Rny

• 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 This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

Rnases, biofilm formation, membrane proteins

The gene

Basic information

• Locus tag: BSU16960

Phenotypes of a mutant

• 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

• BsubCyc: BSU16960

• 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
  • 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):

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

• 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

• BsubCyc: BSU16960

• 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
  • 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

• 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

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 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)