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
Martin Lehnik-Habrink, Henrike Pförtner, Leonie Rempeters, Nico Pietack, Christina Herzberg, Jörg Stülke
The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex.
Mol Microbiol: 2010, 77(4);958-71
[PubMed:20572937]
[WorldCat.org]
[DOI]
(I p)
Irnov Irnov, Cynthia M Sharma, Jörg Vogel, Wade C Winkler
Identification of regulatory RNAs in Bacillus subtilis.
Nucleic Acids Res: 2010, 38(19);6637-51
[PubMed:20525796]
[WorldCat.org]
[DOI]
(I p)
Shiyi Yao, David H Bechhofer
Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y.
J Bacteriol: 2010, 192(13);3279-86
[PubMed:20418391]
[WorldCat.org]
[DOI]
(I p)
Jessica C Zweers, Thomas Wiegert, Jan Maarten van Dijl
Stress-responsive systems set specific limits to the overproduction of membrane proteins in Bacillus subtilis.
Appl Environ Microbiol: 2009, 75(23);7356-64
[PubMed:19820159]
[WorldCat.org]
[DOI]
(I p)
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)
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)
