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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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley & Sons, Inc.
2020
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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. |
format | Online Article Text |
id | pubmed-7317962 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | John Wiley & Sons, Inc. |
record_format | MEDLINE/PubMed |
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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