VAPC_MYCS2
ID VAPC_MYCS2 Reviewed; 129 AA.
AC A0QRY6;
DT 09-JAN-2013, integrated into UniProtKB/Swiss-Prot.
DT 09-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=Ribonuclease VapC;
DE Short=RNase VapC;
DE EC=3.1.-.-;
DE AltName: Full=Endoribonuclease VapC;
DE AltName: Full=Toxin VapC;
GN Name=vapC; OrderedLocusNames=MSMEG_1284, MSMEI_1246;
OS Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium
OS smegmatis).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=246196;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RA Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
RA Fraser C.M.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
RA Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
RA Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
RT "Interrupted coding sequences in Mycobacterium smegmatis: authentic
RT mutations or sequencing errors?";
RL Genome Biol. 8:R20.1-R20.9(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=18955433; DOI=10.1101/gr.081901.108;
RA Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
RA Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
RT "Ortho-proteogenomics: multiple proteomes investigation through orthology
RT and a new MS-based protocol.";
RL Genome Res. 19:128-135(2009).
RN [4]
RP FUNCTION AS A TOXIN, SUBUNIT, INDUCTION, DNA-BINDING, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=19445953; DOI=10.1016/j.jmb.2009.05.006;
RA Robson J., McKenzie J.L., Cursons R., Cook G.M., Arcus V.L.;
RT "The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin-
RT antitoxin module that controls growth via inhibition of translation.";
RL J. Mol. Biol. 390:353-367(2009).
RN [5]
RP FUNCTION AS AN ENDORIBONUCLEASE, SUBSTRATES, SUBUNIT, COFACTOR,
RP RNA-BINDING, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=22366418; DOI=10.1128/jb.06790-11;
RA McKenzie J.L., Robson J., Berney M., Smith T.C., Ruthe A., Gardner P.P.,
RA Arcus V.L., Cook G.M.;
RT "A VapBC toxin-antitoxin module is a posttranscriptional regulator of
RT metabolic flux in mycobacteria.";
RL J. Bacteriol. 194:2189-2204(2012).
RN [6]
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=22199354; DOI=10.1074/jbc.m111.286856;
RA Frampton R., Aggio R.B., Villas-Boas S.G., Arcus V.L., Cook G.M.;
RT "Toxin-antitoxin systems of Mycobacterium smegmatis are essential for cell
RT survival.";
RL J. Biol. Chem. 287:5340-5356(2012).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=24417293; DOI=10.1111/1574-6968.12380;
RA Demidenok O.I., Kaprelyants A.S., Goncharenko A.V.;
RT "Toxin-antitoxin vapBC locus participates in formation of the dormant state
RT in Mycobacterium smegmatis.";
RL FEMS Microbiol. Lett. 352:69-77(2014).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system. A
CC sequence-specific endoribonuclease, cleavage occurs after the first AU
CC in the consensus sequence AUA(U/A); RNA secondary structure is probably
CC important in substrate choice. Cuts in 5' and 3' UTRs. The TA system
CC acts as a post-transcriptional regulator of carbon metabolism; in
CC M.smegmatis 3 TA systems (VapB-VapC, MazE-MazF and Phd-Doc) may be
CC involved in monitoring the nutritional supply and physiological state
CC of the cell, linking catabolic with anabolic reactions. When
CC overexpressed inhibits cell growth, via translation; 10-fold in a wild-
CC type strain, 100-fold in a vapB-vapC disruption mutant
CC (PubMed:19445953). Overexpression of VapC leads to differential
CC expression of 205 genes; many down-regulated genes are predicted to be
CC involved in the transport and catabolism of carbohydrates, while genes
CC involved in phosphate transport and scavenging are up-regulated. VapC
CC is bacteriostatic, not bacteriocidal; cells are ovoid, non-replicating
CC and have decreased transcription, becoming dormant (PubMed:24417293).
CC Digests ssRNA but not tRNA, dsRNA, ssDNA or dsDNA. The VapB-VapC
CC complex binds its own promoter DNA, and VapC alone binds RNA.
CC {ECO:0000269|PubMed:19445953, ECO:0000269|PubMed:22366418,
CC ECO:0000269|PubMed:24417293}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:22366418};
CC -!- SUBUNIT: Forms a complex with VapB. {ECO:0000269|PubMed:19445953,
CC ECO:0000269|PubMed:22366418}.
CC -!- INDUCTION: Expression is low but constitutive, and repressed by VapB-
CC VapC. Translation of vapC mRNA requires VapB. Member of the vapB-vapC
CC operon. {ECO:0000269|PubMed:19445953}.
CC -!- DISRUPTION PHENOTYPE: The vapB-vapC operon is not essential; cells grow
CC faster than wild-type on rich and minimal glycerol-containing medium.
CC The operon deletion mutants die faster than wild-type under potassium-
CC limiting conditions, which is prevented by overexpression of vapB
CC (PubMed:24417293). The vapB antitoxin gene can be disrupted without
CC causing death, however despite elevated vapC transcription, no VapC
CC protein could be detected, suggesting that RNA processing and
CC translational coupling are important in VapC expression. A triple TA
CC mutant (missing vapB-vapC, mazE-mazF and phd-doc TA systems) survives
CC antibiotic challenge, suggesting the TA systems are not required to
CC generate drug-resistant cells. However the triple mutant is more
CC sensitive to oxidative and heat stress, and does not survive long-term
CC starvation during aerobic growth on complex medium. There is a
CC difference in the level of branched-chain amino acids, which may play a
CC role in monitoring the nutritional supply and physiological state of
CC the cell. {ECO:0000269|PubMed:19445953, ECO:0000269|PubMed:22199354,
CC ECO:0000269|PubMed:22366418, ECO:0000269|PubMed:24417293}.
CC -!- SIMILARITY: Belongs to the PINc/VapC protein family. {ECO:0000305}.
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DR EMBL; CP000480; ABK74630.1; -; Genomic_DNA.
DR EMBL; CP001663; AFP37722.1; -; Genomic_DNA.
DR RefSeq; WP_011727564.1; NZ_SIJM01000042.1.
DR RefSeq; YP_885674.1; NC_008596.1.
DR AlphaFoldDB; A0QRY6; -.
DR SMR; A0QRY6; -.
DR STRING; 246196.MSMEI_1246; -.
DR EnsemblBacteria; ABK74630; ABK74630; MSMEG_1284.
DR EnsemblBacteria; AFP37722; AFP37722; MSMEI_1246.
DR GeneID; 66732746; -.
DR KEGG; msg:MSMEI_1246; -.
DR KEGG; msm:MSMEG_1284; -.
DR PATRIC; fig|246196.19.peg.1273; -.
DR eggNOG; COG3742; Bacteria.
DR OMA; AFNEPEA; -.
DR OrthoDB; 1647539at2; -.
DR Proteomes; UP000000757; Chromosome.
DR Proteomes; UP000006158; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004540; F:ribonuclease activity; IEA:InterPro.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR HAMAP; MF_00265; VapC_Nob1; 1.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR002716; PIN_dom.
DR InterPro; IPR022907; VapC_family.
DR Pfam; PF01850; PIN; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
PE 1: Evidence at protein level;
KW DNA-binding; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome; RNA-binding; Toxin-antitoxin system.
FT CHAIN 1..129
FT /note="Ribonuclease VapC"
FT /id="PRO_0000420845"
FT DOMAIN 1..124
FT /note="PINc"
FT BINDING 4
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
FT BINDING 99
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255"
SQ SEQUENCE 129 AA; 13910 MW; 4AF6CB50CB382317 CRC64;
MVIDTSALVA ILTDEPDAEL LEGAVADDPV RTMSTASYLE TAIVIESRFG EPGGRELDLW
LHRASVALVA VDADQADAAR LAYRRYGKGR HRAGLNYGDC FSYALAKVSG QPLLFKGEAF
RLTDVAAVH
