Difference between revisions of "Rny"

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* '''Description:''' RNase Y, endoribonuclease, required for the processing of the ''[[gapA]]'' operon mRNA<br/><br/>
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* '''Description:''' RNase Y, 5' end sensitive endoribonuclease, involved in the degradation/processing of mRNA<br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
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|style="background:#ABCDEF;" align="center"| '''Product''' ||  RNase Y
 
|style="background:#ABCDEF;" align="center"| '''Product''' ||  RNase Y
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || required for the processing <br/>of the ''[[gapA]]'' operon mRNA
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|style="background:#ABCDEF;" align="center"|'''Function''' || Initiates S-box riboswitch RNA turnover, required for the processing <br/>of the ''[[gapA]]'' operon mRNA, depletion of RNase Y increases bulk mRNA stability.
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
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* '''Catalyzed reaction/ biological activity:''' Nucleoside 2',3'-cyclic phosphate + H<sub>2</sub>O = nucleoside 3'-phosphate (according to Swiss-Prot) required for the processing of the ''[[gapA]]'' operon mRNA  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
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* '''Catalyzed reaction/ biological activity:''' RNase Y cleaves S-box riboswitch RNAs ''in vivo'' and ''in vitro''; preference for 5' monophosphorylated substrate ''in vitro'', endonucleolytic cleavageNucleoside 2',3'-cyclic phosphate + H<sub>2</sub>O = nucleoside 3'-phosphate (according to Swiss-Prot) required for the processing of the ''[[gapA]]'' operon mRNA  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed], cleavage activity appears sensitive to downstream secondary structure.
  
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* '''Protein family:''' 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot) 2',3' cyclic nucleotide phosphodiesterase family
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* '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot) 2',3' cyclic nucleotide phosphodiesterase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Modification:'''
 
* '''Modification:'''
  
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* '''Cofactor(s):''' metal-dependent
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* '''Cofactor(s):''' requires Mg+2, which can be replaced by Zn+2 or Mn+2 ions
  
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* '''Effectors of protein activity:'''
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* '''Effectors of protein activity:''' appeares sensitive to downstream secondary structure
  
 
* '''Interactions:''' [[Rny]]-[[PfkA]], [[Rny]]-[[Eno]], [[Rny]]-[[PnpA]], [[Rny]]-[[RnjA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
 
* '''Interactions:''' [[Rny]]-[[PfkA]], [[Rny]]-[[Eno]], [[Rny]]-[[PnpA]], [[Rny]]-[[RnjA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
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=Biological materials =
 
=Biological materials =
  
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* '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control, ''cat''), GP193 (''rny'' under p-xyl control, ''cat''), both available in [[Stülke]] lab
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* '''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:'''  
 
* '''Expression vector:'''  
 
** N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
 
** 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
 
** 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
 
** 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
 
** there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab

Revision as of 14:20, 5 October 2009

  • 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.
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







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; preference for 5' monophosphorylated substrate in vitro, endonucleolytic cleavageNucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate (according to Swiss-Prot) required for the processing of the gapA operon mRNA PubMed, cleavage activity appears sensitive to downstream secondary structure.
  • Protein family: Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot) 2',3' cyclic nucleotide phosphodiesterase family
  • 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
  • Effectors of protein activity: appeares sensitive to downstream secondary structure
  • Localization: cell membrane (according to Swiss-Prot), Single-pass membrane protein PubMed 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

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
  • lacZ fusion: pGP459 (in pAC7), available in Stülke lab
  • GFP fusion: B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in Errington lab
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in 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

Karen Shahbabian, Ailar Jamalli, Léna Zig, Harald Putzer
RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis.
EMBO J: 2009, 28(22);3523-33
[PubMed:19779461] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Fabian M Rothe, Christina Herzberg, Eva Wagner, Daniel Hellwig, Martin Lehnik-Habrink, Elke Hammer, Uwe Völker, Jörg Stülke
Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing.
Mol Cell Proteomics: 2009, 8(6);1350-60
[PubMed:19193632] [WorldCat.org] [DOI] (I p)

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

Alison Hunt, Joy P Rawlins, Helena B Thomaides, Jeff Errington
Functional analysis of 11 putative essential genes in Bacillus subtilis.
Microbiology (Reading): 2006, 152(Pt 10);2895-2907
[PubMed:17005971] [WorldCat.org] [DOI] (P p)

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