Difference between revisions of "Rny"

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(→‎Publications on B. subtilis rny)
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* transcription profile resulting from ''[[rny]]'' depletion: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30430 GEO] {{PubMed|21815947}}
 
* transcription profile resulting from ''[[rny]]'' depletion: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30430 GEO] {{PubMed|21815947}}
 
* defect in spore [[germination]] {{PubMed|22209493}}
 
* defect in spore [[germination]] {{PubMed|22209493}}
 +
* 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|23504012}}
 +
 
=== Database entries ===
 
=== Database entries ===
  
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* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymdA_1767310_1768872_1 rny] {{PubMed|22383849}}
 
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymdA_1767310_1768872_1 rny] {{PubMed|22383849}}
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:''' constitutive
 
* '''Regulation:''' constitutive
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==Publications on ''B. subtilis rny''==
 
==Publications on ''B. subtilis rny''==
−
<pubmed>21862575 22198292 22209493 22412379 23060960 23326572 21908660 21856853 21815947 18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937,21803996 21843271</pubmed>
+
<pubmed>21862575 22198292 22209493 22412379 23060960 23326572 21908660 21856853 21815947 18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937,21803996 21843271 23504012 </pubmed>
  
 
==Publications on homologs from other organisms==
 
==Publications on homologs from other organisms==
 
<pubmed> 17951247  20385762 15853881 </pubmed>
 
<pubmed> 17951247  20385762 15853881 </pubmed>
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 13:16, 27 March 2013

  • 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
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

  • 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
  • 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

Harald Putzer, IBPC Paris, France Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

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 B. subtilis rny


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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