rny

rny
168

RNase Y, 5 end sensitive endoribonuclease, involved in the degradation/ processing of mRNA, part of the putative RNA degradosome

Locus
BSU_16960
Molecular weight
58.75 kDa
Isoelectric point
5.39
Protein length
520 aaSequenceBlast
Gene length
1563 bpSequenceBlast
Function
RNA processing and degradation
Product
RNase Y
Essential
quasi
E.C.
3.1.4.16
Synonyms
rny, ymdA
Outlinks
BsubCyc SubtiList UniProt STRING Genoscapist PaperBLAST

Genomic Context

Categories containing this gene/protein

List of homologs in different organisms, belongs to COG1418 (Galperin et al., 2021)

This gene is a member of the following regulons

Gene
Coordinates
1,767,310  1,768,872
Phenotypes of a mutant
quasi-essential PubMed
transcription profile resulting from rny depletion: GEO PubMed
loss of genetic competence PubMed
defect in spore germination PubMed
the mutant is strongly impaired in sporulation, genetic competence and many other traits PubMed
it is not possible to construct a rnjA rny double mutant  PubMed
the inactivation of the rny gene leads to the rapid accumulation of suppressor mutations that result in strongly reduced transcription PubMed
knockdown of expression results in loss of ICEBs1 conjugation (both in donor cells) PubMed
RNA
Interactions
the rny mRNA binds to RNA polymerase PubMed
The protein
Catalyzed reaction/ biological activity
processing, maturation and degradation of mRNAs, see RNase Y targets
RNase Y cleaves S-box mgtE 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
RNase Y cleaves the leader of the cwlO mRNA at a stem-loop structure PubMed
3' end maturation of RNase P RNA and scRNA PubMed
Protein family
RNase Y family (single member, according to UniProt)
Domains
transmembrane domain\t(aa 524) PubMed
coiled-coiled domain (may form a leucine zipper) (aa 30-150) PubMed
KH domain\t(aa 210-280) PubMed
HD domain (aa 330-430) PubMed
C-terminal domain (aa 430-520)  PubMed
Cofactors
requires Mg2+, which can be replaced by Zn2+ or Mn2+ ions, PubMed
Structure
6F7T (PDB) (the N-teminal part, aa 1 ... 218) PubMed
O31774 (AlphaFold)
Effectors of protein activity
appears sensitive to downstream secondary structure PubMed
interaction of RNase Y with the complex of RicA-RicF-RicT stimulates the degradation and maturation of several polycistronic mRNAs PubMed
interaction of RNase Y with the complex of Eno and SR7P stimulates the degradation and maturation of several target RNAs PubMed
Localization
cell membrane,  single-pass membrane protein  PubMed
forms foci at the site of septation PubMed
Additional information
required for the processing of the gapA operon mRNA
Expression and Regulation
Operons
Genes
rny-ymdB
Description
PubMed
Regulation
constitutive
Additional information
the transcription terminator between ''rny and ymdB'' is strong and NusA-independent Reference
Open in new tab

rny→ymdB

2025-03-21 22:06:43

ghost

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accb38d25050d34785a253e96766189dff0b632b

72F7B633B228E9BCE59B918A835E5A1613D2F9D4

Genes
rny
Description
PubMed
Regulation
constitutive
Additional information
the transcription terminator between ''rny and ymdB'' is strong and NusA-independent Reference
Open in new tab

rny

2025-03-21 22:06:34

ghost

124

21281dca59d9922ef242944ec91108fa9a8a05aa

91BEB4ADBD11915ED36147E1BC802F5F327B5118

Biological materials
Mutant
4043 (rny under p-spac control, cat), GP193 (rny under p-xyl control, cat), both available in Jörg Stülke's lab
GP2501 (Δrny::spc) available in Jörg Stülke's lab PubMed
GP2524 (rny::ermC), available in Jörg Stülke's lab
BKE16960 (rny::erm  trpC2) available at BGSC,  PubMed, upstream reverse: _UP1_CATACTTTCACCTCCTCTTG,  downstream forward: _UP4_TAAAGTGATGCGCTAAGCAT
BKK16960 (rny::kan  trpC2) available at BGSC,  PubMed, upstream reverse: _UP1_CATACTTTCACCTCCTCTTG,  downstream forward: _UP4_TAAAGTGATGCGCTAAGCAT
Expression vectors
N-terminal Strep-tag, expression in E. coli, in pGP172: pGP441, available in Jörg Stülke's lab
pGP2813: IPTG inducible expression, purification in E. coli with N-terminal Strep-tag, in pGP172, 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
Two-hybrid system
B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab, PubMed
FLAG-tag construct
GP1030 (spc, based on pGP1331), available in Jörg Stülke's lab
LacZ fusion
pGP459 (in pAC7), available in Jörg Stülke's lab
Antibody
available in van Dijl and 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
Labs working on this gene/protein
Ciaran Condon, IBPC Paris, France Homepage
Harald Putzer, IBPC Paris, France Homepage
Jörg Stülke, University of Göttingen, Germany Homepage
References
Reviews
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Original Publications
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Page visits: 11352

Time of last update: 2025-04-04 02:08:41

Author of last update: Jstuelk