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Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase

ABSTRACT: Here, we described comparative transcriptomic analysis of B. subtilis strain stably expressing rho with the wild type and rho-deficient strains. We show that maintaining a stable Rho level caused global changes of B. subtilis transcriptome including both strong down-regulation of the antisense transcription and considerable modifications of the sense transcription. The observed changes were more noticeable upon entering the stationary phase and comprised majority of genes controlled by global transcription regulators AbrB and CodY, competence transcription factor ComK, and stringent response. Constitutively expressed rho reprograms stationary phase-specific cellular physiology, affects adaptation of cells to nutrient limitations by attenuating the stringent response and alters cell-fate decision-making to such an extent that it blocks competence development and sporulation.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE195579 | GEO | 2022/02/10

REPOSITORIES: GEO

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A novel feedback loop that controls bimodal expression of genetic competence

Project description:Gene expression can be highly heterogeneous in clonal cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states, and consequently a population will be composed of cells that are ‘ON’ and cells that are ‘OFF’. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by autostimulatory feedback regulation to obtain the bimodal response. A classical model of bistable differentiation is the development of genetic competence in Bacillus subtilis. Noise in expression of the transcription factor ComK ultimately determines the fraction of cells that enter the competent state. Due to its intrinsic random nature, noise is difficult to investigate. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators, to screen for possible factors that affect noise in the bimodal regulation of ComK. This led to the discovery of Kre, a novel factor that controls the bimodal expression of ComK. Kre appears to affect the stability of comK mRNA. Interestingly, ComK itself represses the expression of kre, adding a new double negative feedback loop to the intricate ComK regulation circuit. Our data emphasize that mRNA stability is an important factor in bimodal regulation.

2017-02-10 | GSE61757 | GEO

Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase

Project description:Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase

| PRJNA801272 | ENA

Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence

Project 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.

2021-04-30 | GSE173540 | GEO

Role of Rok in biofilm structure development of Bacillus subtilis 168

Project description:Comparison of the B subtilis rok mutant vs wild type (sample 1-4) and rok-comK mutant vs comK mutant (sample 5-8)

2011-02-01 | GSE22370 | GEO

Role of Rok in biofilm structure development of Bacillus subtilis 168

Project description:Comparison of the B subtilis rok mutant vs wild type (sample 1-4) and rok-comK mutant vs comK mutant (sample 5-8) One condition design comparision of (rok vs wt) and (rok-comK vs comK) including a dye swap, 4 biological replicate

2011-02-01 | E-GEOD-22370 | biostudies-arrayexpress

Transcriptome analysis of a Bacillus subtilis mutant defective in the transcription termination factor Rho.

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2012-03-07 | E-GEOD-27303 | biostudies-arrayexpress

Phosphorylation of Bacillus subtilis gene regulator AbrB modulates its DNA-binding properties

Project description:AbrB is a global gene regulator involved in transition phase phenomena in Bacillus subtilis. It participates in a complex regulatory network governing the expression of stationary phase functions. AbrB was previously found to be phosphorylated on serine 86 located close to its C-terminal oligomerization domain. Here we report that AbrB can be phosphorylated by three B. subtilis serine/threonine kinases expressed during the transition and stationary phase: PrkC, PrkD and YabT. Our in vitro findings suggest that AbrB phosphorylation impedes its DNA binding and abolishes binding cooperativity. In vivo we established that a phospho-mimetic mutation abrB S86D leads to a significant loss of AbrB control over several key target functions: exoprotease production, competence development and sporulation. A wider transcriptome analysis of abrB S86D and S86A mutant strains revealed deregulation of a large number of target genes. We therefore propose that AbrB phosphorylation serves as an additional input for fine-tuning the activity of this ambiactive gene regulator.

2014-04-11 | GSE56723 | GEO

Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis

Project description:Reversible protein phosphorylation is an important and ubiquitous protein modification in all living cells. We report that protein arginine phosphorylation plays a physiological significant role for the regulation of protein activity. We detected 121 arginine phospho-sites for 87 proteins in the Gram-positive model organism Bacillus subtilis in vivo. Moreover, we provide evidences that arginine phosphorylations are involved in the fine-tuned signal transduction of many critical cellular processes, such as protein degradation, motility, competence, stringent and stress response. Our results suggest that in B. subtilis the activity of a protein arginine phosphatase allows a fast regulation of protein activity by protein arginine kinases and that protein arginine phosphorylations play an important role as a reversible post-translational modification in bacteria. Cells were grown under vigorous agitation at 37 M-BM-0C in a defined medium (StM-CM-<lke et al., 1993, J Gen Microbiol 139, 2041-2045). Samples were taken at OD500 0.4 and 1h upon entry into stationary phase. Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 10 samples was labeled with Cy3.

2012-03-31 | E-GEOD-31249 | biostudies-arrayexpress

Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis

Project description:Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown in the presence and absence of amino acids. We show that the change in global RNA structurome is inversely proportional to the change in abundance upon amino acid starvation and that this trend is pronounced in the stringent response and codY regulons. We also use this data to characterize known and novel RNA switches.

2020-07-24 | GSE148936 | GEO

Direct targets of CodY in Staphylococcus aureus

Project description:More than 200 direct CodY target genes in Staphylococcus aureus were identified by genome-wide analysis of in vitro DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules and virulence. The virulence genes regulated by CodY fell into three groups. One group was dependent on the Agr system for its expression; these genes were indirectly regulated by CodY through its repression of the agr locus. A second group was regulated directly by CodY. The third group, which includes genes for alpha-toxin and capsule synthesis, was regulated by CodY in two ways, i.e., by direct repression and by repression of the agr locus. Since S. aureus CodY was activated in vitro by the branched chain amino acids and GTP, CodY appears to link changes in intracellular metabolite pools with the induction of numerous adaptive responses, including virulence. Affymetrix GeneChips were used to compare the transcript titers of S. aureus strains UAMS-1 (wild type) and corresponding agr- (strain CM18), codY- (strain MS1), and agr- codY- (strain CM19) isogenic mutant strains during exponential and stationary phase growth. At least two biological replicates were assessed for each strain and each growth phase.

2010-04-13 | E-GEOD-20973 | biostudies-arrayexpress

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