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Regulatory roles of sRNAs in pathogenesis of Vibrio cholerae
Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). (Sun Nyunt Wai)
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The Gram-negative pathogen Vibrio cholerae uses variety of regulatory molecules to modulate expression of virulence factors. One important regulatory element of microorganisms is small non-coding RNAs (sRNAs), which control various cell functions such as expression of cell membrane proteins, mRNA decay and riboswitches. In this thesis studies, we demonstrated the roles of the sRNAs VrrA in regulation of outer membrane protein expression, biofilm formation and expression of ribosome binding proteins. In addition, we showed that VrrB, a newly discovered sRNA, played a role in amino acid dependent starvation survival of V. cholerae and might functioned as a riboswitch.

VrrA, a 140-nt sRNAs in V. cholerae, was controlled by the alternative sigma factor σE. The outer membrane protein, OmpT is known to be regulated by environmental signals such as pH and temperature via the ToxR regulon and carbon source signals via the cAMP–CRP complex. Our studies provide new insight into the regulation of OmpT by signals received via the σE regulon through VrrA. We demonstrated that VrrA down-regulate ompT translation by base-pairing with the 5′ region of the ompT mRNA in a Hfq (RNA chaperone protein) dependent manner.

V. cholerae biofilms contain three matrix proteins—RbmA, RbmC and Bap1—and exopolysaccharide. While much is known about exopolysaccharide regulation, little is known about the mechanisms by which the matrix protein components of biofilms are regulated. In our studies, we demonstrated that VrrA negatively regulated rbmC translation by pairing to the 5' untranslated region of the rbmC transcript and that this regulation was not stringently dependent on Hfq.

In V. cholerae, VC0706 (Vrp) and VC2530 proteins are homologous to ribosome-associated inhibitor A (RaiA) and hibernation promoting factor (HPF) of Escherichia coli, respectively. HPF facilitates stationary phase survival through ribosome hibernation. We showed that VrrA repressed Vrp protein expression by base-pairing to the 5´ region of vrp mRNA and that this regulation required Hfq. We also showed that Vrp was highly expressed during stationary phase growth and associated with the ribosomes of V. cholerae. We further demonstrated that Vrp and VC2530 were important for V. cholerae starvation survival under nutrient-deficient conditions. While VC2530 was down-regulated in bacterial cells lacking vrrA, mutation of vrp resulted in increased expression of VC2530.

Riboswitches are an important class of regulators in bacteria, which are most often located in the 5' untranslated region (5´ UTR) of bacterial mRNA. In this study, we discovered the novel non-coding sRNA, VrrB located at the 5´ UTR of a downstream gene encoding Vibrio auxotropic factor A (VafA) for phenylalanine. In V. cholerae, reduced production of VafA was observed in the presence of phenylalanine and phenylpyruvate in the culture media. Some analogs of phenylalanine and phenylpyruvate could also modulate the expression of VafA. Furthermore, bacterial cells lacking the vrrB gene exhibited high production of VafA, suggesting that VrrB might function as a riboswitch that controls VafA expression.

Place, publisher, year, edition, pages
Umeå: Umeå University , 2015. , 57 p.
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 1704
Keyword [en]
Vibrio cholerae, sRNA, Biofilm, OmpT, RbmC, Vrp, VafA
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Microbiology
Identifiers
URN: urn:nbn:se:umu:diva-100528ISBN: 978-91-7601-230-7 (print)OAI: oai:DiVA.org:umu-100528DiVA: diva2:792550
Public defence
2015-03-27, E04 Unod R1, Norrlands universitetssjukhus, Umeå, 09:00 (English)
Opponent
Supervisors
Available from: 2015-03-06 Created: 2015-03-04 Last updated: 2015-03-06Bibliographically approved
List of papers
1. VrrA mediates Hfq-dependent regulation of OmpT synthesis in Vibrio cholerae
Open this publication in new window or tab >>VrrA mediates Hfq-dependent regulation of OmpT synthesis in Vibrio cholerae
2010 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 400, no 4, 682-688 p.Article in journal (Refereed) Published
Abstract [en]

OmpT, an outer membrane porin of Vibrio cholerae, is tightly regulated by the organism in response to different environments. Two transcriptional regulators, cAMP receptor protein (CRP) and ToxR, compete at the ompT promoter region. CRP activates ompT transcription by a loop-forming mechanism, while ToxR functions as an antiactivator and repressor, depending on its interplay with CRP. VrrA, a 140-nt small noncoding RNA in V. cholerae, is controlled by the alternative sigma factor sigma(E). We have demonstrated previously that VrrA represses ompA translation by base-pairing with the 5’ region of the mRNA, thereby affecting the release of outer membrane vesicles and modulating the colonization ability of V. cholerae. In this study, we demonstrate that VrrA RNA represses ompT translation by base-pairing with the 5’ region of the mRNA and that regulation requires the RNA chaperone protein Hfq. These results add new insight into the regulation of OmpT. In addition to pH/temperature signals via the ToxR regulon and carbon source signals via the cAMP-CRP complex, OmpT is further regulated by signals received via the sigma(E) regulon through VrrA.

Keyword
Vibrio cholerae, VrrA; OmpT, outer membrane protein, sRNA
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-43198 (URN)10.1016/j.jmb.2010.05.061 (DOI)000280652300004 ()20595045 (PubMedID)
Note

Journal of molecular biology J Mol Biol. 2010 Jul 23;400(4):682-8. Epub 2010 Jun 2.

Available from: 2011-04-22 Created: 2011-04-22 Last updated: 2017-12-11Bibliographically approved
2. Vibrio cholerae Utilizes Direct sRNA Regulation in Expression of a Biofilm Matrix Protein
Open this publication in new window or tab >>Vibrio cholerae Utilizes Direct sRNA Regulation in Expression of a Biofilm Matrix Protein
Show others...
2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 7, e101280Article in journal (Refereed) Published
Abstract [en]

Vibrio cholerae biofilms contain exopolysaccharide and three matrix proteins RbmA, RbmC and Bap1. While much is known about exopolysaccharide regulation, little is known about the mechanisms by which the matrix protein components of biofilms are regulated. VrrA is a conserved, 140-nt sRNA of V. cholerae, whose expression is controlled by sigma factor sigma(E). In this study, we demonstrate that VrrA negatively regulates rbmC translation by pairing to the 5' untranslated region of the rbmC transcript and that this regulation is not stringently dependent on the RNA chaperone protein Hfq. These results point to VrrA as a molecular link between the sigma(E)-regulon and biofilm formation in V. cholerae. In addition, VrrA represents the first example of direct regulation of sRNA on biofilm matrix component, by-passing global master regulators.

Place, publisher, year, edition, pages
PLOS, 2014
National Category
Cell and Molecular Biology Infectious Medicine Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-92947 (URN)10.1371/journal.pone.0101280 (DOI)000339614100012 ()
Available from: 2014-09-15 Created: 2014-09-09 Last updated: 2017-12-05Bibliographically approved
3. The VrrA sRNA controls stationary phase survival factor Vrp of Vibrio cholerae
Open this publication in new window or tab >>The VrrA sRNA controls stationary phase survival factor Vrp of Vibrio cholerae
2015 (English)In: RNA Biology, ISSN 1547-6286, E-ISSN 1555-8584, Vol. 12, no 2, 186-196 p.Article in journal (Refereed) Published
Abstract [en]

Small non-coding RNAs (sRNAs) are emerging regulatory elements in bacteria. The Vibrio cholerae sRNA VrrA has previously been shown to down-regulate outer membrane proteins (OmpA and OmpT) and biofilmmatrix protein (RbmC) by base-pairing with the 50 region of the corresponding mRNAs. In this study, we present an additional target of VrrA in V. cholerae, the mRNA coding for the ribosome binding protein Vrp. Vrp is homologous to ribosome-associated inhibitor A (RaiA) of Escherichia coli which facilitates stationary phase survival through ribosome hibernation. We show that VrrA downregulates Vrp protein synthesis by base-pairing to the 50 region of vrp mRNA and that the regulation requires the RNA chaperone protein, Hfq. We further demonstrate that Vrp is highly expressed during stationary phase growth and associates with the ribosome of V. cholerae. The effect of the Vrp protein in starvation survival is synergistic with that of the VC2530 protein, a homolog of the E. coli hibernation promoting factor HPF, suggesting a combined role for these proteins in ribosome hibernation in V. cholerae. Vrp and VC2530 are important for V. cholerae starvation survival under nutrient deficient conditions. While VC2530 is down-regulated in cells lacking vrrA, mutation of vrp results in VC2530 activation. This is the first report indicating a regulatory role for an sRNA, modulating stationary factors involved in bacterial ribosome hibernation.

Keyword
Hfq, Ribosome hibernation, sRNA, Vibrio cholerae, VrrA, Vrp
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Cell and Molecular Biology
Research subject
Medicine; Microbiology
Identifiers
urn:nbn:se:umu:diva-100522 (URN)10.1080/15476286.2015.1017211 (DOI)000352238900009 ()25826569 (PubMedID)
Available from: 2015-03-04 Created: 2015-03-04 Last updated: 2017-12-04Bibliographically approved
4. A new sRNA, VrrB, acts as a regulator for vafA, a gene involved in amino acid starvation survival of Vibrio cholerae
Open this publication in new window or tab >>A new sRNA, VrrB, acts as a regulator for vafA, a gene involved in amino acid starvation survival of Vibrio cholerae
(English)Manuscript (preprint) (Other academic)
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Microbiology
Identifiers
urn:nbn:se:umu:diva-100525 (URN)
Available from: 2015-03-04 Created: 2015-03-04 Last updated: 2015-03-05

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