Difference between revisions of "Rny"
Line 56: | Line 56: | ||
* essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] | * essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] | ||
* transcription profile resulting from ''[[rny]]'' depletion: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30430 GEO] {{PubMed|21815947}} | * transcription profile resulting from ''[[rny]]'' depletion: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30430 GEO] {{PubMed|21815947}} | ||
+ | * defect in spore [[germination]] {{PubMed|22209493}} | ||
=== Database entries === | === Database entries === | ||
Line 77: | Line 78: | ||
** cleavage activity appears sensitive to downstream secondary structure {{PubMed|19779461}} | ** cleavage activity appears sensitive to downstream secondary structure {{PubMed|19779461}} | ||
** [[RNase]] Y initiates the degradation of ''[[rpsO]]'' mRNA {{PubMed|20418391}} | ** [[RNase]] Y initiates the degradation of ''[[rpsO]]'' mRNA {{PubMed|20418391}} | ||
+ | ** [[RNase]] Y is responsible for the degradation of [[23S rRNA]], [[16S rRNA]], and mRNAs in aging spores {{PubMed|22209493}} | ||
* '''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 175: | Line 177: | ||
==Publications on ''B. subtilis rny''== | ==Publications on ''B. subtilis rny''== | ||
'''Additional publications:''' {{PubMed|21908660}} | '''Additional publications:''' {{PubMed|21908660}} | ||
− | <pubmed>21862575 22198292 </pubmed> | + | <pubmed>21862575 22198292 22209493 </pubmed> |
<big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big> | <big>''Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J'' </big> | ||
<big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big> | <big>'''A Novel Factor Controlling Bistability in ''Bacillus subtilis'': The YmdB Protein Affects</big> |
Revision as of 11:45, 3 January 2012
- 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 | RNA processing and degradation |
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, biofilm formation, 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
- transcription profile resulting from rny depletion: GEO PubMed
- defect in spore germination 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
- RNase Y is responsible for the degradation of 23S rRNA, 16S rRNA, and mRNAs in aging spores 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:
- 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: [3]
- 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
Reviews
Additional reviews: PubMed
Publications on B. subtilis rny
Additional publications: PubMed
Einat Segev, Yoav Smith, Sigal Ben-Yehuda
RNA dynamics in aging bacterial spores.
Cell: 2012, 148(1-2);139-49
[PubMed:22209493]
[WorldCat.org]
[DOI]
(I p)
Joseph A Newman, Lorraine Hewitt, Cecilia Rodrigues, Alexandra S Solovyova, Colin R Harwood, Richard J Lewis
Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome.
J Mol Biol: 2012, 416(1);121-36
[PubMed:22198292]
[WorldCat.org]
[DOI]
(I p)
Gintaras Deikus, David H Bechhofer
5' End-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA.
J Biol Chem: 2011, 286(40);34932-40
[PubMed:21862575]
[WorldCat.org]
[DOI]
(I p)
Diethmaier C, Pietack N, Gunka K, Wrede C, Lehnik-Habrink M, Herzberg C, Hübner S, Stülke J A Novel Factor Controlling Bistability in Bacillus subtilis: The YmdB Protein Affects Flagellin Expression and Biofilm Formation. J Bacteriol.: 2011, 193(21):5997-6007. PubMed:21856853
Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. Mol Microbiol. 2011 81(6): 1459-1473. PubMed:21815947
Patrice Bruscella, Karen Shahbabian, Soumaya Laalami, Harald Putzer
RNase Y is responsible for uncoupling the expression of translation factor IF3 from that of the ribosomal proteins L35 and L20 in Bacillus subtilis.
Mol Microbiol: 2011, 81(6);1526-41
[PubMed:21843271]
[WorldCat.org]
[DOI]
(I p)
Martin Lehnik-Habrink, Joseph Newman, Fabian M Rothe, Alexandra S Solovyova, Cecilia Rodrigues, Christina Herzberg, Fabian M Commichau, Richard J Lewis, Jörg Stülke
RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli.
J Bacteriol: 2011, 193(19);5431-41
[PubMed:21803996]
[WorldCat.org]
[DOI]
(I p)
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