Daniel Jarosz

All Publications

• Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae. Molecular cell Itakura, A. K., Chakravarty, A. K., Jakobson, C. M., Jarosz, D. F. 2019

  Abstract

  Theory and experiments suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors, but the mechanisms driving pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.

  View details for DOI 10.1016/j.molcel.2019.10.027

  View details for PubMedID 31757756

• A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program. Molecular cell Chakravarty, A. K., Smejkal, T., Itakura, A. K., Garcia, D. M., Jarosz, D. F. 2019

  Abstract

  Spatiotemporal gene regulation is often driven by RNA-binding proteins that harbor long intrinsically disordered regions in addition to folded RNA-binding domains. We report that the disordered region of theevolutionarily ancient developmental regulator Vts1/Smaug drives self-assembly into gel-like condensates. These proteinaceous particles are not composed of amyloid, yet they are infectious, allowing them to act as a protein-based epigenetic element: a prion [SMAUG+]. In contrast to many amyloid prions, condensation of Vts1 enhances its function in mRNA decay, and its self-assembly properties are conserved over large evolutionary distances. Yeast cells harboring [SMAUG+] downregulate a coherent network of mRNAs and exhibit improved growth under nutrient limitation. Vts1 condensates formed from purified protein can transform naive cells to acquire [SMAUG+]. Our data establish that non-amyloid self-assembly of RNA-binding proteins can drive a form of epigenetics beyond the chromosome, instilling adaptive gene expression programs that are heritable over long biological timescales.

  View details for DOI 10.1016/j.molcel.2019.10.028

  View details for PubMedID 31757755

• Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships CELL SYSTEMS Jakobson, C. M., Jarosz, D. F. 2019; 8 (5): 363-+

  View details for DOI 10.1016/j.cels.2019.04.002

  View details for Web of Science ID 000468628000003

• Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae. Nature communications Jakobson, C. M., She, R., Jarosz, D. F. 2019; 10 (1): 1222

  Abstract

  Quantitative genetics aims to map genotype to phenotype, often with the goal of understanding how organisms evolved. However, it remains unclear whether the genetic variants identified are exemplary of evolution. Here we analyzed progeny of two wild Saccharomyces cerevisiae isolates to identify 195 loci underlying complex metabolic traits, resolving 107 to single polymorphisms with diverse molecular mechanisms. More than 20% of causal variants exhibited patterns of emergence inconsistent with neutrality. Moreover, contrary to drift-centric expectation, variation in diverse wild yeast isolates broadly exhibited this property: over 30% of shared natural variants exhibited phylogenetic signatures suggesting that they are not neutral. This pattern is likely attributable to both homoplasy and balancing selection on ancestral polymorphism. Variants that emerged repeatedly were more likely to have done so in isolates from the same ecological niche. Our results underscore the power of super-resolution mapping of ecologically relevant traits in understanding adaptation and evolution.

  View details for PubMedID 30874558

• It's not magic - Hsp90 and its effects on genetic and epigenetic variation. Seminars in cell & developmental biology Zabinsky, R. A., Mason, G. A., Queitsch, C., Jarosz, D. F. 2018

  Abstract

  Canalization, or phenotypic robustness in the face of environmental and genetic perturbation, is an emergent property of living systems. Although this phenomenon has long been recognized, its molecular underpinnings have remained enigmatic until recently. Here, we review the contributions of the molecular chaperone Hsp90, a protein that facilitates the folding of many key regulators of growth and development, to canalization of phenotype - and de-canalization in times of stress - drawing on studies in eukaryotes as diverse as baker's yeast, mouse ear cress, and blind Mexican cavefish. Hsp90 is a hub of hubs that interacts with many so-called 'client proteins' that affect virtually every aspect of cell signaling and physiology. As Hsp90 facilitates client folding and stability, it can epistatically suppress or enable the expression of genetic variants in its clients and other proteins that acquire client status through mutation. Hsp90's vast interaction network explains the breadth of its phenotypic reach, including Hsp90-dependent de novo mutations and epigenetic effects on gene regulation. Intrinsic links between environmental stress and Hsp90 function thus endow living systems with phenotypic plasticity in fluctuating environments. As environmental perturbations alter Hsp90 function, they also alter Hsp90's interaction with its client proteins, thereby re-wiring networks that determine the genotype-to-phenotype map. Ensuing de-canalization of phenotype creates phenotypic diversity that is not simply stochastic, but often has an underlying genetic basis. Thus, extreme phenotypes can be selected, and assimilated so that they no longer require environmental stress to manifest. In addition to acting on standing genetic variation, Hsp90 perturbation has also been linked to increased frequency of de novo variation and several epigenetic phenomena, all with the potential to generate heritable phenotypic change. Here, we aim to clarify and discuss the multiple means by which Hsp90 can affect phenotype and possibly evolutionary change, and identify their underlying common feature: at its core, Hsp90 interacts epistatically through its chaperone function with many other genes and their gene products. Its influence on phenotypic diversification is thus not magic but rather a fundamental property of genetics.

  View details for PubMedID 29807130

• It Pays To Be in Phase BIOCHEMISTRY Itakura, A. K., Futia, R. A., Jarosz, D. F. 2018; 57 (17): 2520–29

  Abstract

  To survive, organisms must orchestrate competing biochemical and regulatory processes in time and space. Recent work has suggested that the underlying chemical properties of some biomolecules allow them to self-organize and that life may have exploited this property to organize biochemistry in space and time. Such phase separation is ubiquitous, particularly among the many regulatory proteins that harbor prion-like intrinsically disordered domains. And yet, despite evident regulation by post-translational modification and myriad other stimuli, the biological significance of many phase-separated compartments remains uncertain. Many potential functions have been proposed, but far fewer have been demonstrated. A burgeoning subfield at the intersection of cell biology and polymer physics has defined the biophysical underpinnings that govern the genesis and stability of these particles. The picture is complex: many assemblies are composed of multiple proteins that each have the capacity to phase separate. Here, we briefly discuss this foundational work and survey recent efforts combining targeted biochemical perturbations and quantitative modeling to specifically address the diverse roles that phase separation processes may play in biology.

  View details for DOI 10.1021/acs.biochem.8b00205

  View details for Web of Science ID 000431466700014

  View details for PubMedID 29509425

• Mapping Causal Variants with Single-Nucleotide Resolution Reveals Biochemical Drivers of Phenotypic Change CELL She, R., Jarosz, D. F. 2018; 172 (3): 478-+

  Abstract

  Understanding the sequence determinants that give rise to diversity among individuals and species is the central challenge of genetics. However, despite ever greater numbers of sequenced genomes, most genome-wide association studies cannot distinguish causal variants from linked passenger mutations spanning many genes. We report that this inherent challenge can be overcome in model organisms. By pushing the advantages of inbred crossing to its practical limit in Saccharomyces cerevisiae, we improved the statistical resolution of linkage analysis to single nucleotides. This "super-resolution" approach allowed us to map 370 causal variants across 26 quantitative traits. Missense, synonymous, and cis-regulatory mutations collectively gave rise to phenotypic diversity, providing mechanistic insight into the basis of evolutionary divergence. Our data also systematically unmasked complex genetic architectures, revealing that multiple closely linked driver mutations frequently act on the same quantitative trait. Single-nucleotide mapping thus complements traditional deletion and overexpression screening paradigms and opens new frontiers in quantitative genetics.

  View details for PubMedID 29373829

  View details for PubMedCentralID PMC5788306

• Protein-Based Inheritance: Epigenetics beyond the Chromosome MOLECULAR CELL Harvey, Z. H., Chen, Y., Jarosz, D. F. 2018; 69 (2): 195–202

  Abstract

  Epigenetics refers to changes in phenotype that are not rooted in DNA sequence. This phenomenon has largely been studied in the context of chromatin modification. Yet many epigenetic traits are instead linked to self-perpetuating changes in the individual or collective activity of proteins. Most such proteins are prions (e.g., [PSI+], [URE3], [SWI+], [MOT3+], [MPH1+], [LSB+], and [GAR+]), which have the capacity to adopt at least one conformation that self-templates over long biological timescales. This allows them to serve as protein-based epigenetic elements that are readily broadcast through mitosis and meiosis. In some circumstances, self-templating can fuel disease, but it also permits access to multiple activity states from the same polypeptide and transmission of that information across generations. Ensuing phenotypic changes allow genetically identical cells to express diverse and frequently adaptive phenotypes. Although long thought to be rare, protein-based epigenetic inheritance has now been uncovered in all domains of life.

  View details for PubMedID 29153393

  View details for PubMedCentralID PMC5775936

• Specification of Physiologic and Disease States by Distinct Proteins and Protein Conformations CELL Jarosz, D. F., Khurana, V. 2017; 171 (5): 1001–14

  Abstract

  Protein conformational states-from intrinsically disordered ensembles to amyloids that underlie the self-templating, infectious properties of prion-like proteins-have attracted much attention. Here, we highlight the diversity, including differences in biophysical properties, that drive distinct biological functions and pathologies among self-templating proteins. Advances in chemical genomics, gene editing, and model systems now permit deconstruction of the complex interplay between these protein states and the host factors that react to them. These methods reveal that conformational switches modulate normal and abnormal information transfer and that intimate relationships exist between the intrinsic function of proteins and the deleterious consequences of their misfolding.

  View details for PubMedID 29149602

• Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA She, R., Chakravarty, A. K., Layton, C. J., Chircus, L. M., Andreasson, J. O., Damaraju, N., McMahon, P. L., Buenrostro, J. D., Jarosz, D. F., Greenleaf, W. J. 2017; 114 (14): 3619-3624

  Abstract

  RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying these posttranscriptional gene regulators combines transcriptome-wide throughput and biophysical precision. Here, we describe an assay that accomplishes this. Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. We used the platform to quantitatively measure the binding affinity of the prototypical RBP Vts1 for every transcript in the Saccharomyces cerevisiae genome. The scale and precision of these measurements revealed many previously unknown features of this well-studied RBP. Our transcribed genome array (TGA) assayed both rare and abundant transcripts with equivalent proficiency, revealing hundreds of low-abundance targets missed by previous approaches. These targets regulated diverse biological processes including nutrient sensing and the DNA damage response, and implicated Vts1 in de novo gene "birth." TGA provided single-nucleotide resolution for each binding site and delineated a highly specific sequence and structure motif for Vts1 binding. Changes in transcript levels in vts1Δ cells established the regulatory function of these binding sites. The impact of Vts1 on transcript abundance was largely independent of where it bound within an mRNA, challenging prevailing assumptions about how this RBP drives RNA degradation. TGA thus enables a quantitative description of the relationship between variant RNA structures, affinity, and in vivo phenotype on a transcriptome-wide scale. We anticipate that TGA will provide similarly comprehensive and quantitative insights into the function of virtually any RBP.

  View details for DOI 10.1073/pnas.1618370114

  View details for Web of Science ID 000398159000041

  View details for PubMedID 28325876

• A common bacterial metabolite elicits prion-based bypass of glucose repression. eLife Garcia, D. M., Dietrich, D., Clardy, J., Jarosz, D. F. 2016; 5

  Abstract

  Robust preference for fermentative glucose metabolism has motivated domestication of the budding yeast Saccharomyces cerevisiae. This program can be circumvented by a protein-based genetic element, the [GAR(+)] prion, permitting simultaneous metabolism of glucose and other carbon sources. Diverse bacteria can elicit yeast cells to acquire [GAR(+)], although the molecular details of this interaction remain unknown. Here we identify the common bacterial metabolite lactic acid as a strong [GAR(+)] inducer. Transient exposure to lactic acid caused yeast cells to heritably circumvent glucose repression. This trait had the defining genetic properties of [GAR(+)], and did not require utilization of lactic acid as a carbon source. Lactic acid also induced [GAR(+)]-like epigenetic states in fungi that diverged from S. cerevisiae ~200 million years ago, and in which glucose repression evolved independently. To our knowledge, this is the first study to uncover a bacterial metabolite with the capacity to potently induce a prion.

  View details for DOI 10.7554/eLife.17978

  View details for PubMedID 27906649

  View details for PubMedCentralID PMC5132342

• Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits. Cell Chakrabortee, S., Byers, J. S., Jones, S., Garcia, D. M., Bhullar, B., Chang, A., She, R., Lee, L., Fremin, B., Lindquist, S., Jarosz, D. F. 2016; 167 (2): 369-381 e12

  Abstract

  Prions are a paradigm-shifting mechanism of inheritance in which phenotypes are encoded by self-templating protein conformations rather than nucleic acids. Here, we examine the breadth of protein-based inheritance across the yeast proteome by assessing the ability of nearly every open reading frame (ORF; ∼5,300 ORFs) to induce heritable traits. Transient overexpression of nearly 50 proteins created traits that remained heritable long after their expression returned to normal. These traits were beneficial, had prion-like patterns of inheritance, were common in wild yeasts, and could be transmitted to naive cells with protein alone. Most inducing proteins were not known prions and did not form amyloid. Instead, they are highly enriched in nucleic acid binding proteins with large intrinsically disordered domains that have been widely conserved across evolution. Thus, our data establish a common type of protein-based inheritance through which intrinsically disordered proteins can drive the emergence of new traits and adaptive opportunities.

  View details for DOI 10.1016/j.cell.2016.09.017

  View details for PubMedID 27693355

  View details for PubMedCentralID PMC5066306

• Hsp90: A Global Regulator of the Genotype-to-Phenotype Map in Cancers. Advances in cancer research Jarosz, D. 2016; 129: 225-247

  Abstract

  Cancer cells have the unusual capacity to limit the cost of the mutation load that they harbor and simultaneously harness its evolutionary potential. This property fuels drug resistance, a key failure mode in oncogene-directed therapy. However, the factors that regulate this capacity might also provide an Achilles' heel that could be exploited therapeutically. Recently, insight has come from a seemingly distant field: protein folding. It is now clear that protein homeostasis broadly supports malignancy and fuels the rapid evolution of drug resistance. Among protein homeostatic mechanisms that influence cancer biology, the essential ATP-driven molecular chaperone heat-shock protein 90 (Hsp90) is especially important. Hsp90 catalyzes folding of many proteins that regulate growth and development. These "client" kinases, transcription factors, and ubiquitin ligases often play critical roles in human disease, especially cancer. Studies in a wide range of systems-from single-celled organisms to human tumor samples-suggest that Hsp90 can broadly reshape the map between genotype and phenotype, acting as a "capacitor" and "potentiator" of genetic variation. Indeed, it has likely done so to such a degree that it has left an impress on diverse genome sequences. Hsp90 can constitute as much as 5% of total protein in transformed cells and increased levels of heat-shock activation correlate with poor prognosis in breast cancer. These findings and others have motivated a flurry of interest in Hsp90 inhibitors as cancer therapeutics, which have met with rather limited success as single agents, but may eventually prove invaluable in limiting the emergence of resistance to other chemotherapeutics, both genotoxic and molecularly targeted. Here, we provide an overview of Hsp90 function, review its relationship to genetic variation and the evolution of new traits, and discuss the importance of these findings for cancer biology and future efforts to drug this pathway.

  View details for DOI 10.1016/bs.acr.2015.11.001

  View details for PubMedID 26916007

• An Evolutionarily Conserved Prion-like Element Converts Wild Fungi from Metabolic Specialists to Generalists. Cell Jarosz, D. F., Lancaster, A. K., Brown, J. C., Lindquist, S. 2014; 158 (5): 1072-1082

  Abstract

  [GAR(+)] is a protein-based element of inheritance that allows yeast (Saccharomyces cerevisiae) to circumvent a hallmark of their biology: extreme metabolic specialization for glucose fermentation. When glucose is present, yeast will not use other carbon sources. [GAR(+)] allows cells to circumvent this "glucose repression." [GAR(+)] is induced in yeast by a factor secreted by bacteria inhabiting their environment. We report that de novo rates of [GAR(+)] appearance correlate with the yeast's ecological niche. Evolutionarily distant fungi possess similar epigenetic elements that are also induced by bacteria. As expected for a mechanism whose adaptive value originates from the selective pressures of life in biological communities, the ability of bacteria to induce [GAR(+)] and the ability of yeast to respond to bacterial signals have been extinguished repeatedly during the extended monoculture of domestication. Thus, [GAR(+)] is a broadly conserved adaptive strategy that links environmental and social cues to heritable changes in metabolism.

  View details for DOI 10.1016/j.cell.2014.07.024

  View details for PubMedID 25171408

• Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformation of metabolism. Cell Jarosz, D. F., Brown, J. C., Walker, G. A., Datta, M. S., Ung, W. L., Lancaster, A. K., Rotem, A., Chang, A., Newby, G. A., Weitz, D. A., Bisson, L. F., Lindquist, S. 2014; 158 (5): 1083-1093

  Abstract

  In experimental science, organisms are usually studied in isolation, but in the wild, they compete and cooperate in complex communities. We report a system for cross-kingdom communication by which bacteria heritably transform yeast metabolism. An ancient biological circuit blocks yeast from using other carbon sources in the presence of glucose. [GAR(+)], a protein-based epigenetic element, allows yeast to circumvent this "glucose repression" and use multiple carbon sources in the presence of glucose. Some bacteria secrete a chemical factor that induces [GAR(+)]. [GAR(+)] is advantageous to bacteria because yeast cells make less ethanol and is advantageous to yeast because their growth and long-term viability is improved in complex carbon sources. This cross-kingdom communication is broadly conserved, providing a compelling argument for its adaptive value. By heritably transforming growth and survival strategies in response to the selective pressures of life in a biological community, [GAR(+)] presents a unique example of Lamarckian inheritance.

  View details for DOI 10.1016/j.cell.2014.07.025

  View details for PubMedID 25171409

• Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish SCIENCE Rohner, N., Jarosz, D. F., Kowalko, J. E., Yoshizawa, M., Jeffery, W. R., Borowsky, R. L., Lindquist, S., Tabin, C. J. 2013; 342 (6164): 1372-1375

  Abstract

  In the process of morphological evolution, the extent to which cryptic, preexisting variation provides a substrate for natural selection has been controversial. We provide evidence that heat shock protein 90 (HSP90) phenotypically masks standing eye-size variation in surface populations of the cavefish Astyanax mexicanus. This variation is exposed by HSP90 inhibition and can be selected for, ultimately yielding a reduced-eye phenotype even in the presence of full HSP90 activity. Raising surface fish under conditions found in caves taxes the HSP90 system, unmasking the same phenotypic variation as does direct inhibition of HSP90. These results suggest that cryptic variation played a role in the evolution of eye loss in cavefish and provide the first evidence for HSP90 as a capacitor for morphological evolution in a natural setting.

  View details for DOI 10.1126/science.1240276

  View details for Web of Science ID 000328196000051

  View details for PubMedID 24337296

• Prions are a common mechanism for phenotypic inheritance in wild yeasts NATURE Halfmann, R., Jarosz, D. F., Jones, S. K., Chang, A., Lancaster, A. K., Lindquist, S. 2012; 482 (7385): 363-U1507

  Abstract

  The self-templating conformations of yeast prion proteins act as epigenetic elements of inheritance. Yeast prions might provide a mechanism for generating heritable phenotypic diversity that promotes survival in fluctuating environments and the evolution of new traits. However, this hypothesis is highly controversial. Prions that create new traits have not been found in wild strains, leading to the perception that they are rare 'diseases' of laboratory cultivation. Here we biochemically test approximately 700 wild strains of Saccharomyces for [PSI(+)] or [MOT3(+)], and find these prions in many. They conferred diverse phenotypes that were frequently beneficial under selective conditions. Simple meiotic re-assortment of the variation harboured within a strain readily fixed one such trait, making it robust and prion-independent. Finally, we genetically screened for unknown prion elements. Fully one-third of wild strains harboured them. These, too, created diverse, often beneficial phenotypes. Thus, prions broadly govern heritable traits in nature, in a manner that could profoundly expand adaptive opportunities.

  View details for DOI 10.1038/nature10875

  View details for Web of Science ID 000300287100038

  View details for PubMedID 22337056

• Hsp90 and Environmental Stress Transform the Adaptive Value of Natural Genetic Variation SCIENCE Jarosz, D. F., Lindquist, S. 2010; 330 (6012): 1820-1824

  Abstract

  How can species remain unaltered for long periods yet also undergo rapid diversification? By linking genetic variation to phenotypic variation via environmental stress, the Hsp90 protein-folding reservoir might promote both stasis and change. However, the nature and adaptive value of Hsp90-contingent traits remain uncertain. In ecologically and genetically diverse yeasts, we find such traits to be both common and frequently adaptive. Most are based on preexisting variation, with causative polymorphisms occurring in coding and regulatory sequences alike. A common temperature stress alters phenotypes similarly. Both selective inhibition of Hsp90 and temperature stress increase correlations between genotype and phenotype. This system broadly determines the adaptive value of standing genetic variation and, in so doing, has influenced the evolution of current genomes.

  View details for DOI 10.1126/science.1195487

  View details for Web of Science ID 000285603700040

  View details for PubMedID 21205668

• Protein Homeostasis and the Phenotypic Manifestation of Genetic Diversity: Principles and Mechanisms ANNUAL REVIEW OF GENETICS, VOL 44 Jarosz, D. F., Taipale, M., Lindquist, S. 2010; 44: 189-216

  Abstract

  Changing a single nucleotide in a genome can have profound consequences under some conditions, but the same change can have no consequences under others. Indeed, organisms can be surprisingly robust to environmental and genetic perturbations. Yet, the mechanisms underlying such robustness are controversial. Moreover, how they might affect evolutionary change remains enigmatic. Here, we review the recently appreciated central role of protein homeostasis in buffering and potentiating genetic variation and discuss how these processes mediate the critical influence of the environment on the relationship between genotype and phenotype. Deciphering how robustness emerges from biological organization and the mechanisms by which it is overcome in changing environments will lead to a more complete understanding of both fundamental evolutionary processes and diverse human diseases.

  View details for DOI 10.1146/annurev.genet.40.110405.090412

  View details for Web of Science ID 000286042600009

  View details for PubMedID 21047258

• A single amino acid governs enhanced activity of DinB DNA polymerases on damaged templates NATURE Jarosz, D. F., Godoy, V. G., Delaney, J. C., Essigmann, J. M., Walker, G. C. 2006; 439 (7073): 225-228

  Abstract

  Translesion synthesis (TLS) by Y-family DNA polymerases is a chief mechanism of DNA damage tolerance. Such TLS can be accurate or error-prone, as it is for bypass of a cyclobutane pyrimidine dimer by DNA polymerase eta (XP-V or Rad30) or bypass of a (6-4) TT photoproduct by DNA polymerase V (UmuD'2C), respectively. Although DinB is the only Y-family DNA polymerase conserved among all domains of life, the biological rationale for this striking conservation has remained enigmatic. Here we report that the Escherichia coli dinB gene is required for resistance to some DNA-damaging agents that form adducts at the N2-position of deoxyguanosine (dG). We show that DinB (DNA polymerase IV) catalyses accurate TLS over one such N2-dG adduct (N2-furfuryl-dG), and that DinB and its mammalian orthologue, DNA polymerase kappa, insert deoxycytidine (dC) opposite N2-furfuryl-dG with 10-15-fold greater catalytic proficiency than opposite undamaged dG. We also show that mutating a single amino acid, the 'steric gate' residue of DinB (Phe13 --> Val) and that of its archaeal homologue Dbh (Phe12 --> Ala), separates the abilities of these enzymes to perform TLS over N2-dG adducts from their abilities to replicate an undamaged template. We propose that DinB and its orthologues are specialized to catalyse relatively accurate TLS over some N2-dG adducts that are ubiquitous in nature, that lesion bypass occurs more efficiently than synthesis on undamaged DNA, and that this specificity may be achieved at least in part through a lesion-induced conformational change.

  View details for DOI 10.1038/nature04318

  View details for Web of Science ID 000234538400045

  View details for PubMedID 16407906

• Remembering the past: a new form of protein-based inheritance Jarosz, D. F. TAYLOR & FRANCIS INC. 2019: 10

  View details for Web of Science ID 000477005700018

• Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships. Cell systems Jakobson, C. M., Jarosz, D. F. 2019

  Abstract

  The statistical complexity of heredity has long been evident, but its molecular origins remain elusive. Toinvestigate, we charted 90 comprehensive genotype-to-phenotype maps in a large population of wild diploid yeast. In contrast to long-standing assumptions, all types of genetic variation contributed similarly to phenotype. Causal synonymous and regulatory variants exhibited distinct molecular signatures, as did nonlinearities in heterozygote fitness that likely contribute to hybrid vigor. Highly pleiotropic variants altered disordered sequences within signaling hubs, and their effects correlated across environments-even when antagonistic-suggesting that large fitness gains bring concomitant costs. Naturalgenetic networks defined by the causal loci differed from those determined by precise gene deletionsor protein-protein interactions. Finally, we found that traits that would appear omnigenic in less powered studies do in fact have finite genetic determinants.Integrating these molecular principles will be crucial as genome reading and writing become routine in research, industry, and medicine.

  View details for PubMedID 31054809

• It's not magic-Hsp90 and its effects on genetic and epigenetic variation SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY Zabinsky, R. A., Mason, G., Queitsch, C., Jarosz, D. F. 2019; 88: 21–35

  View details for DOI 10.1016/j.semcdb.2018.05.015

  View details for Web of Science ID 000460291000004

• Molecular drivers and epigenetic modifiers of complex heritability revealed by a natural genotype-to-phenotype map Jakobson, C., Aguilar-Rodriguez, J., Jarosz, D. AMER CHEMICAL SOC. 2019

  View details for Web of Science ID 000478860501518

• More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change JOURNAL OF MOLECULAR BIOLOGY Chakravarty, A. K., Jarosz, D. F. 2018; 430 (23): 4607–18

  View details for DOI 10.1016/j.jmb.2018.07.017

  View details for Web of Science ID 000449898500002

• Mutations, protein homeostasis, and epigenetic control of genome integrity. DNA repair Xie, J. L., Jarosz, D. F. 2018

  Abstract

  From bacteria to humans, ancient stress responses enable organisms to contend with damage to both the genome and the proteome. These pathways have long been viewed as fundamentally separate responses. Yet recent discoveries from multiple fields have revealed surprising links between the two. Many DNA-damaging agents also target proteins, and mutagenesis induced by DNA damage produces variant proteins that are prone to misfolding, degradation, and aggregation. Likewise, recent studies have observed pervasive engagement of a p53-mediated response, and other factors linked to maintenance of genomic integrity, in response to misfolded protein stress. Perhaps most remarkably, protein aggregation and self-assembly has now been observed in multiple proteins that regulate the DNA damage response. The importance of these connections is highlighted by disease models of both cancer and neurodegeneration, in which compromised DNA repair machinery leads to profound defects in protein quality control, and vice versa.

  View details for PubMedID 30181040

• More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change. Journal of molecular biology Chakravarty, A. K., Jarosz, D. F. 2018

  Abstract

  A central tenet of molecular biology is that heritable information is stored in nucleic acids. But this paradigm has been overturned by a group of proteins called 'prions'. Prion proteins, many of which are intrinsically disordered, can adopt multiple conformations, at least one of which has the capacity to self-template. This unusual folding landscape drives a form of extreme epigenetic inheritance that can be stable through both mitotic and meiotic cell divisions. Although the first prion discovered - mammalian PrP - is the causative agent of debilitating neuropathies, many additional prions have now been identified that are not obviously detrimental and can even be adaptive. Intrinsically disordered regions, which endow proteins with the bulk property of 'phase-separation,' can also be drivers of prion formation. Indeed, many protein domains that promote phase separation have been described as prion-like. In this review, we describe how prions lie at the crossroads of phase-separation, epigenetic inheritance and evolutionary adaptation.

  View details for PubMedID 30031007

• Organizing biochemistry in space and time using prion-like self-assembly. Current opinion in systems biology Jakobson, C. M., Jarosz, D. F. 2018; 8: 16–24

  Abstract

  Prion-like proteins have the capacity to adopt multiple stable conformations, at least one of which can recruit proteins from the native conformation into the alternative fold. Although classically associated with disease, prion-like assembly has recently been proposed to organize a range of normal biochemical processes in space and time. Organisms from bacteria to mammals use prion-like mechanisms to (re)organize their proteome in response to intracellular and extracellular stimuli. Prion-like behavior is an economical means to control biochemistry and gene regulation at the systems level, and prions can act as protein-based genes to facilitate quasi-Lamarckian inheritance of induced traits. These mechanisms allow individual cells to express distinct heritable traits using the same complement of polypeptides. Understanding and controlling prion-like behavior is therefore a promising strategy to combat diverse pathologies and organize engineered biological systems.

  View details for PubMedID 29725624

• High-throughput Screening for Protein-based Inheritance in S. cerevisiae JOVE-JOURNAL OF VISUALIZED EXPERIMENTS Byers, J. S., Jarosz, D. F. 2017

  Abstract

  The encoding of biological information that is accessible to future generations is generally achieved via changes to the DNA sequence. Long-lived inheritance encoded in protein conformation (rather than sequence) has long been viewed as paradigm-shifting but rare. The best characterized examples of such epigenetic elements are prions, which possess a self-assembling behavior that can drive the heritable manifestation of new phenotypes. Many archetypal prions display a striking N/Q-rich sequence bias and assemble into an amyloid fold. These unusual features have informed most screening efforts to identify new prion proteins. However, at least three known prions (including the founding prion, PrPSc) do not harbor these biochemical characteristics. We therefore developed an alternative method to probe the scope of protein-based inheritance based on a property of mass action: the transient overexpression of prion proteins increases the frequency at which they acquire a self-templating conformation. This paper describes a method for analyzing the capacity of the yeast ORFeome to elicit protein-based inheritance. Using this strategy, we previously found that >1% of yeast proteins could fuel the emergence of biological traits that were long-lived, stable, and arose more frequently than genetic mutation. This approach can be employed in high throughput across entire ORFeomes or as a targeted screening paradigm for specific genetic networks or environmental stimuli. Just as forward genetic screens define numerous developmental and signaling pathways, these techniques provide a methodology to investigate the influence of protein-based inheritance in biological processes.

  View details for PubMedID 28809826

• Old moms say, no Sir. Science (New York, N.Y.) Gitler, A. D., Jarosz, D. F. 2017; 355 (6330): 1126-1127

  View details for DOI 10.1126/science.aam9740

  View details for PubMedID 28302810

• Meeting Report on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems. G3 (Bethesda, Md.) Jarosz, D., Dudley, A. M. 2017

  Abstract

  The fourth EMBO-sponsored conference on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems (https://www.embl.de/training/events/2016/EAE16-01/), was held at the EMBL in Heidelberg, Germany, October 19-23, 2016. The conference was organized by Judith Berman (Tel Aviv University), Maitreya Dunham (University of Washington), Jun-Yi Leu (Academia Sinica), and Lars Steinmetz (EMBL Heidelberg and Stanford University). The meeting attracted ~120 researchers from 28 countries and covered a wide range of topics in the fields of genetics, evolutionary biology, and ecology with a unifying focus on yeast as a model system. Attendees enjoyed the Keith Haring inspired yeast florescence microscopy artwork (Figure 1), a unique feature of the meeting since its inception, and the one-minute flash talks that catalyzed discussions at two vibrant poster sessions. The meeting coincided with the 20th anniversary of the publication describing the sequence of the first eukaryotic genome, Saccharomyces cerevisiae (Goffeau et al. 1996). Many of the conference talks focused on important questions about what is contained in the genome, how genomes evolve, and the architecture and behavior of communities of phenotypically and genotypically diverse microorganisms. Here, we summarize highlights of the research talks around these themes. Nearly all presentations focused on novel findings, and we refer the reader to relevant manuscripts that have subsequently been published.

  View details for PubMedID 28814445

• Pernicious pathogens or expedient elements of inheritance: the significance of yeast prions. PLoS pathogens Byers, J. S., Jarosz, D. F. 2014; 10 (4)

  View details for DOI 10.1371/journal.ppat.1003992

  View details for PubMedID 24722628

  View details for PubMedCentralID PMC3983059

• Pernicious pathogens or expedient elements of inheritance: the significance of yeast prions. PLoS pathogens Byers, J. S., Jarosz, D. F. 2014; 10 (4)

  View details for DOI 10.1371/journal.ppat.1003992

  View details for PubMedID 24722628

• Rebels with a cause: molecular features and physiological consequences of yeast prions FEMS YEAST RESEARCH Garcia, D. M., Jarosz, D. F. 2014; 14 (1): 136-147

  View details for DOI 10.1111/1567-1364.12116

  View details for Web of Science ID 000330816300013

• HSP90 at the hub of protein homeostasis: emerging mechanistic insights NATURE REVIEWS MOLECULAR CELL BIOLOGY Taipale, M., Jarosz, D. F., Lindquist, S. 2010; 11 (7): 515-528

  Abstract

  Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone that facilitates the maturation of a wide range of proteins (known as clients). Clients are enriched in signal transducers, including kinases and transcription factors. Therefore, HSP90 regulates diverse cellular functions and exerts marked effects on normal biology, disease and evolutionary processes. Recent structural and functional analyses have provided new insights on the transcriptional and biochemical regulation of HSP90 and the structural dynamics it uses to act on a diverse client repertoire. Comprehensive understanding of how HSP90 functions promises not only to provide new avenues for therapeutic intervention, but to shed light on fundamental biological questions.

  View details for DOI 10.1038/nrm2918

  View details for Web of Science ID 000280076000016

  View details for PubMedID 20531426

• A DinB variant reveals diverse physiological consequences of incomplete TLS extension by a Y-family DNA polymerase PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Jarosz, D. F., Cohen, S. E., Delaney, J. C., Essigmann, J. M., Walker, G. C. 2009; 106 (50): 21137-21142

  Abstract

  The only Y-family DNA polymerase conserved among all domains of life, DinB and its mammalian ortholog pol kappa, catalyzes proficient bypass of damaged DNA in translesion synthesis (TLS). Y-family DNA polymerases, including DinB, have been implicated in diverse biological phenomena ranging from adaptive mutagenesis in bacteria to several human cancers. Complete TLS requires dNTP insertion opposite a replication blocking lesion and subsequent extension with several dNTP additions. Here we report remarkably proficient TLS extension by DinB from Escherichia coli. We also describe a TLS DNA polymerase variant generated by mutation of an evolutionarily conserved tyrosine (Y79). This mutant DinB protein is capable of catalyzing dNTP insertion opposite a replication-blocking lesion, but cannot complete TLS, stalling three nucleotides after an N(2)-dG adduct. Strikingly, expression of this variant transforms a bacteriostatic DNA damaging agent into a bactericidal drug, resulting in profound toxicity even in a dinB(+) background. We find that this phenomenon is not exclusively due to a futile cycle of abortive TLS followed by exonucleolytic reversal. Rather, gene products with roles in cell death and metal homeostasis modulate the toxicity of DinB(Y79L) expression. Together, these results indicate that DinB is specialized to perform remarkably proficient insertion and extension on damaged DNA, and also expose unexpected connections between TLS and cell fate.

  View details for DOI 10.1073/pnas.0907257106

  View details for Web of Science ID 000272795300025

  View details for PubMedID 19948952

• Song: SOS (To the Tune of ABBA's "SOS"). Biochemistry and molecular biology education Simon, S. M., Waters, L. S., Jarosz, D. F., Beuning, P. J. 2009; 37 (5): 316-?

  View details for DOI 10.1002/bmb.20305

  View details for PubMedID 21567763

• UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB MOLECULAR CELL Godoy, V. G., Jarosz, D. F., Simon, S. M., Abyzov, A., Ilyin, V., Walker, G. C. 2007; 28 (6): 1058-1070

  Abstract

  DinB is the only translesion Y family DNA polymerase conserved among bacteria, archaea, and eukaryotes. DinB and its orthologs possess a specialized lesion bypass function but also display potentially deleterious -1 frameshift mutagenic phenotypes when overproduced. We show that the DNA damage-inducible proteins UmuD(2) and RecA act in concert to modulate this mutagenic activity. Structural modeling suggests that the relatively open active site of DinB is enclosed by interaction with these proteins, thereby preventing the template bulging responsible for -1 frameshift mutagenesis. Intriguingly, residues that define the UmuD(2)-interacting surface on DinB statistically covary throughout evolution, suggesting a driving force for the maintenance of a regulatory protein-protein interaction at this site. Together, these observations indicate that proteins like RecA and UmuD(2) may be responsible for managing the mutagenic potential of DinB orthologs throughout evolution.

  View details for DOI 10.1016/j.molcel.2007.10.025

  View details for Web of Science ID 000252170000012

  View details for PubMedID 18158902

• DNA polymerase V allows bypass of toxic guanine oxidation products in vivo JOURNAL OF BIOLOGICAL CHEMISTRY Neeley, W. L., Delaney, S., Alekseyev, Y. O., Jarosz, D. F., Delaney, J. C., Walker, G. C., Essigmann, J. M. 2007; 282 (17): 12741-12748

  Abstract

  Reactive oxygen and nitrogen radicals produced during metabolic processes, such as respiration and inflammation, combine with DNA to form many lesions primarily at guanine sites. Understanding the roles of the polymerases responsible for the processing of these products to mutations could illuminate molecular mechanisms that correlate oxidative stress with cancer. Using M13 viral genomes engineered to contain single DNA lesions and Escherichia coli strains with specific polymerase (pol) knockouts, we show that pol V is required for efficient bypass of structurally diverse, highly mutagenic guanine oxidation products in vivo. We also find that pol IV participates in the bypass of two spiroiminodihydantoin lesions. Furthermore, we report that one lesion, 5-guanidino-4-nitroimidazole, is a substrate for multiple SOS polymerases, whereby pol II is necessary for error-free replication and pol V for error-prone replication past this lesion. The results spotlight a major role for pol V and minor roles for pol II and pol IV in the mechanism of guanine oxidation mutagenesis.

  View details for DOI 10.1074/jbc.M700575200

  View details for Web of Science ID 000245942800044

  View details for PubMedID 17322566

• Proficient and accurate bypass of persistent DNA lesions by DinB DNA polymerases CELL CYCLE Jarosz, D. F., Godoy, V. G., Walker, G. C. 2007; 6 (7): 817-822

  Abstract

  Despite nearly universal conservation through evolution, the precise function of the DinB/pol kappa branch of the Y-family of DNA polymerases has remained unclear. Recent results suggest that DinB orthologs from all domains of life proficiently bypass replication blocking lesions that may be recalcitrant to DNA repair mechanisms. Like other translesion DNA polymerases, the error frequency of DinB and its orthologs is higher than the DNA polymerases that replicate the majority of the genome. However, recent results suggest that some Y-family polymerases, including DinB and pol kappa, bypass certain types of DNA damage with greater proficiency than an undamaged template. Moreover, they do so relatively accurately. The ability to employ this mechanism to manage DNA damage may be especially important for types of DNA modification that elude repair mechanisms. For these lesions, translesion synthesis may represent a more important line of defense than for other types of DNA damage that are more easily dealt with by other more accurate mechanisms.

  View details for Web of Science ID 000245577800012

  View details for PubMedID 17377496

• Y-family DNA polymerases in Escherichia coli TRENDS IN MICROBIOLOGY Jarosz, D. F., Beuning, P. J., Cohen, S. E., Walker, G. C. 2007; 15 (2): 70-77

  Abstract

  The observation that mutations in the Escherichia coli genes umuC+ and umuD+ abolish mutagenesis induced by UV light strongly supported the counterintuitive notion that such mutagenesis is an active rather than passive process. Genetic and biochemical studies have revealed that umuC+ and its homolog dinB+ encode novel DNA polymerases with the ability to catalyze synthesis past DNA lesions that otherwise stall replication--a process termed translesion synthesis (TLS). Similar polymerases have been identified in nearly all organisms, constituting a new enzyme superfamily. Although typically viewed as unfaithful copiers of DNA, recent studies suggest that certain TLS polymerases can perform proficient and moderately accurate bypass of particular types of DNA damage. Moreover, various cellular factors can modulate their activity and mutagenic potential.

  View details for DOI 10.1016/j.tim.2006.12.004

  View details for Web of Science ID 000244535900004

  View details for PubMedID 17207624

• Y-family DNA polymerases respond to DNA damage-independent inhibition of replication fork progression EMBO JOURNAL Godoy, V. G., Jarosz, D. F., Walker, F. L., Simmons, L. A., Walker, G. C. 2006; 25 (4): 868-879

  Abstract

  In Escherichia coli, the Y-family DNA polymerases Pol IV (DinB) and Pol V (UmuD2'C) enhance cell survival upon DNA damage by bypassing replication-blocking DNA lesions. We report a unique function for these polymerases when DNA replication fork progression is arrested not by exogenous DNA damage, but with hydroxyurea (HU), thereby inhibiting ribonucleotide reductase, and bringing about damage-independent DNA replication stalling. Remarkably, the umuC122::Tn5 allele of umuC, dinB, and certain forms of umuD gene products endow E. coli with the ability to withstand HU treatment (HUR). The catalytic activities of the UmuC122 and DinB proteins are both required for HUR. Moreover, the lethality brought about by such stalled replication forks in the wild-type derivatives appears to proceed through the toxin/antitoxin pairs mazEF and relBE. This novel function reveals a role for Y-family polymerases in enhancing cell survival under conditions of nucleotide starvation, in addition to their established functions in response to DNA damage.

  View details for DOI 10.1038/sj.emboj.7600986

  View details for Web of Science ID 000236225000020

  View details for PubMedID 16482223

• Characterization of Escherichia coli translesion synthesis polymerases and their accessory factors DNA REPAIR, PT A Beuning, P. J., Simon, S. M., Godoy, V. G., Jarosz, D. F., Walker, G. C. 2006; 408: 318-340

  Abstract

  Members of the Y family of DNA polymerases are specialized to replicate lesion-containing DNA. However, they lack 3'-5' exonuclease activity and have reduced fidelity compared to replicative polymerases when copying undamaged templates, and thus are potentially mutagenic. Y family polymerases must be tightly regulated to prevent aberrant mutations on undamaged DNA while permitting replication only under conditions of DNA damage. These polymerases provide a mechanism of DNA damage tolerance, confer cellular resistance to a variety of DNA-damaging agents, and have been implicated in bacterial persistence. The Y family polymerases are represented in all domains of life. Escherichia coli possesses two members of the Y family, DNA pol IV (DinB) and DNA pol V (UmuD'(2)C), and several regulatory factors, including those encoded by the umuD gene that influence the activity of UmuC. This chapter outlines procedures for in vivo and in vitro analysis of these proteins. Study of the E. coli Y family polymerases and their accessory factors is important for understanding the broad principles of DNA damage tolerance and mechanisms of mutagenesis throughout evolution. Furthermore, study of these enzymes and their role in stress-induced mutagenesis may also give insight into a variety of phenomena, including the growing problem of bacterial antibiotic resistance.

  View details for DOI 10.1016/S0076-6879(06)08020-7

  View details for Web of Science ID 000238224100020

  View details for PubMedID 16793378