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

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 prov...

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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102598/
https://www.ncbi.nlm.nih.gov/pubmed/37065130
http://dx.doi.org/10.3389/fmicb.2023.1095191
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author 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.
author_facet 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.
author_sort Trotter, Valentine V.
collection PubMed
description 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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spelling pubmed-101025982023-04-15 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. Front Microbiol Microbiology 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. Frontiers Media S.A. 2023-03-31 /pmc/articles/PMC10102598/ /pubmed/37065130 http://dx.doi.org/10.3389/fmicb.2023.1095191 Text en Copyright © 2023 Trotter, Shatsky, Price, Juba, Zane, De León, Majumder, Gui, Ali, Wetmore, Kuehl, Arkin, Wall, Deutschbauer, Chandonia and Butland. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
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.
Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
title Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
title_full Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
title_fullStr Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
title_full_unstemmed Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
title_short Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
title_sort large-scale genetic characterization of the model sulfate-reducing bacterium, desulfovibrio vulgaris hildenborough
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102598/
https://www.ncbi.nlm.nih.gov/pubmed/37065130
http://dx.doi.org/10.3389/fmicb.2023.1095191
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