Genome-wide analysis of the general stress response in Bacillus subtilis

ABSTRACTStudies of how microorganisms respond to pressure have been limited mostly to the extreme high pressures of the deep sea (i.e., the piezosphere). In contrast, despite the fact that the growth of most bacteria is inhibited at pressures below ∼2.5 kPa, little is known of microbial responses to low pressure (LP). To study the global LP response, we performed transcription microarrays onBacillus subtiliscells grown under normal atmospheric pressure (∼101 kPa) and a nearly inhibitory LP (5 kPa), equivalent to the pressure found at an altitude of ∼20 km. Microarray analysis revealed altered levels of 363 transcripts belonging to several global regulons (AbrB, CcpA, CodY, Fur, IolR, ResD, Rok, SigH, Spo0A). Notably, the highest number of upregulated genes, 86, belonged to the SigB-mediated general stress response (GSR) regulon. Upregulation of the GSR by LP was confirmed by monitoring the expression of the SigB-dependentctc-lacZreporter fusion. Measuring transcriptome changes resulting from exposure of bacterial cells to LP reveals insights into cellular processes that may respond to LP exposure.

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The Blue-Light Receptor YtvA Acts in the Environmental Stress Signaling Pathway of Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.00691-06 ◽

2006 ◽

Vol 188 (17) ◽

pp. 6387-6395 ◽

Cited By ~ 100

Author(s):

Tatiana A. Gaidenko ◽

Tae-Jong Kim ◽

Andrea L. Weigel ◽

Margaret S. Brody ◽

Chester W. Price

Keyword(s):

Bacillus Subtilis ◽

Stress Response ◽

Signaling Pathway ◽

Blue Light ◽

Stress Signaling ◽

Negative Regulators ◽

General Stress Response ◽

Signaling Complex ◽

General Stress ◽

Stress Signaling Pathway

ABSTRACT The general stress response of the bacterium Bacillus subtilis is regulated by a partner-switching mechanism in which serine and threonine phosphorylation controls protein interactions in the stress-signaling pathway. The environmental branch of this pathway contains a family of five paralogous proteins that function as negative regulators. Here we present genetic evidence that a sixth paralog, YtvA, acts as a positive regulator in the same environmental signaling branch. We also present biochemical evidence that YtvA and at least three of the negative regulators can be isolated from cell extracts in a large environmental signaling complex. YtvA differs from these associated negative regulators by its flavin mononucleotide (FMN)-containing light-oxygen-voltage domain. Others have shown that this domain has the photochemistry expected for a blue-light sensor, with the covalent linkage of the FMN chromophore to cysteine 62 composing a critical part of the photocycle. Consistent with the view that light intensity modifies the output of the environmental signaling pathway, we found that cysteine 62 is required for YtvA to exert its positive regulatory role in the absence of other stress. Transcriptional analysis of the ytvA structural gene indicated that it provides the entry point for at least one additional environmental input, mediated by the Spx global regulator of disulfide stress. These results support a model in which the large signaling complex serves to integrate multiple environmental signals in order to modulate the general stress response.

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Global Transcriptional Response of Bacillus subtilis to Heat Shock

Journal of Bacteriology ◽

10.1128/jb.183.24.7318-7328.2001 ◽

2001 ◽

Vol 183 (24) ◽

pp. 7318-7328 ◽

Cited By ~ 187

Author(s):

John D. Helmann ◽

Ming Fang Winston Wu ◽

Phil A. Kobel ◽

Francisco-Javier Gamo ◽

Michael Wilson ◽

...

Keyword(s):

Bacillus Subtilis ◽

Stress Response ◽

Heat Shock ◽

Dna Sequences ◽

Stress Responses ◽

Transcriptional Response ◽

Transcriptional Responses ◽

General Stress Response ◽

General Stress ◽

Induced Genes

ABSTRACT In response to heat stress, Bacillus subtilisactivates the transcription of well over 100 different genes. Many of these genes are members of a general stress response regulon controlled by the secondary sigma factor, ςB, while others are under control of the HrcA or CtsR heat shock regulators. We have used DNA microarrays to monitor the global transcriptional response to heat shock. We find strong induction of known ςB-dependent genes with a characteristic rapid induction followed by a return to near prestimulus levels. The HrcA and CtsR regulons are also induced, but with somewhat slower kinetics. Analysis of DNA sequences proximal to newly identified heat-induced genes leads us to propose ∼70 additional members of the ςB regulon. We have also identified numerous heat-induced genes that are not members of known heat shock regulons. Notably, we observe very strong induction of arginine biosynthesis and transport operons. Induction of several genes was confirmed by quantitative reverse transcriptase PCR. In addition, the transcriptional responses measured by microarray hybridization compare favorably with the numerous previous studies of heat shock in this organism. Since many different conditions elicit both specific and general stress responses, knowledge of the heat-induced general stress response reported here will be helpful for interpreting future microarray studies of other stress responses.

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Differentiation of Function among the RsbR Paralogs in the General Stress Response of Bacillus subtilis with Regard to Light Perception

Journal of Bacteriology ◽

10.1128/jb.06705-11 ◽

2012 ◽

Vol 194 (7) ◽

pp. 1708-1716 ◽

Cited By ~ 12

Author(s):

J. B. van der Steen ◽

M. Avila-Perez ◽

D. Knippert ◽

A. Vreugdenhil ◽

P. van Alphen ◽

...

Keyword(s):

Bacillus Subtilis ◽

Stress Response ◽

Light Perception ◽

General Stress Response ◽

General Stress

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Heat‐shock and general stress response in Bacillus subtilis

Molecular Microbiology ◽

10.1046/j.1365-2958.1996.396932.x ◽

1996 ◽

Vol 19 (3) ◽

pp. 417-428 ◽

Cited By ~ 395

Author(s):

Michael Hecker ◽

Wolfgang Schumann ◽

Uwe Völker

Keyword(s):

Bacillus Subtilis ◽

Stress Response ◽

Heat Shock ◽

General Stress Response ◽

General Stress

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Genome-Wide Identification of H-NS-Controlled, Temperature-Regulated Genes in Escherichiacoli K-12

Journal of Bacteriology ◽

10.1128/jb.00599-08 ◽

2008 ◽

Vol 191 (3) ◽

pp. 1106-1110 ◽

Cited By ~ 46

Author(s):

Christine A. White-Ziegler ◽

Talya R. Davis

Keyword(s):

Stress Response ◽

Biofilm Formation ◽

Dna Microarrays ◽

Cold Shock ◽

Nutrient Acquisition ◽

General Stress Response ◽

General Stress ◽

Genome Wide ◽

K 12 ◽

Common Regulator

ABSTRACT DNA microarrays demonstrate that H-NS controls 69% of the temperature regulated genes in Escherichia coli K-12. H-NS is shown to be a common regulator of multiple iron and other nutrient acquisition systems preferentially expressed at 37°C and of general stress response, biofilm formation, and cold shock genes highly expressed at 23°C.

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Genome-Wide Analysis of the General Stress Response Network in Escherichia coli: σS-Dependent Genes, Promoters, and Sigma Factor Selectivity

Journal of Bacteriology ◽

10.1128/jb.187.5.1591-1603.2005 ◽

2005 ◽

Vol 187 (5) ◽

pp. 1591-1603 ◽

Cited By ~ 514

Author(s):

Harald Weber ◽

Tino Polen ◽

Johanna Heuveling ◽

Volker F. Wendisch ◽

Regine Hengge

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Rna Polymerase ◽

Sigma Factor ◽

Regulatory Network ◽

Cell Physiology ◽

Data Set ◽

General Stress Response ◽

General Stress ◽

Genome Wide

ABSTRACT The σS (or RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli. While nearly absent in rapidly growing cells, σS is strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of the E. coli genes are under direct or indirect control of σS and that σS should be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a σS consensus promoter in silico. Moreover, our results suggest that σS-dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect σS and/or σ70 selectivity of many promoters. These observations indicate that certain modules of the σS-dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with σ70 RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.

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