alfalfa. Upon examination of the extended DNA region containing host-specific nodulation genes nodFEG and nodH, we found that the nodG gene of WL131 bears a novel insertion sequence, ISRm3. Complementation studies implied, however, that the phenotype on alfalfa correlated with the nodH locus. We found that nodH in WL131 encodes an altered gene product. Correlation of the WL131 defect with nodH was also supported by phenotypic behavior. Each mutation affected nodulation more severely on alfalfa (Medicago sativa) than on sweet clover (Melilotus albus). However, we found that the degree of requirement for nodH in nodulation varied with the conditions under which the plant was grown.

  View details for Web of Science ID A1991FL18100004

  View details for PubMedID 1850728

• GENETIC AND PHYSICAL ANALYSIS OF THE NODD3 REGION OF RHIZOBIUM-MELILOTI NUCLEIC ACIDS RESEARCH Rushing, B. G., YELTON, M. M., Long, S. R. 1991; 19 (4): 921-927

  Abstract

  The nodulation (nod) genes of the symbiont Rhizobium meliloti are transcriptionally controlled by protein activators in the nodD gene family. While NodD1 and NodD2 act in concert with small molecular weight inducers provided by the host legume plant, NodD3 is an inducer-independent activator of the nod promoters. We determined the sequence of the nodD3 gene, confirmed the expression of a 35 kDa protein in vitro, and determined the insertion points of five Tn5 insertions in the region of the nodD3 gene. We found the NodD3 amino acid sequence to be markedly diverged from the sequences of NodD1 and NodD2, which were more similar to the inducer-dependent NodD of another species, Rhizobium leguminosarum biovar viciae. The expression of nodD3 is not well understood, but involves at least SyrM, another positive activator related to the LysR-NodD family. One of the phenotypically mutant Tn5 insertions used in genetic studies of NodD3-dependent nod regulation lacks NodD3 protein as determined by Western blots, but another expresses about 50-60% of the wild type level. The location of these Tn5 insertions substantially upstream of the open reading frame for NodD3 suggests importance of relatively distant regulatory sequences for nodD3 expression. An insertion that did not cause a NodD3- phenotype is located in the extreme C-terminus of the protein coding region.

  View details for Web of Science ID A1991FA08900034

  View details for PubMedID 2017373

• FUNDING AMERICA SCIENTISTS FORTUNE Long, S. R. 1991; 123 (3): 142-142

  View details for Web of Science ID A1991EU20200016

• RHIZOBIUM-MELILOTI NODULATION GENE-REGULATION AND MOLECULAR SIGNALS 5TH INTERNATIONAL SYMP ON THE MOLECULAR GENETICS OF PLANT-MICROBE INTERACTIONS Long, S. R., Fisher, R. F., Ogawa, J., Swanson, J., Ehrhardt, D. W., Atkinson, E. M., SCHWEDOCK, J. S. KLUWER ACADEMIC PUBL. 1991: 127?133

  View details for Web of Science ID A1991BV46F00020

• ATP SULPHURYLASE ACTIVITY OF THE NODP AND NODQ GENE-PRODUCTS OF RHIZOBIUM-MELILOTI NATURE Schwedock, J., Long, S. R. 1990; 348 (6302): 644-647

  Abstract

  The symbiotic bacterium Rhizobium meliloti stimulates alfalfa (Medicago sativa L.) roots to undergo morphogenesis and form nitrogen-fixing nodules. It has been proposed that the bacterial genes nodABC, common to all Rhizobium, are required for synthesis of an oligosaccharide factor, which is converted to a sulphated form (NodRm-1) by the products of the R. meliloti-specific genes nodH and nodQ1-5; NodRm-1 elicits host-specific plant responses. Previously we have shown that the nodP gene is homologous to a segment of the Escherichia coli genome; when we cloned this E. coli fragment we found that it mapped near 59 minutes, corresponding to the cysDNC locus. The genes cysD and cysN encode proteins that catalyse the synthesis of adenosine 5'-phosphosulphate, the first step in the activation of inorganic sulphate. Here we demonstrate that nodP and nodQ correspond to cysD and cysN, and that their proteins have ATP sulphurylase activity both in vivo and in vitro. We propose that nodP and nodQ synthesize an activated sulphate that is an intermediate in the formation of the alfalfa-specific sulphated nodRm-1 factor.

  View details for Web of Science ID A1990EM76000064

  View details for PubMedID 2250719

• DNA-SEQUENCE AND TRANSLATIONAL PRODUCT OF A NEW NODULATION-REGULATORY LOCUS - SYRM HAS SEQUENCE SIMILARITY TO NODD PROTEINS JOURNAL OF BACTERIOLOGY Barnett, M. J., Long, S. R. 1990; 172 (7): 3695-3700

  Abstract

  Rhizobium meliloti nodulation (nod) genes are expressed when activated by trans-acting proteins in the NodD family. The nodD1 and nodD2 gene products activate nod promoters when cells are exposed to plant-synthesized signal molecules. Alternatively, the same nod promoters are activated by the nodD3 gene when nodD3 is carried in trans along with a closely linked global regulatory locus, syrM (symbiotic regulator) (J. T. Mulligan and S. R. Long, Genetics 122:7-18, 1989). In this article we report the nucleotide sequence of a 2.6-kilobase SphI fragment from R. meliloti SU47 containing syrM. Expression from this locus was confirmed by using in vitro transcription-translation assays. The open reading frame encoded a protein of either 33 or 36 kilodaltons whose sequence shows similarity to NodD regulatory proteins.

  View details for Web of Science ID A1990DM73700021

  View details for PubMedID 2361944

• NUCLEOTIDE-SEQUENCE OF AN ALFALFA CALMODULIN CDNA NUCLEIC ACIDS RESEARCH Barnett, M. J., Long, S. R. 1990; 18 (11): 3395-3395

  View details for Web of Science ID A1990DJ27100034

  View details for PubMedID 2356128

• NITROGEN-FIXATION - RHIZOBIUM SWEET-TALKING NATURE Long, S. R., Atkinson, E. M. 1990; 344 (6268): 712-713

  View details for Web of Science ID A1990CZ67800031

• DNA FOOTPRINT ANALYSIS OF THE TRANSCRIPTIONAL ACTIVATOR PROTEINS NODD1 AND NODD3 ON INDUCIBLE NOD GENE PROMOTERS JOURNAL OF BACTERIOLOGY Fisher, R. F., Long, S. R. 1989; 171 (10): 5492-5502

  Abstract

  The Rhizobium meliloti nodD1 and nodD3 gene products (NodD1 and NodD3) are members of the lysR-nodD gene regulator family. They are functionally distinct in that NodD1 transcriptionally activates other nod genes in the presence of a flavonoid inducer such as luteolin, while NodD3 is capable of activating nod gene expression at high levels in the absence of inducer. NodD1 and NodD3 are DNA-binding proteins which interact with DNA sequences situated upstream of the transcription initiation sites of at least three sets of inducible nod genes. We report the footprinting of NodD1- and NodD3-DNA complexes with both DNase I and the 1,10-phenanthroline-copper ion reagent. NodD1 and NodD3 both interacted with the nodABC, nodFE, and nodH promoters and protected from cleavage an extensive piece of DNA, including the nod box, from approximately -20 to -75 from the transcription start site for each of the three promoters. The constitutively activating protein NodD3 displayed an additional hypersensitive cleavage site in its footprint compared with NodD1.

  View details for Web of Science ID A1989AT16000033

  View details for PubMedID 2793828

• Nucleotide sequence and protein products of two new nodulation genes of Rhizobium meliloti, nodP and nodQ. Molecular plant-microbe interactions Schwedock, J., Long, S. R. 1989; 2 (4): 181-194

  Abstract

  Previous studies had suggested the existence of nodulation (nod) genes downstream of nodG in Rhizobium meliloti strain 1021. We have established the DNA sequence and analyzed the translation products of the genes located in this position. Computer analysis of the DNA sequence revealed a number of overlapping putative open-reading frames (ORFs), so we constructed several clones that contained either full-length or truncated ORFs. The protein products of these clones were expressed in both R. meliloti and Escherichia coli in vitro transcription-translation systems. These assays unambiguously defined the expressed ORFs, which we named nodP and nodQ. In addition, we found homology to these genes, via Southern hybridizations, elsewhere in the genome of R. meliloti strain 1021, and in other species of Rhizobium. The nodP gene also displayed homology to E. coli. A computer search revealed significant homology between NodQ and the GDP binding domain of elongation factor Tu (EF-Tu).

  View details for PubMedID 2520820

• A FAMILY OF ACTIVATOR GENES REGULATES EXPRESSION OF RHIZOBIUM-MELILOTI NODULATION GENES GENETICS Mulligan, J. T., Long, S. R. 1989; 122 (1): 7-18

  Abstract

  Nodulation (nod) gene expression in Rhizobium meliloti requires plant inducers and the activating protein product of the nodD gene. We have examined three genes in R. meliloti which have nodD activity and sequence homology. These three nodD genes are designated nodD1, nodD2 and nodD3, and have distinctive properties. The nodD1 gene product activates expression of the nodABC operon, as measured by a nodC-lacZ fusion or by transcript analysis, in the presence of crude seed or plant wash or the inducer, luteolin. The nodD3 gene product can cause a high basal (uninduced) level of nodC-lacZ expression and nodABC transcripts which is relatively unaffected by inducers. The effect of nodD3 is dependent on the presence of another gene, syrM (symbiotic regulator). By primer extension analysis we determined that the transcription start site is the same for nodD1 plus luteolin or nodD3-syrM mediated expression of nodA and nodH mRNAs. syrM also enhances the expression of another symbiotically important trait, production of extracellular polysaccharide. This regulatory effect of syrM requires locus syrA, which is linked to nodD3 and syrM. The syrM-syrA mediated increase in polysaccharide production requires at least some of the previously identified exo genes and may be a parallel regulatory event to the syrM-nodD3 control of nod promoters.

  View details for Web of Science ID A1989U362600002

  View details for PubMedID 2731734

• NITROGEN-FIXATION - NEW ROUTE TO A STICKY SUBJECT NATURE Long, S. R., Ehrhardt, D. W. 1989; 338 (6216): 545-546

  View details for Web of Science ID A1989U112000037

• RHIZOBIUM-LEGUME NODULATION - LIFE TOGETHER IN THE UNDERGROUND CELL Long, S. R. 1989; 56 (2): 203-214

  View details for Web of Science ID A1989T075800010

  View details for PubMedID 2643474

• RHIZOBIUM GENETICS ANNUAL REVIEW OF GENETICS Long, S. R. 1989; 23: 483-506

  View details for Web of Science ID A1989CE68800020

  View details for PubMedID 2694941

• A NON-NODULATING ALFALFA MUTANT DISPLAYS NEITHER ROOT HAIR CURLING NOR EARLY CELL-DIVISION IN RESPONSE TO RHIZOBIUM-MELILOTI PLANT CELL Dudley, M. E., Long, S. R. 1989; 1 (1): 65-72

  Abstract

  The early events in the alfalfa-Rhizobium meliloti symbiosis include deformation of epidermal root hairs and the approximately concurrent stimulation of cell dedifferentiation and cell division in the root inner cortex. These early steps have been studied previously by analysis of R. meliloti mutants. Bacterial strains mutated in nodABC, for example, fail to stimulate either root hair curling or cell division events in the plant host, whereas exopolysaccharide (exo) mutants of R. meliloti stimulate host cell division but the resulting nodules are uninfected. As a further approach to understanding early symbiotic interactions, we have investigated the phenotype of a non-nodulating alfalfa mutant, MnNC-1008 (NN) (referred to as MN-1008). Nodulating and non-nodulating plants were inoculated with wild-type R. meliloti and scored for root hair curling and cell divisions. MN-1008 was found to be defective in both responses. Mutant plants inoculated with Exo- bacteria also showed no cell division response. Therefore, the genetic function mutated in MN-1008 is required for both root hair curling and cell division, as is true for the R. meliloti nodABC genes. These observations support the model that the distinct cellular processes of root hair curling and cell division are triggered by related mechanisms or components, or are causally linked.

  View details for Web of Science ID A1989U213100007

  View details for PubMedID 2535468

• ALFALFA ROOT EXUDATES AND COMPOUNDS WHICH PROMOTE OR INHIBIT INDUCTION OF RHIZOBIUM-MELILOTI NODULATION GENES PLANT PHYSIOLOGY Peters, N. K., Long, S. R. 1988; 88 (2): 396-400

  Abstract

  Using a plate induction assay, we demonstrate that alfalfa exudes inducer of Rhizobium meliloti nodulation genes. The inducer is exuded from the infectible zone of the root, accumulates to at least 1 micromolar, and is not affected by 10 millimolar nitrate. No zones of inhibition are observed. A nodulation minus mutant line of alfalfa, MN-1008, exudes normal levels of inducer. R. meliloti grown in rich medium requires ten-fold higher concentrations of luteolin to achieve half-maximal induction as compared to cells grown in a minimal medium. Flavonoids other than luteolin are found to have activity in R. meliloti nodulation gene induction assays. The compounds apigenin and eriodictyol have activities two-fifths and one-seventh that of luteolin, respectively. Several of the flavonoids tested (morin = naringenin > kaempferol = chrysin > quercetin = fisetin = hesperitin) demonstrate antagonistic activity toward induction by luteolin. The most effective antagonist is the coumarin, umbelliferone.

  View details for Web of Science ID A1988Q571600030

  View details for PubMedID 16666315

• SPECIFIC BINDING OF PROTEINS FROM RHIZOBIUM-MELILOTI CELL-FREE-EXTRACTS CONTAINING NODD TO DNA-SEQUENCES UPSTREAM OF INDUCIBLE NODULATION GENES GENES & DEVELOPMENT Fisher, R. F., Egelhoff, T. T., Mulligan, J. T., Long, S. R. 1988; 2 (3): 282-293

  Abstract

  Nodulation (nod) genes in Rhizobium meliloti are transcriptionally induced by flavonoid signal molecules, such as luteolin, produced by its symbiotic host plant, alfalfa. This induction depends on expression of nodD. Upstream of three inducible nod gene clusters, nodABC, nodFE, and nodH, is a highly conserved sequence referred to as a 'nod box.' The upstream sequences have no other obvious similarity. We have found that DNA fragments containing the regions upstream of all three inducible transcripts show altered electrophoretic mobility when treated with R. meliloti extracts. The ability of the extracts to interact specifically with these DNAs correlated with the genetic dosage of nodD1 or nodD3 and with the presence and concentration of the nodD1 or nodD3 protein (NodD1 or NodD3) in the extracts. Antiserum specific to NodD was used to construct an immunoaffinity column that permitted a substantial purification of NodD1; this preparation of NodD1 also displayed specific binding to restriction fragments containing DNA sequences found upstream of inducible nod genes. In addition, NodD-specific antiserum removed the specific DNA-binding activity from total Rhizobium cell extracts. The interaction of total extracts and of partially purified NodD protein with nod promoter sequences was competitive with an oligonucleotide representing the 3' 25-bp portion of the nod box. The interaction of R. meliloti extracts and NodD1 protein with nod gene upstream regions occurred independently of exposure of cells or extracts to flavone inducer.

  View details for Web of Science ID A1988P138300002

  View details for PubMedID 3288541

• EXTENDED REGION OF NODULATION GENES IN RHIZOBIUM-MELILOTI 1021 .1. PHENOTYPES OF TN5 INSERTION MUTANTS GENETICS Swanson, J. A., Tu, J. K., Ogawa, J., Sanga, R., Fisher, R. F., Long, S. R. 1987; 117 (2): 181-189

  Abstract

  Rhizobium meliloti Nod(-) mutant WL131, a derivative of wild-type strain 102F51, was complemented by a clone bank of wild-type R. meliloti 1021 DNA, and clone pRmJT5 was recovered. Transfer of pRmJT5 conferred alfalfa nodulation on other Rhizobium species, indicating a role in host range determination for pRmJT5. Mutagenesis of pRmJT5 revealed several segments in which transposon insertion causes delay in nodulation, and/or marked reduction of the number of nodules formed on host alfalfa plants. The set of mutants indicated five regions in which nod genes are located; one mutant, nod-216, is located in a region not previously reported to encode a nodulation gene. Other mutant phenotypes correlated with the positions of open reading frames for nodH, nodF and nodE , and with a 2.2-kb EcoRI fragment. A mutant in nodG had no altered phenotype in this strain. One nodulation mutant was shown to be a large deletion of the common nod gene region. We present a discussion comparing the various studies made on this extended nod gene region.

  View details for Web of Science ID A1987K367300004

  View details for PubMedID 17246399

• EXTENDED REGION OF NODULATION GENES IN RHIZOBIUM-MELILOTI 1021 .2. NUCLEOTIDE-SEQUENCE, TRANSCRIPTION START SITES AND PROTEIN PRODUCTS GENETICS Fisher, R. F., Swanson, J. A., Mulligan, J. T., Long, S. R. 1987; 117 (2): 191-201

  Abstract

  We have established the DNA sequence and analyzed the transcription and translation products of a series of putative nodulation (nod) genes in Rhizobium meliloti strain 1021. Four loci have been designated nodF, nodE, nodG and nodH. The correlation of transposon insertion positions with phenotypes and open reading frames was confirmed by sequencing the insertion junctions of the transposons. The protein products of these nod genes were visualized by in vitro expression of cloned DNA segments in a R. meliloti transcription-translation system. In addition, the sequence for nodG was substantiated by creating translational fusions in all three reading frames at several points in the sequence; the resulting fusions were expressed in vitro in both E. coli and R. meliloti transcription-translation systems. A DNA segment bearing several open reading frames downstream of nodG corresponds to the putative nod gene mutated in strain nod-216. The transcription start sites of nodF and nodH were mapped by primer extension of RNA from cells induced with the plant flavone, luteolin. Initiation of transcription occurs approximately 25 bp downstream from the conserved sequence designated the "nod box," suggesting that this conserved sequence acts as an upstream regulator of inducible nod gene expression. Its distance from the transcription start site is more suggestive of an activator binding site rather than an RNA polymerase binding site.

  View details for Web of Science ID A1987K367300005

  View details for PubMedID 17246400

• EXPRESSION OF RHIZOBIUM-MELILOTI NOD GENES IN RHIZOBIUM AND AGROBACTERIUM BACKGROUNDS JOURNAL OF BACTERIOLOGY YELTON, M. M., Mulligan, J. T., Long, S. R. 1987; 169 (7): 3094-3098

  Abstract

  Rhizobium meliloti nod genes are required for the infection of alfalfa. Induction of the nodC gene depends on a chemical signal from alfalfa and on nodD gene expression. By using a nodC-lacZ fusion, we have shown that the induction of the R. meliloti nodC gene and the expression of nodD occur at almost normal levels in other Rhizobium backgrounds and in Agrobacterium tumefaciens, but not in Escherichia coli. Xanthomonas campestris, or Pseudomonas savastanoi. Our results suggest that bacterial genes in addition to nodDABC are required for nod gene response to plant cells. We have found that inducing activity is present in other plant species besides alfalfa. Acetosyringone, the A. tumefaciens vir gene inducer, does not induce nodC.

  View details for Web of Science ID A1987H998900029

  View details for PubMedID 3597319

• MICROSCOPIC STUDIES OF CELL DIVISIONS INDUCED IN ALFALFA ROOTS BY RHIZOBIUM-MELILOTI PLANTA Dudley, M. E., Jacobs, T. W., Long, S. R. 1987; 171 (3): 289-301

  View details for Web of Science ID A1987J235400001

• TRANSCRIPTION OF RHIZOBIUM-MELILOTI NODULATION GENES - IDENTIFICATION OF A NODD TRANSCRIPTION INITIATION SITE INVITRO AND INVIVO JOURNAL OF BIOLOGICAL CHEMISTRY Fisher, R. F., BRIERLEY, H. L., Mulligan, J. T., Long, S. R. 1987; 262 (14): 6849-6855

  Abstract

  Nodulation genes in Rhizobium are required for invasion of the host plant. The nodABC operon is induced by plant activator molecules; this activation requires the gene product of the constitutively expressed nodD locus, which is transcribed divergently from nodABC. We are employing in vitro transcription to elucidate the molecular mechanism of nod gene activation. We used a micropurification technique to obtain RNA polymerase from Rhizobium meliloti, and here demonstrate that it initiated and terminated accurately at the Escherichia coli trp promoter-leader region. E. coli RNA polymerase, however, apparently fails to recognize R. meliloti promoters. We used the R. meliloti RNA polymerase in a minimal transcription system to attempt to localize the divergent start sites for nodD and nodABC. Transcript sizing and fingerprinting, together with synchronized single-round transcription experiments permit us to designate an in vitro transcription initiation site for nodD. Primer extension analysis of in vivo mRNA demonstrates that the initiation site which is utilized in vitro is the same site used in vivo. While nodABC is not transcribed in our minimal in vitro transcription system, this system should prove useful for the study of factors in induced cells which promote expression of this inducible promoter.

  View details for Web of Science ID A1987H281900066

  View details for PubMedID 3032978

• A PLANT FLAVONE, LUTEOLIN, INDUCES EXPRESSION OF RHIZOBIUM-MELILOTI NODULATION GENES SCIENCE Peters, N. K., Frost, J. W., Long, S. R. 1986; 233 (4767): 977-980

  Abstract

  The symbiotic interaction of Rhizobium meliloti and alfalfa results in the formation of nitrogen-fixing root nodules. Rhizobium meliloti nodABC genes are required for the early host responses of cortical cell divisions and root hair curling. The induction of nodABC expression by alfalfa exudates demonstrates host-symbiont signaling at an early stage in nodule development. The inducer molecule for nodABC expression was isolated from plant exudate by constructing a nodABC-lacZ fusion to monitor the inducing activity. From ultraviolet-visible absorption spectra, proton nuclear magnetic resonance, and mass spectrometry, the inducer was determined to be 3',4', 5,7-tetrahydroxyflavone (luteolin). Luteolin is a normal secondary plant metabolite found throughout the plant kingdom that may serve to control nodABC expression during nodule development. This regulatory role for a flavone contrasts with the function of some flavonoids as defense compounds.

  View details for Web of Science ID A1986D688600033

  View details for PubMedID 3738520

• REGULATION OF RHIZOBIUM INFECTION GENES Long, S. R. WILEY-LISS. 1986: 7?7

  View details for Web of Science ID A1986A664300011

• RHIZOBIUM MELILOTI NOD GENE-PRODUCTS Egelhoff, T., Long, S. WILEY-LISS. 1986: 32?32

  View details for Web of Science ID A1986A664300081

• CONSERVED NODULATION GENES IN RHIZOBIUM-MELILOTI AND RHIZOBIUM-TRIFOLII APPLIED AND ENVIRONMENTAL MICROBIOLOGY Fisher, R. F., Tu, J. K., Long, S. R. 1985; 49 (6): 1432-1435

  Abstract

  Plasmids which contained wild-type or mutated Rhizobium meliloti nodulation (nod) genes were introduced into NodR. trifolii mutants ANU453 and ANU851 and tested for their ability to nodulate clover. Cloned wild-type and mutated R. meliloti nod gene segments restored ANU851 to Nod, with the exception of nodD mutants. Similarly, wild-type and mutant R. meliloti nod genes complemented ANU453 to Nod, except for nodCII mutants. Thus, ANU851 identifies the equivalent of the R. meliloti nodD genes, and ANU453 specifies the equivalent of the R. meliloti nodCII genes. In addition, cloned wild-type R. trifolii nod genes were introduced into seven R. meliloti Nod mutants. All seven mutants were restored to Nod on alfalfa. Our results indicate that these genes represent common nodulation functions and argue for an allelic relationship between nod genes in R. meliloti and R. trifolii.

  View details for Web of Science ID A1985AJN2900016

  View details for PubMedID 16346809

• RHIZOBIUM-MELILOTI NODULATION GENES - IDENTIFICATION OF NODDABC GENE-PRODUCTS, PURIFICATION OF NODA PROTEIN, AND EXPRESSION OF NODA IN RHIZOBIUM-MELILOTI JOURNAL OF BACTERIOLOGY Egelhoff, T. T., Long, S. R. 1985; 164 (2): 591-599

  Abstract

  A set of conserved, or common, bacterial nodulation (nod) loci is required for host plant infection by Rhizobium meliloti and other Rhizobium species. Four such genes, nodDABC, have been indicated in R. meliloti 1021 by genetic analysis and DNA sequencing. An essential step toward understanding the function of these genes is to characterize their protein products. We used in vitro and maxicell Escherichia coli expression systems, together with gel electrophoresis and autoradiography, to detect proteins encoded by nodDABC. We facilitated expression of genes on these DNA fragments by inserting them downstream of the Salmonella typhimurium trp promoter, both in colE1 and incP plasmid-based vectors. Use of the incP trp promoter plasmid allowed overexpression of a nodABC gene fragment in R. meliloti. We found that nodA encodes a protein of 21 kilodaltons (kDa), and nodB encodes one of 28 kDa; the nodC product appears as two polypeptide bands at 44 and 45 kDa. Expression of the divergently read nodD yields a single polypeptide of 33 kDa. Whether these represent true Rhizobium gene products must be demonstrated by correlating these proteins with genetically defined Rhizobium loci. We purified the 21-kDa putative nodA protein product by gel electrophoresis, selective precipitation, and ion-exchange chromatography and generated antiserum to the purified gene product. This permitted the immunological demonstration that the 21-kDa protein is present in wild-type cells and in nodB- or nodC-defective strains, but is absent from nodA::Tn5 mutants, which confirms that the product expressed in E. coli is identical to that produced by R. meliloti nodA. Using antisera detection, we found that the level of nodA protein is increased by exposure of R. meliloti cells to plant exudate, indicating regulation of the bacterial nod genes by the plant host.

  View details for Web of Science ID A1985ATP6100015

  View details for PubMedID 2997121

• PHYSICAL AND GENETIC-MAP OF A RHIZOBIUM-MELILOTI NODULATION GENE REGION AND NUCLEOTIDE-SEQUENCE OF NODC JOURNAL OF BACTERIOLOGY Jacobs, T. W., Egelhoff, T. T., Long, S. R. 1985; 162 (2): 469-476

  Abstract

  Infection of alfalfa by the soil bacterium Rhizobium meliloti proceeds by deformation of root hairs and bacterial invasion of host tissue by way of an infection thread. We studied an 8.7-kilobase (kb) segment of the R. meliloti megaplasmid, which contains genes required for infection. Site-directed Tn5 mutagenesis was used to examine this fragment for nodulation genes. A total of 81 R. meliloti strains with mapped Tn5 insertions in the 8.7-kb fragment were evaluated for nodulation phenotype on alfalfa plants; 39 of the insertions defined a 3.5-kb segment containing nodulation functions. Of these 39 mutants, 37 were completely nodulation deficient (Nod-), and 2 at the extreme nif-distal end were leaky Nod-. Complementation analysis was performed by inoculating plants with strains carrying a genomic Tn5 at one location and a plasmid-borne Tn5 at another location in the 3.5-kb nodulation segment. Mutations near the right border of the fragment behaved as two distinct complementation groups. The segment in which these mutations are located was analyzed by DNA sequencing. Several open reading frames were found in this region, but the one most likely to function is 1,206 bases long, reading from left to right (nif distal to proximal) and spanning both mutation groups. The genetic behavior of this segment may be due either to the gene product having two functional domains or to a recombinational hot spot between the apparent complementation groups.

  View details for Web of Science ID A1985AGJ1200001

  View details for PubMedID 2985535

• NODULES ARE INDUCED ON ALFALFA ROOTS BY AGROBACTERIUM-TUMEFACIENS AND RHIZOBIUM-TRIFOLII CONTAINING SMALL SEGMENTS OF THE RHIZOBIUM-MELILOTI NODULATION REGION JOURNAL OF BACTERIOLOGY Hirsch, A. M., Drake, D., Jacobs, T. W., Long, S. R. 1985; 161 (1): 223-230

  Abstract

  Regions of the Rhizobium meliloti nodulation genes from the symbiotic plasmid were transferred to Agrobacterium tumefaciens and Rhizobium trifolii by conjugation. The A. tumefaciens and R. trifolii transconjugants were unable to elicit curling of alfalfa root hairs, but were able to induce nodule development at a low frequency. These were judged to be genuine nodules on the basis of cytological and developmental criteria. Like genuine alfalfa nodules, the nodules were initiated from divisions of the inner root cortical cells. They developed a distally positioned meristem and several peripheral vascular bundles. An endodermis separated the inner tissues of the nodule from the surrounding cortex. No infection threads were found to penetrate either root hairs or the nodule cells. Bacteria were found only in intercellular spaces. Thus, alfalfa nodules induced by A. tumefaciens and R. trifolii transconjugants carrying small nodulation clones of R. meliloti were completely devoid of intracellular bacteria. When these strains were inoculated onto white clover roots, small nodule-like protrusions developed that, when examined cytologically, were found to more closely resemble roots than nodules. Although the meristem was broadened and lacked a root cap, the protrusions had a central vascular bundle and other rootlike features. Our results suggest that morphogenesis of alfalfa root nodules can be uncoupled from infection thread formation. The genes encoded in the 8.7-kilobase nodulation fragment are sufficient in A. tumefaciens or R. trifolii backgrounds for nodule morphogenesis.

  View details for Web of Science ID A1985TZ13800035

  View details for PubMedID 3968028

• NUCLEOTIDE-SEQUENCE OF RHIZOBIUM-MELILOTI 1021 NODULATION GENES - NODD IS READ DIVERGENTLY FROM NODABC DNA-A JOURNAL OF MOLECULAR & CELLULAR BIOLOGY Egelhoff, T. T., Fisher, R. F., Jacobs, T. W., Mulligan, J. T., Long, S. R. 1985; 4 (3): 241-248

  Abstract

  Nodulation (nod) genes are required for Rhizobium meliloti to invade and stimulate nodule formation in its host, alfalfa. We have established the DNA sequence of nodD, nodA, and nodB, which are part of a gene cluster located 20 kb downstream of nifHDK on the R. meliloti pSym megaplasmid. The nodD open reading frame (308 amino acids) reads from proximal to nifHDK toward distal to nifHDK, divergently from nodA (196 aa) and nodB (217 aa). These two genes read from distal to nifHDK toward proximal, and are just upstream from the previously defined open reading frame for nodC. Fourteen Tn5 insertion sites have been sequenced in nodD, nodA, and nodB, revealing no major hotspots for insertion, but an overall preference for G/C bases at positions 1 and 9 of the 9-bp repeat.

  View details for Web of Science ID A1985AKH0800006

  View details for PubMedID 4006668

• INDUCTION OF RHOZOBIUM-MELILOTI NODC EXPRESSION BY PLANT EXUDATE REQUIRES NODD PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Mulligan, J. T., Long, S. R. 1985; 82 (19): 6609-6613

  Abstract

  The soil bacterium Rhizobium meliloti invades and establishes a symbiosis with host plants such as alfalfa. Bacterial nodulation (nod) genes are required for this invasion, but their mechanism of action and the timing of their expression are not known. We have used translational lacZ fusions to monitor expression of nodD and nodC, which are located in the cluster of four nod genes on the R. meliloti megaplasmid (pSym). nodD is expressed at comparable levels by broth-grown bacterial cells and by cells exposed to exudates from aseptically grown plants. Activity of the nodC-lacZ protein fusion in broth-grown bacterial cells is very low. nodC-lacZ activity is increased approximately equal to 30-fold by plant exudate when nodD is expressed at a high level but not when nodD expression is low. Both fusions show differences in expression when borne on inc-P vectors as compared to when located on the pSym megaplasmid. nodD expression from vector-borne copies of the nod segment and response of nodC to plant exudate appear to require additional loci on the megaplasmid. Our results suggest that regulation of bacterial nod gene expression is an important control mechanism early in the symbiosis, and that the biochemical nature of some nod gene products may be cryptic except in cells grown in the presence of plant exudate.

  View details for Web of Science ID A1985ARZ4800052

  View details for PubMedID 3931078

• WHY WHIP EGG-WHITES IN COPPER BOWLS NATURE MCGEE, H. J., Long, S. R., Briggs, W. R. 1984; 308 (5960): 667-668

  View details for Web of Science ID A1984SM02100076

• GENERALIZED TRANSDUCTION IN RHIZOBIUM-MELILOTI JOURNAL OF BACTERIOLOGY Martin, M. O., Long, S. R. 1984; 159 (1): 125-129

  Abstract

  Generalized transduction of Rhizobium meliloti 1021 was carried out by bacteriophage N3. Genetic markers on the chromosome and the pSym megaplasmid were transduced, along with markers on several IncP plasmids. Cotransduction between transposon Tn5 insertions and integrated recombinant plasmid markers permitted correlation of cotransductional frequencies and known physical distances. Bacteriophage N3 was capable of infecting several commonly used strains of R. meliloti.

  View details for Web of Science ID A1984SY40800019

  View details for PubMedID 6330025

• GENETIC-ANALYSIS OF RHIZOBIUM INFECTION Long, S. R., Jacobs, T. W., Egelhoff, T. T., deHostos, E. L., Mulligan, J. T., Tu, J. K., Sanga, R., Fisher, R. F. MARY ANN LIEBERT INC. 1984: 56?56

  View details for Web of Science ID A1984SF34100012

• THE MOLECULAR-BIOLOGY OF RHIZOBIUM LEGUME SYMBIOSIS INTERNATIONAL REVIEW OF CYTOLOGY-A SURVEY OF CELL BIOLOGY Verma, D. P., Long, S. 1983: 211-245

  View details for Web of Science ID A1983QK61800008

• Physical and genetic characterization of Rhizobium meliloti symbiotic mutants. Journal of molecular and applied genetics Buikema, W. J., Long, S. R., Brown, S. E., van den Bos, R. C., Earl, C., Ausubel, F. M. 1983; 2 (3): 249-260

  Abstract

  A set of 19 symbiotic mutants of Rhizobium meliloti obtained by a Tn5 "suicide plasmid" mutagenesis procedure was characterized genetically and physically. As part of this characterization, we showed that R. meliloti strain 1021, like other R. meliloti strains, contains a very large indigenous plasmid (greater than 300 Md) that carries the structural genes for nitrogenase (nifHDK genes). Among the 19 symbiotic mutations studied, at least six were shown to reside on the megaplasmid. By a "walking procedure" we obtained from a cosmid clone bank a set of overlapping cosmids that contained megaplasmid sequences contiguous to nifHDK. A 90 kb region of contiguous DNA from these cosmids was used to probe the mutant strains for rearrangements within this region. The same six mutations that were located on the megaplasmid mapped within the 90 kb region examined, which included the structural genes for nitrogenase (nifHDK). A majority of the mutations characterized in this study could not be correlated with a bona fide Tn5 insertion into a symbiotic gene.

  View details for PubMedID 6363587

• GENETIC-ANALYSIS OF SYMBIOTIC NITROGEN-FIXATION DEVELOPMENTS IN INDUSTRIAL MICROBIOLOGY Long, S. R., RUVKUN, G. B., Meade, H. M., BUIKEMA, W. E., Brown, S. E., Friedman, A. M., Ausubel, F. M. 1983; 24: 21-29

  View details for Web of Science ID A1983RZ30600004

• Cloning of Rhizobium meliloti nodulation genes by direct complementation of Nod? mutants Nature Long, S., Buikema, WJ, Ausubel, FM 1982; 298: 485-488
• STRUCTURAL STUDIES OF ALFALFA ROOTS INFECTED WITH NODULATION MUTANTS OF RHIZOBIUM-MELILOTI JOURNAL OF BACTERIOLOGY Hirsch, A. M., Long, S. R., Bang, M., Haskins, N., Ausubel, F. M. 1982; 151 (1): 411-419

  Abstract

  Alfalfa roots infected with four nodulation defective (Nod-) mutants of Rhizobium meliloti which were generated by transposon Tn5 mutagenesis were examined by light and electron microscopy. In one class of Nod- mutants, which we can nonreactive, the bacteria did not induce root hair curling or penetrate host cells. In a second class of Nod- mutants, which we call reactive, the bacteria induced some root hair curling and entered root epidermal cells, although no infection threads were formed. In addition, reactive Nod- mutants induced extensive root hair proliferation and hypertrophied roots. This study presents the details of the phenotype of the association between each mutant strain and alfalfa roots.

  View details for Web of Science ID A1982NW54100052

  View details for PubMedID 7085566

• PHYSICAL AND GENETIC-CHARACTERIZATION OF SYMBIOTIC AND AUXOTROPHIC MUTANTS OF RHIZOBIUM-MELILOTI INDUCED BY TRANSPOSON TN5 MUTAGENESIS JOURNAL OF BACTERIOLOGY Meade, H. M., Long, S. R., RUVKUN, G. B., Brown, S. E., Ausubel, F. M. 1982; 149 (1): 114-122

  Abstract

  We have physically and genetically characterized 20 symbiotic and 20 auxotrophic mutants of Rhizobium meliloti, the nitrogen-fixing symbiont of alfalfa (Medicago sativa), isolated by transposon Tn5 mutagenesis. A "suicide plasmid" mutagenesis procedure was used to generate TN-5-induced mutants, and both auxotrophic and symbiotic mutants were found at a frequency of 0.3% among strains containing random TN5 insertions. Two classes of symbiotic mutants were isolated: 4 of the 20 formed no nodules at all (Nod-), and 16 formed nodules which failed to fix nitrogen (Fix-). We used a combination of physical and genetic criteria to determine that in most cases the auxotrophic and symbiotic phenotypes could be correlated with the insertion of a single Tn5 elements. Once the Tn5 element was inserted into the R. meliloti genome, the frequency of its transposition to a new site was approximately 10-8 and the frequency of precise excision was less than 10-9. In approximately 25% of the mutant strains, phage Mu DNA sequences, which originated from the suicide plasmid used to generate the Tn5 transpositions, were also found in the R. meliloti genome contiguous with Tn5. These later strains exhibited anomalous conjugation properties, and therefore we could not correlate the symbiotic phenotype with a Tn5 insertion. In general, we found that both physical and genetic tests were required to fully characterize transposon-induced mutations.

  View details for Web of Science ID A1982MX09200015

  View details for PubMedID 6274841

• ISRm1: A Rhizobium meliloti insertion sequence that transposes preferentially into nitrogen fixation genes. Journal of molecular and applied genetics RUVKUN, G. B., Long, S. R., Meade, H. M., van den Bos, R. C., Ausubel, F. M. 1982; 1 (5): 405-418

  Abstract

  After transposon Tn5 mutagenesis, a high proportion of Rhizobium meliloti symbiotic mutants do not contain Tn5 insertions in symbiotic genes. Instead, the mutations in these strains are correlated with the presence of an endogenous insertion sequence (ISRm1) in nitrogen fixation (nif) or symbiotic genes which are adjacent to the nif genes. ISRm1 is 1.4 kb and transposes to at least three restriction fragments in the nif region at a frequency between 10(-2) and 10(-3). A nif region restriction fragment containing ISRm1 was cloned from one of the mutant strains unable to fix nitrogen symbiotically (Fix-) and the resulting plasmid was used as a hybridization probe. ISRm1 is present at least ten times in the R. meliloti genome but is not present in any other R. meliloti strains, E. coli strains, or Rhizobium species tested. We demonstrated that the Fix- phenotype correlated with ISRm1 transposition is indeed caused by ISRm1 insertion by conjugating a cloned fragment containing ISRm1 into a wild type Fix+ R. meliloti host and replacing the normal genomic nif fragment with the nif::ISRm1 fragment. The resulting strain was Fix-.

  View details for PubMedID 6296251

• CONSTRUCTION OF A BROAD HOST RANGE COSMID CLONING VECTOR AND ITS USE IN THE GENETIC-ANALYSIS OF RHIZOBIUM MUTANTS GENE Friedman, A. M., Long, S. R., Brown, S. E., Buikema, W. J., Ausubel, F. M. 1982; 18 (3): 289-296

  Abstract

  We have constructed a cosmid derivative of the low copy-number broad host-range cloning vector pRK290 (Ditta et al., 1980) by inserting a 1.6-kb Bg/II fragment containing lambda cos into the unique Bg/II site in pRK290. The new vector, pLAFR1, is 21.6 kb long, confers tetracycline resistance, contains a unique EcoRI site, and can be mobilized into and stably replicates within many Gram-negative hosts. We constructed a clone bank of Rhizobium meliloti DNA in pLAFR1 using a partial EcoRI digest. The mean insert size was 23.1 kb. When the clone bank was mated (en masse) from Escherichia coli to various R. meliloti auxotrophic mutants, tetracycline-resistant (Tcr) transconjugants were obtained at frequencies ranging from 0.1 to 0.8, and among these, prototrophic colonies were obtained at frequencies ranging from 0.001 to 0.007. pLAFR1 cosmids were mobilized from R. meliloti prototrophic colonies into E. coli and then reintroduced into R. meliloti auxotrophs. In most cases, 100% of these latter Tcr transconjugants were prototrophic.

  View details for Web of Science ID A1982PG36600011

  View details for PubMedID 6290332

• CLONING OF RHIZOBIUM-MELILOTI NODULATION GENES BY DIRECT COMPLEMENTATION OF NOD- MUTANTS NATURE Long, S. R., Buikema, W. J., Ausubel, F. M. 1982; 298 (5873): 485-488

  View details for Web of Science ID A1982NZ37500057

• MOLECULAR-GENETICS OF SYMBIOTIC NITROGEN-FIXATION COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY RUVKUN, G. B., Long, S. R., Meade, H. M., Ausubel, F. M. 1980; 45: 492-499

  View details for Web of Science ID A1980MG40600007