Rny

• Description: RNase Y, endoribonuclease, required for the processing of the gapA operon mRNA
  
  

Gene name	rny
Synonyms	ymdA
Essential	yes
Product	RNase Y
Function	required for the processing of the gapA operon mRNA
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

The gene

Basic information

• Locus tag: BSU16960

Phenotypes of a mutant

essential PubMed

Database entries

• DBTBS entry: no entry

• SubtiList entry: [1]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: Nucleoside 2',3'-cyclic phosphate + H₂O = nucleoside 3'-phosphate (according to Swiss-Prot) required for the processing of the gapA operon mRNA PubMed

• Protein family: 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): metal-dependent

• Effectors of protein activity:

• Interactions: Rny-PfkA, Rny-Eno, Rny-PnpA, Rny-RnjA PubMed

• Localization: cell membrane (according to Swiss-Prot), Single-pass membrane protein PubMed 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

• Operon: rny-ymdB

• 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

• 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
  • 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

• Antibody: available in van Dijl and Stülke labs

Labs working on this gene/protein

Harald Putzer, IBPC Paris, France Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

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)