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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Published in:PloS one Vol. 6; no. 11; p. e27160
Main Authors: Blom, Evert-Jan, Ridder, Anja N J A, Lulko, Andrzej T, Roerdink, Jos B T M, Kuipers, Oscar P
Format: Journal Article
Language:English
Published: United States Public Library of Science 08-11-2011
Public Library of Science (PLoS)
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Summary: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.
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Current address: Department of Pharmacy, Pharmaceutical Biology/Pharmaceutical Gene Modulation, University of Groningen, Groningen, The Netherlands
Conceived and designed the experiments: EJB ANJAR ATL. Performed the experiments: EJB ANJAR ATL. Analyzed the data: EJB ANJAR. Contributed reagents/materials/analysis tools: EJB ANJAR ATL. Wrote the paper: EJB ANJAR JBTMR OPK.
Current address: Keygene N.V., Wageningen, The Netherlands
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0027160