All Publications

  • Engineered sigma factors increase full-length antibody expression in Escherichia coli METABOLIC ENGINEERING McKenna, R., Lombana, T., Yamada, M., Mukhyala, K., Veeravalli, K. 2019; 52: 315–23


    Escherichia coli (E. coli) is a promising platform for expression of full-length antibodies owing to its several advantages as a production host (fast growth, well characterized genetics, low manufacturing cost), however, low titers from shake flask (typically < 5 mg/L) has limited its use for production of research-grade material in antibody discovery programs. In this work, we used global transcriptional machinery engineering (gTME) with high throughput screening to increase the expression of full-length antibodies in E. coli. A library of E. coli mutants carrying mutations in the global sigma factor RpoD were generated and screened using the Bacterial Antibody Display (BAD) method for enhanced expression. RpoD mutants were isolated that resulted in full-length antibody titers of up to 130.7 ± 6.6 mg/L of shake flask culture with chaperone co-expression. These results could be useful for production of several antibodies quickly in shake flasks for characterization (e.g. antigen binding, biological function) during the early discovery phase.

    View details for DOI 10.1016/j.ymben.2018.12.009

    View details for Web of Science ID 000457633200029

    View details for PubMedID 30610917

  • Strain Engineering to Reduce Acetate Accumulation during Microaerobic Growth Conditions in Escherichia coli BIOTECHNOLOGY PROGRESS Veeravalli, K., Schindler, T., Dong, E., Yamada, M., Hamilton, R., Laird, M. W. 2018; 34 (2): 303–14


    Microaerobic (oxygen limited) conditions are advantageous for several industrial applications since a majority of the carbon atoms can be directed for synthesis of desired products. Oxygen limited conditions, however, can result in high levels of undesirable by-products such as acetate, which subsequently can have an impact on biomass and product yields. The molecular mechanisms involved in acetate accumulation under oxygen limited conditions are not well understood. Our results indicate that a majority of the genetic modifications known to decrease acetate under aerobic conditions results in similar or even higher acetate under oxygen limitation. Deletion of arcA, whose gene product is a global transcriptional regulator, was the only modification among those evaluated that significantly decreased acetate under both transient and prolonged oxygen limitation. Transcriptome results indicate that the arcA deletion results in an increased expression of the operon involving acs and actP (whose gene products are involved in acetate assimilation and uptake respectively) and some genes in the TCA cycle, thereby promoting increased acetate assimilation. These results provide useful cues for strain design for improved manufacturing of biopharmaceuticals under oxygen limited conditions. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:303-314, 2018.

    View details for DOI 10.1002/btpr.2592

    View details for Web of Science ID 000430490800001

    View details for PubMedID 29193870

  • A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy ACS SYNTHETIC BIOLOGY Chen, R., Rishi, H. S., Potapov, V., Yamada, M. R., Yeh, V. J., Chow, T., Cheung, C. L., Jones, A. T., Johnson, T. D., Keating, A. E., DeLoache, W. C., Dueber, J. E. 2015; 4 (11): 1205–16


    Dramatic progress has been made in the design and build phases of the design-build-test cycle for engineering cells. However, the test phase usually limits throughput, as many outputs of interest are not amenable to rapid analytical measurements. For example, phenotypes such as motility, morphology, and subcellular localization can be readily measured by microscopy, but analysis of these phenotypes is notoriously slow. To increase throughput, we developed microscopy-readable barcodes (MiCodes) composed of fluorescent proteins targeted to discernible organelles. In this system, a unique barcode can be genetically linked to each library member, making possible the parallel analysis of phenotypes of interest via microscopy. As a first demonstration, we MiCoded a set of synthetic coiled-coil leucine zipper proteins to allow an 8 × 8 matrix to be tested for specific interactions in micrographs consisting of mixed populations of cells. A novel microscopy-readable two-hybrid fluorescence localization assay for probing candidate interactions in the cytosol was also developed using a bait protein targeted to the peroxisome and a prey protein tagged with a fluorescent protein. This work introduces a generalizable, scalable platform for making microscopy amenable to higher-throughput library screening experiments, thereby coupling the power of imaging with the utility of combinatorial search paradigms.

    View details for DOI 10.1021/acssynbio.5b00060

    View details for Web of Science ID 000365461200006

    View details for PubMedID 26155738

    View details for PubMedCentralID PMC4654675

  • Enhancing Tolerance to Short-Chain Alcohols by Engineering the Escherichia coli AcrB Efflux Pump to Secrete the Non-native Substrate n-Butanol ACS SYNTHETIC BIOLOGY Fisher, M. A., Boyarskiy, S., Yamada, M. R., Kong, N., Bauer, S., Tullman-Ercek, D. 2014; 3 (1): 30–40


    The microbial conversion of sugars to fuels is a promising technology, but the byproducts of biomass pretreatment processes and the fuels themselves are often toxic at industrially relevant levels. One promising solution to these problems is to engineer efflux pumps to secrete fuels and inhibitory chemicals from the cell, increasing microbial tolerance and enabling higher fuel titer. Toward that end, we used a directed evolution strategy to generate variants of the Escherichia coli AcrB efflux pump that act on the non-native substrate n-butanol, enhancing growth rates of E. coli in the presence of this biofuel by up to 25%. Furthermore, these variants confer improved tolerance to isobutanol and straight-chain alcohols up to n-heptanol. Single amino acid changes in AcrB responsible for this phenotype were identified. We have also shown that both the chemical and genetic inactivation of pump activity eliminate the tolerance conferred by AcrB pump variants, supporting our assertion that the variants secrete the non-native substrates. This strategy can be applied to create an array of efflux pumps that modulate the intracellular concentrations of small molecules of interest to microbial fuel and chemical production.

    View details for DOI 10.1021/sb400065q

    View details for Web of Science ID 000330098600004

    View details for PubMedID 23991711

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