Rnc

• Description: RNase III; required for the degradation of sense/antisense transcripts in Gram positive, low GC bacteria
  
  

Gene name	rnc
Synonyms	rncS
Essential	yes
Product	endoribonuclease III
Function	cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (scr)
Gene expression levels in SubtiExpress: rnc
Metabolic function and regulation of this protein in SubtiPathways: Rnc
MW, pI	28 kDa, 8.076
Gene length, protein length	747 bp, 249 aa
Immediate neighbours	acpA, smc
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

Rnases, translation, protein secretion, essential genes

This gene is a member of the following regulons

stringent response

The gene

Basic information

• Locus tag: BSU15930

Phenotypes of a mutant

• essential PubMed
• the rnc gene can be deleted in strains cured of the Skin element and SPß prophage (or upon deletion of the toxin genes txpA and yonT) PubMed

Database entries

• BsubCyc: BSU15930

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity:
  • Endonucleolytic cleavage of double-stranded RNA to 5'-phosphomonoester (according to Swiss-Prot)
  • cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor (scr)
  • degradation of txpA mRNA-RatA RNA duplex (encoded on the Skin element) PubMed
  • degradation of yonT mRNA-as-yonT RNA duplex (encoded on the SP-beta prophage) PubMed
  • degradation of the roxS-ppnKB and roxS-sucC RNA duplexes PubMed

• Protein family:

• Paralogous protein(s):

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactor(s):

• Effectors of protein activity:

• Interactions:

• Localization: cytoplasm (according to Swiss-Prot)

Database entries

• BsubCyc: BSU15930

• Structure:

• UniProt: P51833

• KEGG entry: [3]

• E.C. number: 3.1.26.3

Expression and regulation

• Operon: rnc-smc-ftsY PubMed

• Expression browser: rnc PubMed

• Sigma factor: SigA PubMed

• Regulation:
  • RelA dependent downregulation (Class I) during stringent response PubMed

• Regulatory mechanism:

• Additional information:
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 314 PubMed
  • number of protein molecules per cell (complex medium with amino acids, without glucose): 605 PubMed

Biological materials

• Mutant:

• Expression vector:

• lacZ fusion:

• GFP fusion:

• two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

• Antibody:

Labs working on this gene/protein

David Bechhofer, Mount Sinai School, New York, USA Homepage

Ciaran Condon, IBPC, Paris, France Homepage

References

Reviews

Sabine Brantl, Natalie Jahn
sRNAs in bacterial type I and type III toxin-antitoxin systems.
FEMS Microbiol Rev: 2015, 39(3);413-27
[PubMed:25808661] [WorldCat.org] [DOI] (I p)

Monica P Hui, Patricia L Foley, Joel G Belasco
Messenger RNA degradation in bacterial cells.
Annu Rev Genet: 2014, 48;537-59
[PubMed:25292357] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Jörg Stülke
A mystery unraveled: essentiality of RNase III in Bacillus subtilis is caused by resident prophages.
PLoS Genet: 2012, 8(12);e1003199
[PubMed:23300472] [WorldCat.org] [DOI] (I p)

Ian J MacRae, Jennifer A Doudna
Ribonuclease revisited: structural insights into ribonuclease III family enzymes.
Curr Opin Struct Biol: 2007, 17(1);138-45
[PubMed:17194582] [WorldCat.org] [DOI] (P p)

Xinhua Ji
Structural basis for non-catalytic and catalytic activities of ribonuclease III.
Acta Crystallogr D Biol Crystallogr: 2006, 62(Pt 8);933-40
[PubMed:16855311] [WorldCat.org] [DOI] (P p)

Djamel Drider, Ciarán Condon
The continuing story of endoribonuclease III.
J Mol Microbiol Biotechnol: 2004, 8(4);195-200
[PubMed:16179796] [WorldCat.org] [DOI] (P p)

R A Srivastava, N Srivastava
The multifaceted roles of the RNA processing enzyme ribonuclease III.
Indian J Biochem Biophys: 1996, 33(4);253-60
[PubMed:8936814] [WorldCat.org] (P p)

Original publications

Sylvain Durand, Frédérique Braun, Efthimia Lioliou, Cédric Romilly, Anne-Catherine Helfer, Laurianne Kuhn, Noé Quittot, Pierre Nicolas, Pascale Romby, Ciarán Condon
A nitric oxide regulated small RNA controls expression of genes involved in redox homeostasis in Bacillus subtilis.
PLoS Genet: 2015, 11(2);e1004957
[PubMed:25643072] [WorldCat.org] [DOI] (I e)

Sylvain Durand, Laetitia Gilet, Ciarán Condon
The essential function of B. subtilis RNase III is to silence foreign toxin genes.
PLoS Genet: 2012, 8(12);e1003181
[PubMed:23300471] [WorldCat.org] [DOI] (I p)

Sylvain Durand, Laetitia Gilet, Philippe Bessières, Pierre Nicolas, Ciarán Condon
Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs.
PLoS Genet: 2012, 8(3);e1002520
[PubMed:22412379] [WorldCat.org] [DOI] (I p)

Iñigo Lasa, Alejandro Toledo-Arana, Alexander Dobin, Maite Villanueva, Igor Ruiz de los Mozos, Marta Vergara-Irigaray, Víctor Segura, Delphine Fagegaltier, José R Penadés, Jaione Valle, Cristina Solano, Thomas R Gingeras
Genome-wide antisense transcription drives mRNA processing in bacteria.
Proc Natl Acad Sci U S A: 2011, 108(50);20172-7
[PubMed:22123973] [WorldCat.org] [DOI] (I p)

Shiyi Yao, Joshua B Blaustein, David H Bechhofer
Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site.
Nucleic Acids Res: 2007, 35(13);4464-73
[PubMed:17576666] [WorldCat.org] [DOI] (I p)

M A Herskovitz, D H Bechhofer
Endoribonuclease RNase III is essential in Bacillus subtilis.
Mol Microbiol: 2000, 38(5);1027-33
[PubMed:11123676] [WorldCat.org] [DOI] (P p)

Hiroshi Kakeshita, Akihiro Oguro, Reiko Amikura, Kouji Nakamura, Kunio Yamane
Expression of the ftsY gene, encoding a homologue of the alpha subunit of mammalian signal recognition particle receptor, is controlled by different promoters in vegetative and sporulating cells of Bacillus subtilis.
Microbiology (Reading): 2000, 146 ( Pt 10);2595-2603
[PubMed:11021934] [WorldCat.org] [DOI] (P p)

A Oguro, H Kakeshita, K Nakamura, K Yamane, W Wang, D H Bechhofer
Bacillus subtilis RNase III cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor.
J Biol Chem: 1998, 273(31);19542-7
[PubMed:9677377] [WorldCat.org] [DOI] (P p)

W Wang, D H Bechhofer
Bacillus subtilis RNase III gene: cloning, function of the gene in Escherichia coli, and construction of Bacillus subtilis strains with altered rnc loci.
J Bacteriol: 1997, 179(23);7379-85
[PubMed:9393702] [WorldCat.org] [DOI] (P p)

S Mitra, D H Bechhofer
Substrate specificity of an RNase III-like activity from Bacillus subtilis.
J Biol Chem: 1994, 269(50);31450-6
[PubMed:7527387] [WorldCat.org] (P p)

A T Panganiban, H R Whiteley
Bacillus subtilis RNAase III cleavage sites in phage SP82 early mRNA.
Cell: 1983, 33(3);907-13
[PubMed:6409421] [WorldCat.org] [DOI] (P p)