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Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence

Upon competence‐inducing nutrient‐limited conditions, only part of the Bacillus subtilis population becomes competent. Here, we separated the two subpopulations by fluorescence‐assisted cell sorting (FACS). Using RNA‐seq, we confirmed the previously described ComK regulon. We also found for the firs...

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Autores principales: Boonstra, Mirjam, Schaffer, Marc, Sousa, Joana, Morawska, Luiza, Holsappel, Siger, Hildebrandt, Petra, Sappa, Praveen Kumar, Rath, Hermann, de Jong, Anne, Lalk, Michael, Mäder, Ulrike, Völker, Uwe, Kuipers, Oscar P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317962/
https://www.ncbi.nlm.nih.gov/pubmed/32249531
http://dx.doi.org/10.1111/1462-2920.15005
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author Boonstra, Mirjam
Schaffer, Marc
Sousa, Joana
Morawska, Luiza
Holsappel, Siger
Hildebrandt, Petra
Sappa, Praveen Kumar
Rath, Hermann
de Jong, Anne
Lalk, Michael
Mäder, Ulrike
Völker, Uwe
Kuipers, Oscar P.
author_facet Boonstra, Mirjam
Schaffer, Marc
Sousa, Joana
Morawska, Luiza
Holsappel, Siger
Hildebrandt, Petra
Sappa, Praveen Kumar
Rath, Hermann
de Jong, Anne
Lalk, Michael
Mäder, Ulrike
Völker, Uwe
Kuipers, Oscar P.
author_sort Boonstra, Mirjam
collection PubMed
description Upon competence‐inducing nutrient‐limited conditions, only part of the Bacillus subtilis population becomes competent. Here, we separated the two subpopulations by fluorescence‐assisted cell sorting (FACS). Using RNA‐seq, we confirmed the previously described ComK regulon. We also found for the first time significantly downregulated genes in the competent subpopulation. The downregulated genes are not under direct control by ComK but have higher levels of corresponding antisense RNAs in the competent subpopulation. During competence, cell division and replication are halted. By investigating the proteome during competence, we found higher levels of the regulators of cell division, MinD and Noc. The exonucleases SbcC and SbcD were also primarily regulated at the post‐transcriptional level. In the competent subpopulation, yhfW was newly identified as being highly upregulated. Its absence reduces the expression of comG, and has a modest, but statistically significant effect on the expression of comK. Although expression of yhfW is higher in the competent subpopulation, no ComK‐binding site is present in its promoter region. Mutants of yhfW have a small but significant defect in transformation. Metabolomic analyses revealed significant reductions in tricarboxylic acid (TCA) cycle metabolites and several amino acids in a ΔyhfW mutant. RNA‐seq analysis of ΔyhfW revealed higher expression of the NAD synthesis genes nadA, nadB and nadC.
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spelling pubmed-73179622020-06-29 Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence Boonstra, Mirjam Schaffer, Marc Sousa, Joana Morawska, Luiza Holsappel, Siger Hildebrandt, Petra Sappa, Praveen Kumar Rath, Hermann de Jong, Anne Lalk, Michael Mäder, Ulrike Völker, Uwe Kuipers, Oscar P. Environ Microbiol Research Articles Upon competence‐inducing nutrient‐limited conditions, only part of the Bacillus subtilis population becomes competent. Here, we separated the two subpopulations by fluorescence‐assisted cell sorting (FACS). Using RNA‐seq, we confirmed the previously described ComK regulon. We also found for the first time significantly downregulated genes in the competent subpopulation. The downregulated genes are not under direct control by ComK but have higher levels of corresponding antisense RNAs in the competent subpopulation. During competence, cell division and replication are halted. By investigating the proteome during competence, we found higher levels of the regulators of cell division, MinD and Noc. The exonucleases SbcC and SbcD were also primarily regulated at the post‐transcriptional level. In the competent subpopulation, yhfW was newly identified as being highly upregulated. Its absence reduces the expression of comG, and has a modest, but statistically significant effect on the expression of comK. Although expression of yhfW is higher in the competent subpopulation, no ComK‐binding site is present in its promoter region. Mutants of yhfW have a small but significant defect in transformation. Metabolomic analyses revealed significant reductions in tricarboxylic acid (TCA) cycle metabolites and several amino acids in a ΔyhfW mutant. RNA‐seq analysis of ΔyhfW revealed higher expression of the NAD synthesis genes nadA, nadB and nadC. John Wiley & Sons, Inc. 2020-04-15 2020-06 /pmc/articles/PMC7317962/ /pubmed/32249531 http://dx.doi.org/10.1111/1462-2920.15005 Text en © 2020 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Boonstra, Mirjam
Schaffer, Marc
Sousa, Joana
Morawska, Luiza
Holsappel, Siger
Hildebrandt, Petra
Sappa, Praveen Kumar
Rath, Hermann
de Jong, Anne
Lalk, Michael
Mäder, Ulrike
Völker, Uwe
Kuipers, Oscar P.
Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence
title Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence
title_full Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence
title_fullStr Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence
title_full_unstemmed Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence
title_short Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence
title_sort analyses of competent and non‐competent subpopulations of bacillus subtilis reveal yhfw, yhxc and ncrnas as novel players in competence
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317962/
https://www.ncbi.nlm.nih.gov/pubmed/32249531
http://dx.doi.org/10.1111/1462-2920.15005
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