Zweers, Jessica C., Nicolas, Pierre, Wiegert, Thomas, Dijl, Jan Maarten van and Denham, Emma (2012) Definition of the σW regulon of Bacillus subtilis in the absence of stress. PLoS One, Volume 7 (Number 11). Article number e48471. doi:10.1371/journal.pone.0048471 ISSN 1932-6203.

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Abstract

Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that activate the different ECF sigma factors. Here we have employed tiling arrays to single out the ECF σW regulon of the Gram-positive bacterium Bacillus subtilis from the overlapping ECF σX, σY, and σM regulons. For this purpose, we profiled the transcriptome of a B. subtilis sigW mutant under non-stress conditions to select candidate genes that are strictly σW-regulated. Under these conditions, σW exhibits a basal level of activity. Subsequently, we verified the σW-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental B. subtilis strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of rasP or prsW mutant strains that lack the proteases involved in the degradation of the σW anti-sigma factor RsiW and subsequent activation of the σW-regulon. Taken together, our studies identify 89 genes as being strictly σW-regulated, including several genes for non-coding RNAs. The effects of rasP or prsW mutations on the expression of σW-dependent genes were relatively mild, which implies that σW-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of rasP mutant cells, which have defects in competence development, protein secretion and membrane protein production, is not mirrored in the transcript profile of these cells. This implies that RasP is not only important for transcriptional regulation via σW, but that this membrane protease also exerts other important post-transcriptional regulatory functions.

Item Type:	Journal Article
Subjects:	Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics
Divisions:	Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School
Library of Congress Subject Headings (LCSH):	Bacterial genetics, Bacillus subtilis
Journal or Publication Title:	PLoS One
Publisher:	Public Library of Science
ISSN:	1932-6203
Official Date:	2012
Dates:	Date Event 2012 Published
Volume:	Volume 7
Number:	Number 11
Page Range:	Article number e48471
DOI:	10.1371/journal.pone.0048471
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access (Creative Commons)
Date of first compliant deposit:	26 December 2015
Date of first compliant Open Access:	26 December 2015
Funder:	European Science Foundation (ESF), Nederlandse Organisatie voor Wetenschappelijk Onderzoek [Netherlands Organisation for Scientific Research] (NWO), European Commission (EC), Systems Biology of Microorganisms (SysMo), Deutsche Forschungsgemeinschaft (DFG)
Grant number:	04-EScope 01-011 (NWO) ; LSHM-CT-2006-019064, LSHG-CT-2006-037469, PITN-GA-2008-215524, 244093 (EC) ; WI 1771/5-1 (DFG)

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