Difference between revisions of "Rny"
| 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 
This image was kindly provided by SubtiList
| |
Contents
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
- Localization:
- cell membrane, single-pass membrane protein PubMed
Database entries
- Structure:
- UniProt: O31774
- KEGG entry: [2]
- E.C. number: 3.1.4.16
Additional information
required for the processing of the gapA operon mRNA
Expression and regulation
- Sigma factor:
- Regulation: constitutive
- Regulatory mechanism:
- Additional information:
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
- 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
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
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)
