Difference between revisions of "Rny"

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** [[RNase]] Y is responsible for the degradation of [[23S rRNA]], [[16S rRNA]], and mRNAs in aging spores {{PubMed|22209493}}
 
** [[RNase]] Y is responsible for the degradation of [[23S rRNA]], [[16S rRNA]], and mRNAs in aging spores {{PubMed|22209493}}
 
** [[RNase]] Y cleaves the leader of the ''[[cwlO]]'' mRNA at a stem-loop structure {{PubMed|24163346}}
 
** [[RNase]] Y cleaves the leader of the ''[[cwlO]]'' mRNA at a stem-loop structure {{PubMed|24163346}}
 +
** 3' end maturation of [[rnpB|RNase P RNA]] and [[scr|scRNA]] {{PubMed|25402410}}
  
 
* '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot)  
 
* '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot)  
Line 199: Line 200:
  
 
==Publications on ''B. subtilis rny''==
 
==Publications on ''B. subtilis rny''==
<pubmed>21862575 22198292 22209493 22412379 23060960 23326572 21908660 21856853 21815947 24163346 18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937,21803996 21843271 23504012 </pubmed>
+
<pubmed>21862575 22198292 22209493 22412379 23060960 23326572 21908660 21856853 21815947 24163346 18763711,19193632,17005971 19779461 19820159 20418391 20525796 20572937,21803996 21843271 23504012 25402410</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 12:40, 18 November 2014

  • 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
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, 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

  • 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

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
    • 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
  • 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

Your additional remarks

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 B. subtilis rny


Publications on homologs from other organisms