Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough

Trotter, Valentine V.; Shatsky, Maxim; Price, Morgan N.; Juba, Thomas R.; Zane, Grant M.; De León, Kara B.; Majumder, Erica L.-W.; Gui, Qin; Ali, Rida; Wetmore, Kelly M.; Kuehl, Jennifer V.; Arkin, Adam P.; Wall, Judy D.; Deutschbauer, Adam M.; Chandonia, John-Marc; Butland, Gareth P.

doi:10.3389/fmicb.2023.1095191

Title: Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough

Journal Article · Fri Mar 31 00:00:00 EDT 2023 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2023.1095191· OSTI ID:2229335

Trotter, Valentine V. ^[1]; Shatsky, Maxim ^[1]; Price, Morgan N. ^[1]; Juba, Thomas R. ^[2]; Zane, Grant M. ^[2]; De León, Kara B. ^[3]; Majumder, Erica L.-W. ^[4]; Gui, Qin ^[2]; Ali, Rida ^[1]; Wetmore, Kelly M. ^[1]; Kuehl, Jennifer V. ^[1]; Arkin, Adam P. ^[5]; Wall, Judy D. ^[2]; Deutschbauer, Adam M. ^[5]; Chandonia, John-Marc ^[1]; Butland, Gareth P. ^[1]

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Univ. of Missouri, Columbia, MO (United States)
Univ. of Oklahoma, Norman, OK (United States)
Univ. of Wisconsin, Madison, WI (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231; S10 OD018174

OSTI ID:: 2229335

Journal Information:: Frontiers in Microbiology, Vol. 14; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough

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