SubtiBank SubtiBank

Categories containing this gene/protein


RNAses, biofilm formation, membrane proteins

This gene is a member of the following regulons


RNase Y targets


Gene


  • Coordinates on the chromosome (coding sequence): 1,767,310 -> 1,768,872
  • Phenotypes of a mutant

  • transcription profile resulting from rny depletion: GEO PubMed
  • defect in spore germination PubMed
  • the mutant is strongly impaired in sporulation, genetic competence and many other phenotypes PubMed
  • it is not possible to construct a rnjA rny double mutant PubMed
  • The protein


    Catalyzed reaction/ biological activity

  • RNase Y cleaves S-box riboswitch RNAs in vivo and in vitro PubMed
  • preference for 5' monophosphorylated substrate in vitro PubMed
  • endonucleolytic cleavage PubMed
  • required for the processing of the gapA operon mRNA PubMed
  • cleavage activity appears sensitive to downstream secondary structure PubMed
  • RNase Y initiates the degradation of rpsO mRNA PubMed
  • RNase Y is responsible for the degradation of 23S rRNA, 16S rRNA, and mRNAs in aging spores PubMed
  • RNase Y cleaves the leader of the cwlO mRNA at a stem-loop structure PubMed
  • 3' end maturation of RNase P RNA and scRNA PubMed
  • Protein family

  • Member of the HD superfamily of metal-dependent phosphohydrolases; 2,3 cyclic nucleotide phosphodiesterase family (according to Swiss-Prot)
  • Paralogous protein(s)

    Kinetic information

    Domains

  • transmembrane domain (aa 5–24) PubMed
  • coiled-coiled domain (may form a leucine zipper) (aa 30-150) PubMed
  • KH domain (aa 210–280) PubMed
  • HD domain (aa 330–430) PubMed
  • C-terminal domain (aa 430-520) PubMed
  • Modification

    Cofactors

  • requires Mg 2, which can be replaced by Zn 2 or Mn 2 ions, PubMed
  • Effectors of protein activity

  • appears sensitive to downstream secondary structure, PubMed
  • interaction of RNase Y with the complex of YmcA-YlbF-YaaT was reported to stimulate the degradation of the sinR and cggR-gapA mRNAs PubMed
  • Structure

    Localization

  • cell membrane, single-pass membrane protein PubMed
  • forms foci at the site of septation PubMed
  • Interactions

  • RNase Y forms dimers PubMed
  • part of the RNA degradosome
  • RNase Y-PfkA PubMed
  • RNase Y-Eno PubMed, K(D) of the interaction: 100 nM PubMed
  • RNase Y-PnpA PubMed, K(D) of the interaction: 5 nM PubMed
  • RNase Y-RnjA PubMed
  • RNase Y-CshA PubMed
  • DynA-RNase Y PubMed
  • GapA-Rny PubMed, about 2% of all GapA molecules participate in this interaction PubMed
  • interaction of RNase Y with the complex of YmcA-YlbF-YaaT was reported to stimulate the degradation of the sinR and cggR-gapA mRNAs PubMed
  • Additional information

  • required for the processing of the gapA operon mRNA
  • Expression and Regulation


    Operon

  • rny-ymdB PubMed
  • rny PubMed
  • Sigma factor

    Regulation

  • constitutive
  • Regulatory mechanism

    Additional information

  • the transcription terminator between rny and ymdB is strong and NusA-independent Reference
  • Biological materials


    Mutant

  • 4043 (rny under p-spac control, cat), GP193 (rny under p-xyl control, cat), both available in Jörg Stülke's lab
  • SSB447 (rny under P-spac control, "erm") available in Putzer lab
  • GP2501 (rny::spc), available in Jörg Stülke's lab
  • Expression vector

  • N-terminal Strep-tag, expression in E. coli, in pGP172: pGP441, available in Jörg Stülke's lab
  • pGP2813: IPTG inducible expression, purification in E. coli with N-terminal Strep-tag, in pGP172, available in Jörg Stülke's lab
  • N-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP380: pGP775, available in Jörg Stülke's lab
  • C-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP382: pGP1852, available in Jörg Stülke's lab
  • Expression of RNase Y missing the N-terminal transmembrane domain (25aa) as an intein fusion in E. coli (no tag left in the purified protein) available in the Putzer lab
  • wild type rny, expression in B. subtilis, in pBQ200: pGP1201, available in Jörg Stülke's lab
  • there is also a series of domain constructs present in pBQ200, all available in Jörg Stülke's lab
  • chromosomal expression of Rny-Strep, spc: GP1033, available in Jörg Stülke's lab
  • lacZ fusion

  • pGP459 (in pAC7), available in Jörg Stülke's lab
  • GFP fusion

  • B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in Errington lab
  • pGP1368 for chromosomal expression of rny-YFP, available in Jörg Stülke's lab
  • two-hybrid system

  • B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab
  • FLAG-tag construct

  • GP1030 (spc, based on pGP1331), available in Jörg Stülke's lab
  • Antibody

  • available in van Dijl and in Jörg Stülke's lab
  • Labs working on this gene/protein


  • Ciaran Condon, IBPC Paris, France Homepage
  • Harald Putzer, IBPC Paris, France Homepage
  • Jörg Stülke, University of Göttingen, Germany Homepage
  • References


    Reviews

    Hui MP, Foley PL, Belasco JG

    Messenger RNA degradation in bacterial cells

    Annu Rev Genet. 2014;48:537-59. doi: 10.1146/annurev-genet-120213-092340. Epub 2014 Oct 1. Review. PubMed PMID: 25292357; PubMed Central PMCID: PMC4431577.
    Laalami S, Zig L, Putzer H

    Initiation of mRNA decay in bacteria

    Cell Mol Life Sci. 2014 May;71(10):1799-828. doi: 10.1007/s00018-013-1472-4. Epub 2013 Sep 25. Review. PubMed PMID: 24064983; PubMed Central PMCID: PMC3997798.
    Lehnik-Habrink M, Lewis RJ, Mäder U, Stülke J

    RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases

    Mol Microbiol. 2012 Jun;84(6):1005-17. doi: 10.1111/j.1365-2958.2012.08072.x. Epub 2012 May 8. Review. PubMed PMID: 22568516.
    Bechhofer DH

    Bacillus subtilis mRNA decay: new parts in the toolkit

    Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):387-94. doi: 10.1002/wrna.66. Epub 2010 Dec 16. Review. PubMed PMID: 21957024.
    Valverde R, Edwards L, Regan L

    Structure and function of KH domains

    FEBS J. 2008 Jun;275(11):2712-26. doi: 10.1111/j.1742-4658.2008.06411.x. Epub 2008 Apr 15. Review. PubMed PMID: 18422648.
    Aravind L, Koonin EV

    The HD domain defines a new superfamily of metal-dependent phosphohydrolases

    Trends Biochem Sci. 1998 Dec;23(12):469-72. PubMed PMID: 9868367.

    Original publications

    Cascante-Estepa N, Gunka K, Stülke J

    Localization of Components of the RNA-Degrading Machine in Bacillus subtilis

    Front Microbiol. 2016 Sep 21;7:1492. eCollection 2016. PubMed PMID: 27708634; PubMed Central PMCID: PMC5030255.
    Gimpel M, Brantl S

    Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B

    subtilis GapA. RNA Biol. 2016 Sep;13(9):916-26. doi: 10.1080/15476286.2016.1208894. Epub 2016 Jul 22. PubMed PMID: 27449348; PubMed Central PMCID: PMC5013986.
    Müller P, Jahn N, Ring C, Maiwald C, Neubert R, Meißner C, Brantl S

    A multistress responsive type I toxin-antitoxin system: bsrE/SR5 from the B

    subtilis chromosome. RNA Biol. 2016 May 3;13(5):511-23. doi: 10.1080/15476286.2016.1156288. Epub 2016 Mar 3. PubMed PMID: 26940229; PubMed Central PMCID: PMC4962801.
    Ogura M

    Post-transcriptionally generated cell heterogeneity regulates biofilm formation in Bacillus subtilis

    Genes Cells. 2016 Apr;21(4):335-49. doi: 10.1111/gtc.12343. Epub 2016 Jan 28. PubMed PMID: 26819068.
    Jahn N, Brantl S

    Heat-shock-induced refolding entails rapid degradation of bsrG toxin mRNA by RNases Y and J1

    Microbiology. 2016 Mar;162(3):590-9. doi: 10.1099/mic.0.000247. Epub 2016 Jan 22. PubMed PMID: 26802042.
    Salvo E, Alabi S, Liu B, Schlessinger A, Bechhofer DH

    Interaction of Bacillus subtilis Polynucleotide Phosphorylase and RNase Y: STRUCTURAL MAPPING AND EFFECT ON mRNA TURNOVER

    J Biol Chem. 2016 Mar 25;291(13):6655-63. doi: 10.1074/jbc.M115.711044. Epub 2016 Jan 21. PubMed PMID: 26797123; PubMed Central PMCID: PMC4807252.
    Khemici V, Prados J, Linder P, Redder P

    Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation

    PLoS Genet. 2015 Oct 16;11(10):e1005577. doi: 10.1371/journal.pgen.1005577. eCollection 2015 Oct. Erratum in: PLoS Genet. 2016 Sep;12(9):e1006320. PubMed PMID: 26473962; PubMed Central PMCID: PMC4608709.
    DeLoughery A, Dengler V, Chai Y, Losick R

    Biofilm formation by Bacillus subtilis requires an endoribonuclease-containing multisubunit complex that controls mRNA levels for the matrix gene repressor SinR

    Mol Microbiol. 2016 Jan;99(2):425-37. doi: 10.1111/mmi.13240. Epub 2015 Oct 26. PubMed PMID: 26434553; PubMed Central PMCID: PMC4989519.
    Gilet L, DiChiara JM, Figaro S, Bechhofer DH, Condon C

    Small stable RNA maturation and turnover in Bacillus subtilis

    Mol Microbiol. 2015 Jan;95(2):270-82. doi: 10.1111/mmi.12863. Epub 2014 Dec 19. PubMed PMID: 25402410; PubMed Central PMCID: PMC4364036.
    Noone D, Salzberg LI, Botella E, Bäsell K, Becher D, Antelmann H, Devine KM

    A highly unstable transcript makes CwlO D,L-endopeptidase expression responsive to growth conditions in Bacillus subtilis

    J Bacteriol. 2014 Jan;196(2):237-47. doi: 10.1128/JB.00986-13. Epub 2013 Oct 25. PubMed PMID: 24163346; PubMed Central PMCID: PMC3911235.
    Figaro S, Durand S, Gilet L, Cayet N, Sachse M, Condon C

    Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence

    J Bacteriol. 2013 May;195(10):2340-8. doi: 10.1128/JB.00164-13. Epub 2013 Mar 15. PubMed PMID: 23504012; PubMed Central PMCID: PMC3650553.
    Laalami S, Bessières P, Rocca A, Zig L, Nicolas P, Putzer H

    Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays

    PLoS One. 2013;8(1):e54062. doi: 10.1371/journal.pone.0054062. Epub 2013 Jan 10. PubMed PMID: 23326572; PubMed Central PMCID: PMC3542257.
    Bürmann F, Sawant P, Bramkamp M

    Identification of interaction partners of the dynamin-like protein DynA from Bacillus subtilis

    Commun Integr Biol. 2012 Jul 1;5(4):362-9. doi: 10.4161/cib.20215. PubMed PMID: 23060960; PubMed Central PMCID: PMC3460841.
    Durand S, Gilet L, Bessières P, Nicolas P, Condon C

    Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs

    PLoS Genet. 2012;8(3):e1002520. doi: 10.1371/journal.pgen.1002520. Epub 2012 Mar 8. PubMed PMID: 22412379; PubMed Central PMCID: PMC3297567.
    Segev E, Smith Y, Ben-Yehuda S

    RNA dynamics in aging bacterial spores

    Cell. 2012 Jan 20;148(1-2):139-49. doi: 10.1016/j.cell.2011.11.059. Epub 2011 Dec 29. PubMed PMID: 22209493.
    Newman JA, Hewitt L, Rodrigues C, Solovyova AS, Harwood CR, Lewis RJ

    Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome

    J Mol Biol. 2012 Feb 10;416(1):121-36. doi: 10.1016/j.jmb.2011.12.024. Epub 2011 Dec 16. PubMed PMID: 22198292.
    Yao S, Richards J, Belasco JG, Bechhofer DH

    Decay of a model mRNA in Bacillus subtilis by a combination of RNase J1 5' exonuclease and RNase Y endonuclease activities

    J Bacteriol. 2011 Nov;193(22):6384-6. doi: 10.1128/JB.05939-11. Epub 2011 Sep 9. PubMed PMID: 21908660; PubMed Central PMCID: PMC3209221.
    Deikus G, Bechhofer DH

    5' End-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA

    J Biol Chem. 2011 Oct 7;286(40):34932-40. doi: 10.1074/jbc.M111.287409. Epub 2011 Aug 23. PubMed PMID: 21862575; PubMed Central PMCID: PMC3186403.
    Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J

    A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation

    J Bacteriol. 2011 Nov;193(21):5997-6007. doi: 10.1128/JB.05360-11. Epub 2011 Aug 19. PubMed PMID: 21856853; PubMed Central PMCID: PMC3194898.
    Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J

    RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y

    Mol Microbiol. 2011 Sep;81(6):1459-73. doi: 10.1111/j.1365-2958.2011.07777.x. Epub 2011 Aug 4. PubMed PMID: 21815947.
    Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C, Herzberg C, Commichau FM, Lewis RJ, Stülke J

    RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli

    J Bacteriol. 2011 Oct;193(19):5431-41. doi: 10.1128/JB.05500-11. Epub 2011 Jul 29. PubMed PMID: 21803996; PubMed Central PMCID: PMC3187381.
    Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C, Herzberg C, Commichau FM, Lewis RJ, Stülke J

    RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli

    J Bacteriol. 2011 Oct;193(19):5431-41. doi: 10.1128/JB.05500-11. Epub 2011 Jul 29. PubMed PMID: 21803996; PubMed Central PMCID: PMC3187381.
    Lehnik-Habrink M, Pförtner H, Rempeters L, Pietack N, Herzberg C, Stülke J

    The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex

    Mol Microbiol. 2010 Aug;77(4):958-71. doi: 10.1111/j.1365-2958.2010.07264.x. Epub 2010 Jun 21. PubMed PMID: 20572937.
    Irnov I, Sharma CM, Vogel J, Winkler WC

    Identification of regulatory RNAs in Bacillus subtilis

    Nucleic Acids Res. 2010 Oct;38(19):6637-51. doi: 10.1093/nar/gkq454. Epub 2010 Jun 4. PubMed PMID: 20525796; PubMed Central PMCID: PMC2965217.
    Yao S, Bechhofer DH

    Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y

    J Bacteriol. 2010 Jul;192(13):3279-86. doi: 10.1128/JB.00230-10. Epub 2010 Apr 23. PubMed PMID: 20418391; PubMed Central PMCID: PMC2897663.
    Zweers JC, Wiegert T, van Dijl JM

    Stress-responsive systems set specific limits to the overproduction of membrane proteins in Bacillus subtilis

    Appl Environ Microbiol. 2009 Dec;75(23):7356-64. doi: 10.1128/AEM.01560-09. Epub 2009 Oct 9. PubMed PMID: 19820159; PubMed Central PMCID: PMC2786430.
    Shahbabian K, Jamalli A, Zig L, Putzer H

    RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis

    EMBO J. 2009 Nov 18;28(22):3523-33. doi: 10.1038/emboj.2009.283. Epub 2009 Sep 24. PubMed PMID: 19779461; PubMed Central PMCID: PMC2782095.
    Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, Lehnik-Habrink M, Hammer E, Völker U, Stülke J

    Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing

    Mol Cell Proteomics. 2009 Jun;8(6):1350-60. doi: 10.1074/mcp.M800546-MCP200. Epub 2009 Feb 3. PubMed PMID: 19193632; PubMed Central PMCID: PMC2690492.
    Hahne H, Wolff S, Hecker M, Becher D

    From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches

    Proteomics. 2008 Oct;8(19):4123-36. doi: 10.1002/pmic.200800258. PubMed PMID: 18763711.
    Hunt A, Rawlins JP, Thomaides HB, Errington J

    Functional analysis of 11 putative essential genes in Bacillus subtilis

    Microbiology. 2006 Oct;152(Pt 10):2895-907. PubMed PMID: 17005971.

    Publications on homologs from other organisms

    Khemici V, Prados J, Linder P, Redder P

    Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation

    PLoS Genet. 2015 Oct 16;11(10):e1005577. doi: 10.1371/journal.pgen.1005577. eCollection 2015 Oct. Erratum in: PLoS Genet. 2016 Sep;12(9):e1006320. PubMed PMID: 26473962; PubMed Central PMCID: PMC4608709.
    Kang SO, Caparon MG, Cho KH

    Virulence gene regulation by CvfA, a putative RNase: the CvfA-enolase complex in Streptococcus pyogenes links nutritional stress, growth-phase control, and virulence gene expression

    Infect Immun. 2010 Jun;78(6):2754-67. doi: 10.1128/IAI.01370-09. Epub 2010 Apr 12. PubMed PMID: 20385762; PubMed Central PMCID: PMC2876558.
    Nagata M, Kaito C, Sekimizu K

    Phosphodiesterase activity of CvfA is required for virulence in Staphylococcus aureus

    J Biol Chem. 2008 Jan 25;283(4):2176-84. Epub 2007 Oct 18. PubMed PMID: 17951247.
    Kaito C, Kurokawa K, Matsumoto Y, Terao Y, Kawabata S, Hamada S, Sekimizu K

    Silkworm pathogenic bacteria infection model for identification of novel virulence genes

    Mol Microbiol. 2005 May;56(4):934-44. PubMed PMID: 15853881.
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