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The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae

ABSTRACT: The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae

PROVIDER: PRJNA803738 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17893371.fastq.gz	Fastqsanger.gz
	SRR17893372.fastq.gz	Fastqsanger.gz
	SRR17893373.fastq.gz	Fastqsanger.gz
	SRR17893374.fastq.gz	Fastqsanger.gz
	SRR17893375.fastq.gz	Fastqsanger.gz

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The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae

Project description:In this study, we determined the expression profile of V. cholerae strain A1552 and its varA-deficient mutant at two different growth stages (OD600 of 0.2 or 2.5)

2022-02-08 | GSE196185 | GEO

The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae.

Project description:Despite extensive studies on the curve-shaped bacterium Vibrio cholerae, the causative agent of the diarrheal disease cholera, its virulence-associated regulatory two-component signal transduction system VarS/VarA is not well understood. This pathway, which mainly signals through the downstream protein CsrA, is highly conserved among gamma-proteobacteria, indicating there is likely a broader function of this system beyond virulence regulation. In this study, we investigated the VarA-CsrA signaling pathway and discovered a previously unrecognized link to the shape of the bacterium. We observed that varA-deficient V. cholerae cells showed an abnormal spherical morphology during late-stage growth. Through peptidoglycan (PG) composition analyses, we discovered that these mutant bacteria contained an increased content of disaccharide dipeptides and reduced peptide crosslinks, consistent with the atypical cellular shape. The spherical shape correlated with the CsrA-dependent overproduction of aspartate ammonia lyase (AspA) in varA mutant cells, which likely depleted the cellular aspartate pool; therefore, the synthesis of the PG precursor amino acid meso-diaminopimelic acid was impaired. Importantly, this phenotype, and the overall cell rounding, could be prevented by means of cell wall recycling. Collectively, our data provide new insights into how V. cholerae use the VarA-CsrA signaling system to adjust its morphology upon unidentified external cues in its environment.

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CLIP-seq of CsrA foci in Enteropathogenic E. coli

Project description:The RNA content of the CsrA foci. EPEC (E2348/69 (strain O127:H6)) expressing CsrA-FLAGx3-GFP or wild-type EPEC expressing untagged CsrA (negative control) were grown to OD 0.6 in DMEM and subjected to the foci-enrichment protocol, followed by RNA extraction and library preparation. Six libraries were prepared, containing three biological repeats of csrA-3 x flag-gfp and three repeats of wt.

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The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system

Project description:The RNA binding protein CsrA is the master regulator of the bi-phasic life cycle of Legionella pneumophila governing virulence expression in this intracellular pathogen. The goal of the study was to use deep sequencing of RNA enriched by co-immunoprecipitation with epitope tagged CsrA to identify CsrA-associated transcripts at the genome level. We found 478 mRNAs or non-coding RNAs to be targets of CsrA. Among those major regulators including FleQ, the regulator of flagella expression, LqsR, the regulator of quorum sensing and RpoS implicated in stress response were identified. The expression of over 40 type IV secreted effector proteins important for intracellular survival and virulence are under the control of CsrA. Combined with transcriptomics, whole shotgun proteomics of a wild type and a CsrA mutant strain and functional analyses of several CsrA-targeted RNAs we identified the first riboswitch in L. pneumophila, a thiamine pyrophosphate riboswitch, and discovered a new mode of regulation by CsrA that allows L. pneumophila to regulate the pentose phosphate pathway and the glycolysis combined or individually although they share genes in a single operon. Our results further underline the indispensable role of CsrA in the life cycle of L. pneumophila and provide new insights into its regulatory roles and mechanisms.

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Extensive mutual influences of SMC complexes shape 3D genome folding

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Proteomics identification of CsrA-regulated proteins in Legionella pneumophila

Project description:The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. In this dataset we identified proteins regulated by CsrA in the human bacterial pathogen Legionella pneumophila by labelfree shotgun proteomics. WT and ∆csrA bacteria were grown to exponential phase in three biological replicates. Bacteria were lysed by sonication and extracted proteins were reducted, alkylated and digested with trypsin. The resulting peptide mixtures were analyzed by LC-MS/MS and proteins were identified by the MaxQuant software. In total of 1,448 proteins were quantified by the MaxLFQ algorithm in a labelfree approach. Cluster analysis showed that expression of almost all proteins was affected by the mutation of CsrA as about half of the identified proteins were up and half were down regulated. About 15% of the proteome (238 proteins) was strongly affected with 132 proteins significantly up and 109 significantly down regulated dependent on CsrA.

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The interplay between a protein and an mRNA antagonist controls CsrA-mediated regulation of flagella genes in Campylobacter jejuni

Project description:This study investigates the CsrA regulon of the food-borne pathogen Campylobacter jejuni. Direct RNA binding targets of CsrA in two strains of C. jejuni, NCTC11168 and 81-176, were determined using RIP-seq. Identification of CsrA binding sites in two C. jejuni strains using RIP-seq

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RNA binding partners of the post-transcriptional regulator CsrA

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