Rny

• 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
Gene expression levels in SubtiExpress: rny
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 This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

Rnases, biofilm formation, essential genes, membrane proteins

The gene

Basic information

• Locus tag: BSU16960

Phenotypes of a mutant

• essential PubMed
• transcription profile resulting from rny depletion: GEO PubMed
• defect in spore germination PubMed
• a study from the lab of Ciaran Condon reports that rny is non-essential and that the mutant is strongly impaired in sporulation, genetic competence and many other phenotypes PubMed

Database entries

• DBTBS entry: no entry

• SubtiList entry: [1]

• GEO entry: [2] (rny depletion vs. normal rny expression) PubMed

The protein

Basic information/ Evolution

• 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

• 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

• 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

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

Database entries

• Structure:

• UniProt: O31774

• KEGG entry: [3]

• E.C. number: 3.1.4.16

Additional information

required for the processing of the gapA operon mRNA

Expression and regulation

• Operon:
  • rny-ymdB PubMed
  • rny PubMed

• Expression browser: rny PubMed

• 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 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

• 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

Harald Putzer, IBPC Paris, France Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

References

Reviews

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)

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)