Rny

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  • Description: RNase Y, 5' end sensitive endoribonuclease, involved in the degradation/ processing of mRNA

Gene name rny
Synonyms ymdA
Essential no PubMed
Product RNase Y
Function RNA processing and degradation
Gene expression levels in SubtiExpress: rny
Interactions involving this protein in SubtInteract: Rny
Regulatory function of this protein in SubtiPathways:
rny
Metabolic function and regulation of this protein in SubtiPathways:
Rny
MW, pI 58,7 kDa, 5.39
Gene length, protein length 1560 bp, 520 amino acids
Immediate neighbours pbpX, ymdB
Sequences Protein DNA DNA_with_flanks
Genetic context
Rny context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
Rny expression.png















Categories containing this gene/protein

Rnases, biofilm formation, membrane proteins

This gene is a member of the following regulons

Targets of RNase Y

The gene

Basic information

  • Locus tag: BSU16960

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

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

Extended information on the protein

  • 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

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

required for the processing of the gapA operon mRNA

Expression and regulation

  • Regulation: constitutive
  • Regulatory mechanism:
  • Additional information:
    • there is a terminator between rny and ymdB, most transcripts terminate there PubMed
    • The mRNA has a long 5' leader region. This may indicate RNA-based regulation PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 222 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 1386 PubMed

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.
  • Expression vector:
    • N-terminal Strep-tag, expression in E. coli, in pGP172: pGP441, 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
  • 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

Labs working on this gene/protein

Your additional remarks

References

Reviews

Soumaya Laalami, Léna Zig, Harald Putzer
Initiation of mRNA decay in bacteria.
Cell Mol Life Sci: 2014, 71(10);1799-828
[PubMed:24064983] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Richard J Lewis, Ulrike Mäder, Jörg Stülke
RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases.
Mol Microbiol: 2012, 84(6);1005-17
[PubMed:22568516] [WorldCat.org] [DOI] (I p)

David H Bechhofer
Bacillus subtilis mRNA decay: new parts in the toolkit.
Wiley Interdiscip Rev RNA: 2011, 2(3);387-94
[PubMed:21957024] [WorldCat.org] [DOI] (I p)

Roberto Valverde, Laura Edwards, Lynne Regan
Structure and function of KH domains.
FEBS J: 2008, 275(11);2712-26
[PubMed:18422648] [WorldCat.org] [DOI] (P p)

L Aravind, E V Koonin
The HD domain defines a new superfamily of metal-dependent phosphohydrolases.
Trends Biochem Sci: 1998, 23(12);469-72
[PubMed:9868367] [WorldCat.org] [DOI] (P p)


Publications on B. subtilis rny

Laetitia Gilet, Jeanne M DiChiara, Sabine Figaro, David H Bechhofer, Ciarán Condon
Small stable RNA maturation and turnover in Bacillus subtilis.
Mol Microbiol: 2015, 95(2);270-82
[PubMed:25402410] [WorldCat.org] [DOI] (I p)

David Noone, Letal I Salzberg, Eric Botella, Katrin Bäsell, Dörte Becher, Haike Antelmann, Kevin M Devine
A highly unstable transcript makes CwlO D,L-endopeptidase expression responsive to growth conditions in Bacillus subtilis.
J Bacteriol: 2014, 196(2);237-47
[PubMed:24163346] [WorldCat.org] [DOI] (I p)

Sabine Figaro, Sylvain Durand, Laetitia Gilet, Nadège Cayet, Martin Sachse, Ciarán Condon
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, 195(10);2340-8
[PubMed:23504012] [WorldCat.org] [DOI] (I p)

Soumaya Laalami, Philippe Bessières, Anna Rocca, Léna Zig, Pierre Nicolas, Harald Putzer
Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays.
PLoS One: 2013, 8(1);e54062
[PubMed:23326572] [WorldCat.org] [DOI] (I p)

Frank Bürmann, Prachi Sawant, Marc Bramkamp
Identification of interaction partners of the dynamin-like protein DynA from Bacillus subtilis.
Commun Integr Biol: 2012, 5(4);362-9
[PubMed:23060960] [WorldCat.org] [DOI] (I p)

Sylvain Durand, Laetitia Gilet, Philippe Bessières, Pierre Nicolas, Ciarán Condon
Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs.
PLoS Genet: 2012, 8(3);e1002520
[PubMed:22412379] [WorldCat.org] [DOI] (I p)

Einat Segev, Yoav Smith, Sigal Ben-Yehuda
RNA dynamics in aging bacterial spores.
Cell: 2012, 148(1-2);139-49
[PubMed:22209493] [WorldCat.org] [DOI] (I p)

Joseph A Newman, Lorraine Hewitt, Cecilia Rodrigues, Alexandra S Solovyova, Colin R Harwood, Richard J Lewis
Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome.
J Mol Biol: 2012, 416(1);121-36
[PubMed:22198292] [WorldCat.org] [DOI] (I p)

Shiyi Yao, Jamie Richards, Joel G Belasco, David H Bechhofer
Decay of a model mRNA in Bacillus subtilis by a combination of RNase J1 5' exonuclease and RNase Y endonuclease activities.
J Bacteriol: 2011, 193(22);6384-6
[PubMed:21908660] [WorldCat.org] [DOI] (I p)

Gintaras Deikus, David H Bechhofer
5' End-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA.
J Biol Chem: 2011, 286(40);34932-40
[PubMed:21862575] [WorldCat.org] [DOI] (I p)

Christine Diethmaier, Nico Pietack, Katrin Gunka, Christoph Wrede, Martin Lehnik-Habrink, Christina Herzberg, Sebastian Hübner, Jörg Stülke
A novel factor controlling bistability in Bacillus subtilis: the YmdB protein affects flagellin expression and biofilm formation.
J Bacteriol: 2011, 193(21);5997-6007
[PubMed:21856853] [WorldCat.org] [DOI] (I p)

Patrice Bruscella, Karen Shahbabian, Soumaya Laalami, Harald Putzer
RNase Y is responsible for uncoupling the expression of translation factor IF3 from that of the ribosomal proteins L35 and L20 in Bacillus subtilis.
Mol Microbiol: 2011, 81(6);1526-41
[PubMed:21843271] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Marc Schaffer, Ulrike Mäder, Christine Diethmaier, Christina Herzberg, Jörg Stülke
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y.
Mol Microbiol: 2011, 81(6);1459-73
[PubMed:21815947] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Joseph Newman, Fabian M Rothe, Alexandra S Solovyova, Cecilia Rodrigues, Christina Herzberg, Fabian M Commichau, Richard J Lewis, Jörg Stülke
RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli.
J Bacteriol: 2011, 193(19);5431-41
[PubMed:21803996] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Henrike Pförtner, Leonie Rempeters, Nico Pietack, Christina Herzberg, Jörg Stülke
The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex.
Mol Microbiol: 2010, 77(4);958-71
[PubMed:20572937] [WorldCat.org] [DOI] (I p)

Irnov Irnov, Cynthia M Sharma, Jörg Vogel, Wade C Winkler
Identification of regulatory RNAs in Bacillus subtilis.
Nucleic Acids Res: 2010, 38(19);6637-51
[PubMed:20525796] [WorldCat.org] [DOI] (I p)

Shiyi Yao, David H Bechhofer
Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y.
J Bacteriol: 2010, 192(13);3279-86
[PubMed:20418391] [WorldCat.org] [DOI] (I p)

Jessica C Zweers, Thomas Wiegert, Jan Maarten van Dijl
Stress-responsive systems set specific limits to the overproduction of membrane proteins in Bacillus subtilis.
Appl Environ Microbiol: 2009, 75(23);7356-64
[PubMed:19820159] [WorldCat.org] [DOI] (I p)

Karen Shahbabian, Ailar Jamalli, Léna Zig, Harald Putzer
RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis.
EMBO J: 2009, 28(22);3523-33
[PubMed:19779461] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Fabian M Rothe, Christina Herzberg, Eva Wagner, Daniel Hellwig, Martin Lehnik-Habrink, Elke Hammer, Uwe Völker, Jörg Stülke
Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing.
Mol Cell Proteomics: 2009, 8(6);1350-60
[PubMed:19193632] [WorldCat.org] [DOI] (I p)

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

Alison Hunt, Joy P Rawlins, Helena B Thomaides, Jeff Errington
Functional analysis of 11 putative essential genes in Bacillus subtilis.
Microbiology (Reading): 2006, 152(Pt 10);2895-2907
[PubMed:17005971] [WorldCat.org] [DOI] (P p)


Publications on homologs from other organisms

Song Ok Kang, Michael G Caparon, Kyu Hong Cho
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, 78(6);2754-67
[PubMed:20385762] [WorldCat.org] [DOI] (I p)

Makiko Nagata, Chikara Kaito, Kazuhisa Sekimizu
Phosphodiesterase activity of CvfA is required for virulence in Staphylococcus aureus.
J Biol Chem: 2008, 283(4);2176-84
[PubMed:17951247] [WorldCat.org] [DOI] (P p)

Chikara Kaito, Kenji Kurokawa, Yasuhiko Matsumoto, Yutaka Terao, Shigetada Kawabata, Shigeyuki Hamada, Kazuhisa Sekimizu
Silkworm pathogenic bacteria infection model for identification of novel virulence genes.
Mol Microbiol: 2005, 56(4);934-44
[PubMed:15853881] [WorldCat.org] [DOI] (P p)

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