Difference between revisions of "Rny"

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Revision as of 10:01, 19 April 2012

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

Gene name rny
Synonyms ymdA
Essential yes
Product RNase Y
Function RNA processing and degradation
Interactions involving this protein in SubtInteract: Rny
Regulatory function of this protein in SubtiPathways:
Central C-metabolism
MW, pI 58,7 kDa, 5.39
Gene length, protein length 1560 bp, 520 amino acids
Immediate neighbours pbpX, ymdB
Get the DNA and protein sequences
(Barbe et al., 2009)
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, essential genes, 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

  • Catalyzed reaction/ biological activity:
  • 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:
  • Cofactor(s): 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

  • Sigma factor:
  • 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

Biological materials

  • Mutant: essential!!!!, 4043 (rny under p-spac control, cat), GP193 (rny under p-xyl control, cat), both available in Stülke 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 Stülke lab
    • N-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP380: pGP775 , available in Stülke 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 Stülke lab
    • there is also a series of domain constructs present in pBQ200, all available in Stülke lab
    • chromosomal expression of Rny-Strep, spc: GP1033, available in Jörg Stülke's lab
  • lacZ fusion: pGP459 (in pAC7), available in Stülke 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 Stülke lab
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • FLAG-tag construct: GP1030 (spc, based on pGP1331), available in the Stülke lab

Labs working on this gene/protein

Harald Putzer, IBPC Paris, France Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

Reviews

Additional reviews: PubMed

Publications on B. subtilis rny

Additional publications: PubMed

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)

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)

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, 193(21):5997-6007. 
PubMed:21856853
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 81(6): 1459-1473. 
PubMed:21815947


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)