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Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium

Valentine V. Trotter, Maxim Shatsky, View ORCID ProfileMorgan N. Price, Thomas R. Juba, Grant M. Zane, Kara B. De León, Erica L. Majumder, Qin Gui, Rida Ali, Kelly M. Wetmore, Jennifer V. Kuehl, View ORCID ProfileAdam P. Arkin, Judy D. Wall, Adam M. Deutschbauer, John-Marc Chandonia, Gareth P. Butland
doi: https://doi.org/10.1101/2021.01.13.426591
Valentine V. Trotter
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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  • For correspondence: vvtrotter@lbl.gov jmchandonia@lbl.gov
Maxim Shatsky
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Morgan N. Price
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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  • ORCID record for Morgan N. Price
Thomas R. Juba
2Department of Biochemistry, University of Missouri, Columbia, MO, USA
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Grant M. Zane
2Department of Biochemistry, University of Missouri, Columbia, MO, USA
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Kara B. De León
2Department of Biochemistry, University of Missouri, Columbia, MO, USA
6Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
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Erica L. Majumder
2Department of Biochemistry, University of Missouri, Columbia, MO, USA
5Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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Qin Gui
2Department of Biochemistry, University of Missouri, Columbia, MO, USA
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Rida Ali
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Kelly M. Wetmore
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Jennifer V. Kuehl
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Adam P. Arkin
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
3Department of Bioengineering, University of California, Berkeley, CA, USA
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  • ORCID record for Adam P. Arkin
Judy D. Wall
2Department of Biochemistry, University of Missouri, Columbia, MO, USA
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Adam M. Deutschbauer
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
4Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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John-Marc Chandonia
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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  • For correspondence: vvtrotter@lbl.gov jmchandonia@lbl.gov
Gareth P. Butland
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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ABSTRACT

Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted January 13, 2021.
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Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium
Valentine V. Trotter, Maxim Shatsky, Morgan N. Price, Thomas R. Juba, Grant M. Zane, Kara B. De León, Erica L. Majumder, Qin Gui, Rida Ali, Kelly M. Wetmore, Jennifer V. Kuehl, Adam P. Arkin, Judy D. Wall, Adam M. Deutschbauer, John-Marc Chandonia, Gareth P. Butland
bioRxiv 2021.01.13.426591; doi: https://doi.org/10.1101/2021.01.13.426591
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Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium
Valentine V. Trotter, Maxim Shatsky, Morgan N. Price, Thomas R. Juba, Grant M. Zane, Kara B. De León, Erica L. Majumder, Qin Gui, Rida Ali, Kelly M. Wetmore, Jennifer V. Kuehl, Adam P. Arkin, Judy D. Wall, Adam M. Deutschbauer, John-Marc Chandonia, Gareth P. Butland
bioRxiv 2021.01.13.426591; doi: https://doi.org/10.1101/2021.01.13.426591

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