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SwrA extends DegU over an UP element to activate flagellar gene expression in Bacillus subtilis

ABSTRACT: SwrA extends DegU over an UP element to activate flagellar gene expression in Bacillus subtilis

PROVIDER: PRJNA1003071 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25557446_1.fastq.gz	Fastqsanger.gz
	SRR25557446_2.fastq.gz	Fastqsanger.gz
	SRR25557447_1.fastq.gz	Fastqsanger.gz
	SRR25557447_2.fastq.gz	Fastqsanger.gz
	SRR25557448_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

SwrA extends DegU over an UP element to activate flagellar gene expression in Bacillus subtilis

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

Genome-wide transcriptional regulation by the flagellar sigma factor FliA in Pseudomonas putida

Project description:The sigma factor FliA (σ28) has been described to activate the expression of several chemoreceptor-encoding genes and the late flagellar genes in Pseudomonas putida, enabling synthesis of the filament, an stator complex and completion of the flagella-associated chemotaxis machinery. The activity of FliA is repressed in the cytoplasm by the anti-sigma factor FlgM upon completion of the flagellar hook. In this study we aim to identify genome-wide targets of regulation by FliA in P. putida KT2442 (a spontaneous rifampicin-resistant mutant of the reference strain KT2440) by performing RNA-seq experiments using a fliA deletion mutant and a constitutively active strain that combines the deletion of flgM with ectopic production of FliA.

2024-11-18 | GSE281820 | GEO

MG1655 Flagellar Regulators RNA-seq

Project description:MG1655 Flagellar Regulators RNA-seq

| PRJEB6897 | ENA

The polar flagellar transcriptional regulatory network in Vibrio campbellii deviates from known Vibrio species

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

Transcriptional organization and regulation of the Pseudomonas putida flagellar system

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

MG1655 Flagellar Regulators RNA-seq

Project description:This experiment contains RNA-seq data for a motile derivative of MG1655 and isogenic strains with deletions of each flagellar regulator: flhD, flhC, and fliA. All strains were grown at 37 degrees C in LB. After RNA purification, ribosomal RNA was removed using RiboZero and a library was made of remaining total RNA.

2014-08-01 | E-MTAB-2802 | biostudies-arrayexpress

Flagellar mutants have reduced pilus synthesis in Caulobacter crescentus

Project description:Surface appendages such as flagella and type IV pili mediate a broad range of bacterial behaviors including motility, attachment, and surface sensing. While many species harbor both flagella and type IV pili, little is known about how or if their synthesis is coupled. Here, we show that deletions of genes encoding different flagellum machinery components result in a reduction of pilus synthesis in Caulobacter crescentus. First, we show that different flagellar mutants exhibit different levels of sensitivity to a pilus-dependent phage and that less cells within populations of flagellar mutants make pili. Furthermore, we find that single cells within flagellar mutant populations produce less pili per cell. We demonstrate that these gene deletions result in reduced transcription of pilus-associated genes and have a broad effect on global transcription profiles. Finally, we show that the decrease in pilus production is due to a reduction in the pool of pilin subunits that are polymerized into pilus fibers. These data demonstrate that mutations in flagella gene components affect not only motility but can also have considerable and unexpected consequences on other aspects of cell biology.

2019-07-05 | GSE126478 | GEO

MG1655 flagellar regulator ChIP-seq (FlhD, FlhC, FliA)

Project description:We mapped the genome-wide binding of the flagellar regulators FlhD, FlhC, and FliA in FLAG-tagged derivatives of E. coli K-12 MG1655 using ChIP coupled with deep sequencing (ChIP-seq). We identify new binding sites for each factor.

2014-04-10 | E-MTAB-2457 | biostudies-arrayexpress

MG1655 flagellar regulator ChIP-seq (FlhD, FlhC, FliA)

Project description:MG1655 flagellar regulator ChIP-seq (FlhD, FlhC, FliA)

| PRJEB6080 | ENA

Transcription profiling of Methanobacterium thermautotrophicus after contact with flagellar filament protein (FliC) and flagellar cap protein (FliD) of P. thermopropionicum

Project description:In the syntrophic interaction between fermentative bacteria (Pelotomaculum thermopropionicum) and methanogenic archaea (methanogens: Methanothemobacter thermautotrophicus), reducing equivalents (e.g., H2) produced by fermentative bacteria should efficiently be consumed by methanogens in order for the fermentation of volatile fatty acids (VFA, e.g., butyrate, propionate, and acetate) to be thermodynamically feasible. It has been known that physical approximation (e.g., coaggregation) between VFA-fermenting syntrophic bacteria (syntrophs) and hydrogenotrophic methanogens is necessary for efficient H2 transfer between them. Our previous study has shown that, at an early exponential growth phase of syntrophic coculture, cells of Pelotomaculum thermopropionicum (syntroph) were connected to cells of Methanothermobacter thermautotrophicus (methanogen) via unidentified extracellular filamentous appendages, after which they started to coaggregate, suggesting that the filamentous appendages may have been important for their syntrophic interaction. The filamentous appendages seemed to specifically connect these syntrophic partners, since such pairwise connection has been observed neither in single-species cultures (monocultures) nor in mixtures with other microbes.<br>We found that P. thermopropionicum has putative gene clusters for flagellum and pilus, while no extracellular filament gene was identified in the M. thermautotrophicus genome. So we examined transcriptome responses of M. thermautotrophicus to the contact with flagellar filament protein (FliC) and flagellar cap protein (FliD) of P. thermopropionicum.

2009-01-06 | E-MEXP-1971 | biostudies-arrayexpress

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