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Comparative integrated omics analysis of the Hfq regulon in Bordetella pertussis

ABSTRACT: This study represents the first attempt to characterize the RNA chaperone Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expression profiles were analyzed by RNA-seq and protein amounts in cell-associated and cell-free fractions were determined by LC-MS/MS technique. Comparative analysis of transcriptomic and proteomic data revealed solid correlation considering the role of Hfq in post-transcriptional control of gene expression. Importantly, our study confirms and further enlightens the role of Hfq in pathogenicity of B. pertussis.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Bordetella Pertussis (strain Tohama I / Atcc Baa-589 / Nctc 13251)

SUBMITTER: Denisa Petrackova

LAB HEAD: Branislav Vecerek

PROVIDER: PXD013953 | Pride | 2019-07-02

REPOSITORIES: Pride

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			Action	DRS
	hfq_P1.raw	Raw
	hfq_P2.raw	Raw
	hfq_P3.raw	Raw
	hfq_S1.raw	Raw
	hfq_S2.raw	Raw

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Publications

Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis.

Dienstbier Ana A Amman Fabian F Štipl Daniel D Petráčková Denisa D Večerek Branislav B

International journal of molecular sciences 20190624 12

Bordetella pertussis is a Gram-negative strictly human pathogen of the respiratory tract and the etiological agent of whooping cough (pertussis). Previously, we have shown that RNA chaperone Hfq is required for virulence of B. pertussis. Furthermore, microarray analysis revealed that a large number of genes are affected by the lack of Hfq. This study represents the first attempt to characterize the Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expressi ...[more]

PMID: 31238496

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An integrative, multi-omics analysis of the Hfq regulon

Project description:The ability of bacteria to respond to environmental change is based on the exploration of sophisticated regulatory landscapes. While we can learn a great deal from reductive analyses of individual pathways, and global approaches to gene regulation, a deeper understanding of these complex signalling networks requires the simultaneous consideration of several regulatory layers at the genome-scale. To highlight the power of this approach we analysed the Hfq transcriptional/translational regulatory network in the plant-associated rhizobacterium Pseudomonas fluorescens. Extensive multi-omics analyses including proteomics quantification using isobaric isotope labelling (iTRAQ )were used to assess how hfq deletion affects gene transcription, translation and protein abundance. The subsequent integration of these datasets highlighted the discrete contributions by Hfq to gene regulation at different levels, confirmed previous predictions, and suggested novel regulatory principles for Hfq function. The integrative approach to regulatory analysis described here has significant potential, for both dissecting individual signalling pathways and understanding the strategies bacteria use to cope with external challenges.

2017-10-18 | PXD005621 | Pride

COMPARATIVE OMICS ANALYSIS OF HISTORICAL AND RECENT ISOLATES OF BORDETELLA PERTUSSIS

Project description:Despite high vaccination coverage, pertussis is on the rise in many countries including Czech Republic. To better understand B. pertussis resurgence we compared the changes in genome structures between Czech vaccine and circulating strains and subsequently, we determined how these changes translated into global transcriptomic and proteomic profiles. The whole-genome sequencing revealed that both historical and recent isolates of B. pertussis display substantial variation in genome organization and cluster separately. The RNA-seq and LC-MS/MS analyses indicate that these variations translated into discretely separated transcriptomic and proteomic profiles. Compared to vaccine strains, recent isolates displayed increased expression of flagellar genes and decreased expression of polysaccharide capsule operon. Czech strains (Bp46, K10, Bp155, Bp318 and Bp6242)exhibited increased expression of T3SS and sulphate metabolism genes when compared to Tohama I. In spite of 50 years of vaccination the Czech vaccine strains (VS67, VS393 and VS401) differ from recent isolates to a lesser extent than from another vaccine strain Tohama I.

2021-09-08 | PXD015184 | Pride

Analysis of the Hfq regulon in Pseudomonas fluorescens SBW25.

Project description:Hfq is a transcriptional and translational pleiotropic regulator in several bacteria. RNA-Seq, Ribo-Seq and Proteomic analyses were carried out in the wild-type and a hfq deletion strain of Pseudomonas fluorescens SBW25 with the intention to separate the influence of Hfq on the transcript stability and translation. This submission relates to the RNA-Seq data only. RNA was extracted from two replicate cultures each of SBW25-WT and SBW25-Δhfq strains and, after removal of ribosomal RNA, subjected to RNA-Seq in an Illumina NextSeq500 machine. The resulting sequence data was analysed by mapping to the reference sequence of Pseudomonas fluorescens SBW25 as available in the Genbank accession NC_012660.

2019-02-07 | E-MTAB-5396 | biostudies-arrayexpress

BtcB (BP2265) is a T3SS chaperone of the CesT family in Bordetella pertussis

Project description:Bordetella pertussis is a Gram-negative, strictly human respiratory pathogen and the causative agent of whooping cough (pertussis). Similar to other Gram-negative pathogens, B. pertussis produces a functional type III secretion system, but its role in pathogenesis of B. pertussis is enigmatic and has not yet been elucidated. Here, we applied omics RNA-seq as well as LC-MS/MS techniques and co-immunoprecipitation method to identify and characterize the novel CesT family T3SS chaperone BP2265. Our results show that the chaperone BP2265 specifically interacts with the secreted T3SS anti-sigma factor BtrA. Moreover, in the absence of the chaperone, secretion but not production of BtrA and several early, intermediate, and late T3SS substrates is severely impaired. It appears that the role of BtrA in regulating T3SS is more complex and extends beyond its activity as an antagonist of the sigma factor BtrS. We propose to rename BP2265 as BtcB for the Bordetella type III chaperone of BtrA.

2024-01-26 | PXD044487 | Pride

Blood exposure induces global changes in gene expression and protein secretion of B. pertussis

Project description:This project was focused on transcriptome and secretome of pathogenic bacteria B. pertussis, which were cultivated on solid plates (charcoal agar) with/without blood and subsequently sub-cultured in liquid media. As a standard, Bordetella spp. strain are grown on agar plates supplemented with blood. The main aim of this project was to determine how the cells respond to blood exposure and how the blood treatment impacts on the gene expression profiles in cell inoculated from plates and subcultured in a blood-less medium. Gene expression profiles were analyzed by RNA-seq and proteins secreted by B. pertussis cells grown in liquid media were determined by LC-MS/MS technique. Our results indicate that B. pertussis cells exposed to blood secreted significantly higher amounts of several virulence factors including type III secretion system (T3SS), bifunctional hemolysin/adenylate cyclase CyaA and adhesin FhaS, compared to cells inoculated from plates without blood. Differences in secretion of T3SS needle complex, effector protein BopC and anti-sigma factor BtrA were at least an order of magnitude higher compared to the differences on the transcriptional level, suggesting that post-transcriptional regulation and/or regulation of the protein secretion plays an important role in modulating the function of T3SS in B. pertussis.

2021-09-09 | PXD022760 | Pride

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Hfq-coIP overgrowth

Project description:The small RNAs associated with protein Hfq constitute one of the largest classes of post-transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free-standing genes. Here, deep sequencing of Hfq-bound transcripts from multiple stages of growth of Salmonella Typhimurium revealed a plethora of new small RNA species from within mRNA loci, including DapZ which overlaps with the 3’ region of the biosynthetic gene, dapB. Synthesis of the DapZ small RNA is independent of DapB protein synthesis, and controlled by HilD, the master regulator of Salmonella invasion genes. DapZ carries a short G/U-rich domain similar to that of the globally acting GcvB small RNA, and uses GcvB-like seed pairing to repress translation of the major ABC transporters, DppA and OppA. This exemplifies double functional output from an mRNA locus by the production of both a protein and an Hfq-dependent trans-acting RNA. Our atlas of Hfq targets suggests that the 3’ regions of mRNA genes constitute a rich reservoir to feed the Hfq network with new regulatory small RNAs.

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Functional characterization of the RNA chaperone Hfq in opportunistic human pathogen Stenotrophomonas maltophilia

Project description:Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immuno-compromised hosts. We constructed an hfq deletion mutant (Delta-hfq) of S. maltophilia, and compared the behaviour of wild-type and Delta-hfq S. maltophilia cells in a variety of assays. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from S. maltophilia wild-type and Delta-hfq strains showed that Hfq regulates expression of genes encoding flagellar and fimbrial components, transmembrane proteins, as well as enzymes involved in different metabolic pathways. Moreover, we analysed expression of several sRNAs identified by dRNA-seq in wild-type. The accumulation of two sRNAs was strongly reduced in the absence of Hfq. TEX (terminator exonuclease) treated and untreated libraries of the wild type and the Delta-hfq mutant were sequenced and compared

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