The SinR•SlrR heteromer internally attenuates a long transcript of flagellar genes in B. subtilis [ChIP-seq]
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PROVIDER: PRJNA1201129 | ENA |
REPOSITORIES: ENA
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Project description:The SinR•SlrR heteromer internally attenuates a long transcript of flagellar genes in B. subtilis [RNA-seq]
| PRJNA1201128 | ENA
Project description:Bacillus subtilis differentiates into two cell types during growth, dictated by the activity of the alternative sigma factor SigD. The frequency of SigD-ON motile cells is increased when the heteromeric transcription factor SwrA•DegU activates the promoter of the long fla/che operon that encodes SigD. Conversely, the frequency of SigD-ON cells is decreased by the heteromeric transcription factor SinR•SlrR but the mechanism and location of inhibition is poorly understood. Using ChIP-Seq analysis, we determine the binding sites of the SinR•SlrR heteromer, including five sites within the fla/che operon. The first two sites were found to be both necessary and sufficient to attenuate transcript abundance within the operon upstream of the gene that encodes SigD. We conclude that the SinR•SlrR heteromer inhibits SigD accumulation by binding within the operon by causing RNA polymerase to pause and prematurely terminate. Thus, the development of motile cells, and the motility-to-biofilm transition, depends on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle.
2025-01-04 | GSE285065 | GEO
Project description:Bacillus subtilis differentiates into two cell types during growth, dictated by the activity of the alternative sigma factor SigD. The frequency of SigD-ON motile cells is increased when the heteromeric transcription factor SwrA•DegU activates the promoter of the long fla/che operon that encodes SigD. Conversely, the frequency of SigD-ON cells is decreased by the heteromeric transcription factor SinR•SlrR but the mechanism and location of inhibition is poorly understood. Using ChIP-Seq analysis, we determine the binding sites of the SinR•SlrR heteromer, including five sites within the fla/che operon. The first two sites were found to be both necessary and sufficient to attenuate transcript abundance within the operon upstream of the gene that encodes SigD. We conclude that the SinR•SlrR heteromer inhibits SigD accumulation by binding within the operon by causing RNA polymerase to pause and prematurely terminate. Thus, the development of motile cells, and the motility-to-biofilm transition, depends on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle.
2025-01-04 | GSE285064 | GEO
Project description:SwrA activates flagellar gene expression in Bacillus subtilis to increase the frequency of motile cells in liquid and further increase flagellar density to swarm over solid surfaces. Here we perform ChIP-seq and demonstrate that SwrA interacts with many sites on the chromosome indirectly through the response regulator DegU. We identify a DegU-specific inverted repeat and show that SwrA increased DegU DNA binding affinity in parallel to phosphorylation. Moreover, we show that SwrA increased the size of the DegU footprint expanding the region of protection towards the promoter. The remote location of the DegU inverted repeat was critical such that relocating the binding site by full turns of DNA impaired activation by SwrA/DegU and moving the binding site closer to the promoter severely impaired transcription. We conclude that SwrA/DegU forms a heteromeric complex that enables both remote binding and activator-RNA polymerase interaction in the context of an interceding UP element. We speculate that multimeric activators that resolve similar cis-element spatial conflicts are common in bacteria such as the diverse master activators of flagellar biosynthesis and those that activate long operons of other multi-subunit complexes.
2023-08-15 | GSE240266 | GEO
Project description:Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviated ribosome pausing at sequences encoding tandem prolines, and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.
2019-05-20 | GSE126233 | GEO
Project description:Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviated ribosome pausing at sequences encoding tandem prolines, and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.
2019-05-20 | GSE126234 | GEO
Project description:SwrA extends DegU over an UP element to activate flagellar gene expression in Bacillus subtilis
| PRJNA1003071 | ENA
Project description:MG1655 Flagellar Regulators RNA-seq
| PRJEB6897 | ENA
Project description:Vibrio campbellii is a gram-negative bacterial pathogen that is both free-living and a pathogen of marine organisms and exhibits swimming motility via a single, polar flagellum. Swimming motility is a critical virulence factor in V. campbellii pathogenesis, and disruption of the flagellar motor significantly decreases host mortality. However, while V. campbelli encodes homologs of flagellar and chemotaxis genes conserved by other members of the Vibrionaceae, the regulatory network governing these genes have not been explored. We systematically deleted all 63 known flagellar and chemotaxis genes in V. campbellii and examined their effects on motility compared to their homologs in other Vibrios. We specifically focused on assessing the roles of the core flagellar regulators of the flagellar regulatory hierarchy established in other Vibrios: rpoN, flrA, flrC, and fliA. Although V. campbellii transcription of flagellar and chemotaxis genes is governed by a multi-tiered regulatory hierarchy similar to other Vibrios, we observed two critical differences: the σ54-dependent regulator FlrA is dispensable for motility, and Class II gene expression is independent of σ54 regulation. Our genetic and phenotypic dissection of the V. campbellii flagellar regulatory network highlights the differences that have evolved in flagellar regulation across the Vibrionaceae.
2021-07-26 | GSE167483 | GEO
Project description:The entire set of flagellar structural components and flagellar-specific transcriptional regulators, as well as much of the core chemotaxis machinery, is encoded into a >70 kbp cluster in Pseudomonas putida KT2440 genome. We have performed RNA-seq of the wild-type strain in order to identify operon boundaries and promoters location in this cluster.
2021-05-05 | GSE173832 | GEO