Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis
We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth in a batch fermentor on rich medium. DNA microarrays were used to monitor gene transcription using 10-minute intervals at 40 consecutive time points. From the growth curve and analysis of...
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| Veröffentlicht in: | PloS one 2011-11, Vol.6 (11), p.e27160-e27160 |
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| creator | Blom, Evert-Jan Ridder, Anja N J A Lulko, Andrzej T Roerdink, Jos B T M Kuipers, Oscar P |
| description | We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth in a batch fermentor on rich medium. DNA microarrays were used to monitor gene transcription using 10-minute intervals at 40 consecutive time points. From the growth curve and analysis of all gene expression levels, we identified 4 distinct growth phases and one clear transition point: a lag phase, an exponential growth phase, the transition point and the very clearly separated early and late stationary growth phases. The gene expression profiles suggest the occurrence of stress responses at specific times although no external stresses were applied. The first one is a small induction of the SigB regulon that occurs at the transition point. Remarkably, a very strong response is observed for the SigW regulon, which is highly upregulated at the onset of the late stationary phase. Bioinformatic analyses that were performed on our data set suggest several novel putative motifs for regulator binding. In addition, the expression profiles of several genes appeared to correlate with the oxygen concentration. This data set of the expression profiles of all B. subtilis genes during the entire growth curve on rich medium constitutes a rich repository that can be further mined by the scientific community. |
| doi_str_mv | 10.1371/journal.pone.0027160 |
| format | Article |
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DNA microarrays were used to monitor gene transcription using 10-minute intervals at 40 consecutive time points. From the growth curve and analysis of all gene expression levels, we identified 4 distinct growth phases and one clear transition point: a lag phase, an exponential growth phase, the transition point and the very clearly separated early and late stationary growth phases. The gene expression profiles suggest the occurrence of stress responses at specific times although no external stresses were applied. The first one is a small induction of the SigB regulon that occurs at the transition point. Remarkably, a very strong response is observed for the SigW regulon, which is highly upregulated at the onset of the late stationary phase. Bioinformatic analyses that were performed on our data set suggest several novel putative motifs for regulator binding. In addition, the expression profiles of several genes appeared to correlate with the oxygen concentration. This data set of the expression profiles of all B. subtilis genes during the entire growth curve on rich medium constitutes a rich repository that can be further mined by the scientific community.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0027160</identifier><identifier>PMID: 22087258</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acids ; Analysis ; Bacillus ; Bacillus subtilis ; Bacillus subtilis - growth & development ; Bacillus subtilis - metabolism ; Bacterial Proteins - genetics ; Batch Cell Culture Techniques ; Batch culture ; Bioinformatics ; Biology ; Biotechnology ; Cannibalism ; Carbon ; Computational Biology ; Deoxyribonucleic acid ; DNA ; DNA microarrays ; Gene expression ; Gene Expression Regulation, Bacterial ; Genes ; Genetic aspects ; Genomes ; Genomics ; Laboratories ; Lag phase ; Metabolism ; Oxygen ; Phase transitions ; Physiology ; Proteomics ; Regulon ; Sigma Factor - genetics ; Stationary phase ; Stress, Physiological ; Studies ; Transcription ; Transcription (Genetics) ; Transcriptome</subject><ispartof>PloS one, 2011-11, Vol.6 (11), p.e27160-e27160</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Blom et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Blom et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c691t-f955f7b8216872f754a8afa9423553e6d7465af4f725a04ebd34b844159e613d3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210768/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210768/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22087258$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Driks, Adam</contributor><creatorcontrib>Blom, Evert-Jan</creatorcontrib><creatorcontrib>Ridder, Anja N J A</creatorcontrib><creatorcontrib>Lulko, Andrzej T</creatorcontrib><creatorcontrib>Roerdink, Jos B T M</creatorcontrib><creatorcontrib>Kuipers, Oscar P</creatorcontrib><title>Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth in a batch fermentor on rich medium. DNA microarrays were used to monitor gene transcription using 10-minute intervals at 40 consecutive time points. From the growth curve and analysis of all gene expression levels, we identified 4 distinct growth phases and one clear transition point: a lag phase, an exponential growth phase, the transition point and the very clearly separated early and late stationary growth phases. The gene expression profiles suggest the occurrence of stress responses at specific times although no external stresses were applied. The first one is a small induction of the SigB regulon that occurs at the transition point. Remarkably, a very strong response is observed for the SigW regulon, which is highly upregulated at the onset of the late stationary phase. Bioinformatic analyses that were performed on our data set suggest several novel putative motifs for regulator binding. In addition, the expression profiles of several genes appeared to correlate with the oxygen concentration. This data set of the expression profiles of all B. subtilis genes during the entire growth curve on rich medium constitutes a rich repository that can be further mined by the scientific community.</description><subject>Acids</subject><subject>Analysis</subject><subject>Bacillus</subject><subject>Bacillus subtilis</subject><subject>Bacillus subtilis - growth & development</subject><subject>Bacillus subtilis - metabolism</subject><subject>Bacterial Proteins - genetics</subject><subject>Batch Cell Culture Techniques</subject><subject>Batch culture</subject><subject>Bioinformatics</subject><subject>Biology</subject><subject>Biotechnology</subject><subject>Cannibalism</subject><subject>Carbon</subject><subject>Computational Biology</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA microarrays</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Laboratories</subject><subject>Lag phase</subject><subject>Metabolism</subject><subject>Oxygen</subject><subject>Phase transitions</subject><subject>Physiology</subject><subject>Proteomics</subject><subject>Regulon</subject><subject>Sigma Factor - genetics</subject><subject>Stationary phase</subject><subject>Stress, Physiological</subject><subject>Studies</subject><subject>Transcription</subject><subject>Transcription (Genetics)</subject><subject>Transcriptome</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk9-L1DAQx4so3nn6H4gWBMWHXZMmTdsX4Tz8sXBwoKevIW0nu1nSZk3SxXv3D3fq9o6t3IP0IWXmM9-ZTGaS5DklS8oK-m7rBt8ru9y5HpaEZAUV5EFySiuWLURG2MOj_5PkSQhbQnJWCvE4OckyUhZZXp4mv69NBwsPwdk9tGn0qg-NN7voOtOEVPVtWhtneu18p6Jp0KLsTYCQetiDsqnpozd9QE-IKDPaA5Y0Eu2AnnVaq9hs0mawcfCQOp1-UI2xdghpGOporAlPk0da2QDPpvMs-f7p4_XFl8Xl1efVxfnlohEVjQtd5bku6jKjAqvXRc5VqbSqeMbynIFoCy5ypbnGqynCoW4Zr0vOaV6BoKxlZ8nLg-7OuiCnBgZJGSUVF7wqkFgdiNaprdx50yl_I50y8q_B-bVUHttgQUKREV5oYFAXvG2JopSLUuRl3aiK1AS13k_ZhrqDtgHslLIz0bmnNxu5dnvJMkoKUaLAm0nAu58DhCg7ExqwVvXghiArkgtRlZwh-eof8v7LTdRaYf3jm2LaZtSU5xwTCsaIQGp5D4VfCzgSOGzaoH0W8HYWgEyEX3GthhDk6tvX_2evfszZ10fsBoctbnBMh2hwvOYgP4CNdyF40Hc9pkSOu3LbDTnuipx2BcNeHL_PXdDtcrA_PpMRdg</recordid><startdate>20111108</startdate><enddate>20111108</enddate><creator>Blom, Evert-Jan</creator><creator>Ridder, Anja N J A</creator><creator>Lulko, Andrzej T</creator><creator>Roerdink, Jos B T M</creator><creator>Kuipers, Oscar P</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20111108</creationdate><title>Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis</title><author>Blom, Evert-Jan ; Ridder, Anja N J A ; Lulko, Andrzej T ; Roerdink, Jos B T M ; Kuipers, Oscar P</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c691t-f955f7b8216872f754a8afa9423553e6d7465af4f725a04ebd34b844159e613d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Acids</topic><topic>Analysis</topic><topic>Bacillus</topic><topic>Bacillus subtilis</topic><topic>Bacillus subtilis - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Blom, Evert-Jan</au><au>Ridder, Anja N J A</au><au>Lulko, Andrzej T</au><au>Roerdink, Jos B T M</au><au>Kuipers, Oscar P</au><au>Driks, Adam</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2011-11-08</date><risdate>2011</risdate><volume>6</volume><issue>11</issue><spage>e27160</spage><epage>e27160</epage><pages>e27160-e27160</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth in a batch fermentor on rich medium. DNA microarrays were used to monitor gene transcription using 10-minute intervals at 40 consecutive time points. From the growth curve and analysis of all gene expression levels, we identified 4 distinct growth phases and one clear transition point: a lag phase, an exponential growth phase, the transition point and the very clearly separated early and late stationary growth phases. The gene expression profiles suggest the occurrence of stress responses at specific times although no external stresses were applied. The first one is a small induction of the SigB regulon that occurs at the transition point. Remarkably, a very strong response is observed for the SigW regulon, which is highly upregulated at the onset of the late stationary phase. Bioinformatic analyses that were performed on our data set suggest several novel putative motifs for regulator binding. In addition, the expression profiles of several genes appeared to correlate with the oxygen concentration. This data set of the expression profiles of all B. subtilis genes during the entire growth curve on rich medium constitutes a rich repository that can be further mined by the scientific community.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22087258</pmid><doi>10.1371/journal.pone.0027160</doi><tpages>e27160</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Acids Analysis Bacillus Bacillus subtilis Bacillus subtilis - growth & development Bacillus subtilis - metabolism Bacterial Proteins - genetics Batch Cell Culture Techniques Batch culture Bioinformatics Biology Biotechnology Cannibalism Carbon Computational Biology Deoxyribonucleic acid DNA DNA microarrays Gene expression Gene Expression Regulation, Bacterial Genes Genetic aspects Genomes Genomics Laboratories Lag phase Metabolism Oxygen Phase transitions Physiology Proteomics Regulon Sigma Factor - genetics Stationary phase Stress, Physiological Studies Transcription Transcription (Genetics) Transcriptome |
| title | Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis |
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