Difference between revisions of "Rny"

From SubtiWiki
Jump to: navigation, search
Line 44: Line 44:
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
  
 +
= [[RNase Y targets|Targets of RNase Y]] =
  
 
=The gene=
 
=The gene=
Line 94: Line 95:
 
* '''Effectors of protein activity:''' appears sensitive to downstream secondary structure, [http://www.ncbi.nlm.nih.gov/pubmed/19779461 PubMed]
 
* '''Effectors of protein activity:''' appears sensitive to downstream secondary structure, [http://www.ncbi.nlm.nih.gov/pubmed/19779461 PubMed]
  
* '''[[Interactions]]:''' part of the [[RNA degradosome]]
+
* '''[[SubtInteract|Interactions]]:'''
 +
** part of the [[RNA degradosome]]
 
** [[Rny]]-[[PfkA]] {{PubMed|19193632}}, [[Rny]]-[[Eno]] {{PubMed|19193632}}, [[Rny]]-[[PnpA]] {{PubMed|19193632}}, [[Rny]]-[[RnjA]] {{PubMed|19193632}}, [[Rny]]-[[CshA]] {{PubMed|20572937}}
 
** [[Rny]]-[[PfkA]] {{PubMed|19193632}}, [[Rny]]-[[Eno]] {{PubMed|19193632}}, [[Rny]]-[[PnpA]] {{PubMed|19193632}}, [[Rny]]-[[RnjA]] {{PubMed|19193632}}, [[Rny]]-[[CshA]] {{PubMed|20572937}}
  
* '''Localization:''' cell membrane,  single-pass membrane protein  {{PubMed|18763711,17005971,19820159}}
+
* '''[[Localization]]:'''  
 +
** cell membrane,  single-pass membrane protein  {{PubMed|18763711,17005971,19820159}}
  
 
=== Database entries ===
 
=== Database entries ===

Revision as of 12:05, 23 July 2011

  • 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 Initiates S-box riboswitch RNA turnover, required for the processing
of the gapA operon mRNA, depletion of RNase Y increases bulk
mRNA stability.
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







Categories containing this gene/protein

Rnases, 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

essential PubMed

Database entries

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

Additional information

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
  • 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 (4–24)
    • KH domain (210–273)
    • HD domain (336–429)
  • 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: [2]

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
    • 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

Publications on B. subtilis rny

Publications on homologs from other organisms