YAFQ_ECOLI
ID YAFQ_ECOLI Reviewed; 92 AA.
AC Q47149;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=mRNA interferase toxin YafQ;
DE EC=3.1.-.-;
DE AltName: Full=Endoribonuclease YafQ;
DE AltName: Full=Toxin YafQ;
GN Name=yafQ; OrderedLocusNames=b0225, JW0215;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=7596361; DOI=10.1016/0165-7992(95)90024-1;
RA Ohmori H., Hatada E., Qiao Y., Tsuji M., Fukuda R.;
RT "dinP, a new gene in Escherichia coli, whose product shows similarities to
RT UmuC and its homologues.";
RL Mutat. Res. 347:1-7(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T.,
RA Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S.,
RA Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0
RT - 6.0 min (189,987 - 281,416bp) region.";
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION AS A TOXIN, AND SUBUNIT.
RC STRAIN=K12 / BW25113;
RX PubMed=17263853; DOI=10.1111/j.1574-6968.2006.00563.x;
RA Motiejunaite R., Armalyte J., Markuckas A., Suziedeliene E.;
RT "Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module.";
RL FEMS Microbiol. Lett. 268:112-119(2007).
RN [6]
RP DISRUPTION PHENOTYPE, AND FUNCTION IN ANTIBIOTIC TOLERANCE IN BIOFILM.
RC STRAIN=K12 / BW25113;
RX PubMed=19307375; DOI=10.1128/aac.00043-09;
RA Harrison J.J., Wade W.D., Akierman S., Vacchi-Suzzi C., Stremick C.A.,
RA Turner R.J., Ceri H.;
RT "The chromosomal toxin gene yafQ is a determinant of multidrug tolerance
RT for Escherichia coli growing in a biofilm.";
RL Antimicrob. Agents Chemother. 53:2253-2258(2009).
RN [7]
RP FUNCTION AS AN MRNA INTERFERASE, ENDORIBONUCLEASE ACTIVITY, PROBABLE ACTIVE
RP SITE, RNA SEQUENCE SPECIFICITY, SUBUNIT, LARGE RIBOSOMAL SUBUNIT-BINDING,
RP DNA-BINDING, INDUCTION, AND MUTAGENESIS OF HIS-87.
RC STRAIN=K12 / BW25113, and K12 / DH5-alpha;
RX PubMed=19210620; DOI=10.1111/j.1365-2958.2008.06572.x;
RA Prysak M.H., Mozdzierz C.J., Cook A.M., Zhu L., Zhang Y., Inouye M.,
RA Woychik N.A.;
RT "Bacterial toxin YafQ is an endoribonuclease that associates with the
RT ribosome and blocks translation elongation through sequence-specific and
RT frame-dependent mRNA cleavage.";
RL Mol. Microbiol. 71:1071-1087(2009).
RN [8]
RP FUNCTION IN BIOFILM FORMATION, DEVELOPMENTAL STAGE, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=19707553; DOI=10.1371/journal.pone.0006785;
RA Kolodkin-Gal I., Verdiger R., Shlosberg-Fedida A., Engelberg-Kulka H.;
RT "A differential effect of E. coli toxin-antitoxin systems on cell death in
RT liquid media and biofilm formation.";
RL PLoS ONE 4:E6785-E6785(2009).
RN [9]
RP RETRACTED PAPER.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21788497; DOI=10.1073/pnas.1100186108;
RA Maisonneuve E., Shakespeare L.J., Joergensen M.G., Gerdes K.;
RT "Bacterial persistence by RNA endonucleases.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:13206-13211(2011).
RN [10]
RP RETRACTION NOTICE OF PUBMED:21788497.
RX PubMed=29531044; DOI=10.1073/pnas.1803278115;
RA Maisonneuve E., Shakespeare L.J., Joergensen M.G., Gerdes K.;
RL Proc. Natl. Acad. Sci. U.S.A. 115:E2901-E2901(2018).
RN [11] {ECO:0007744|PDB:4Q2U}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 2-92, FUNCTION, AND SUBUNIT.
RX PubMed=24898247; DOI=10.1074/jbc.m114.573006;
RA Ruangprasert A., Maehigashi T., Miles S.J., Giridharan N., Liu J.X.,
RA Dunham C.M.;
RT "Mechanisms of toxin inhibition and transcriptional repression by
RT Escherichia coli DinJ-YafQ.";
RL J. Biol. Chem. 289:20559-20569(2014).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system
CC (PubMed:17263853). A sequence-specific mRNA endoribonuclease that
CC inhibits translation elongation and induces bacterial stasis
CC (PubMed:19210620). Cleavage occurs between the second and third residue
CC of the Lys codon followed by a G or A (5'AAA(G/A)3'), is reading-frame
CC dependent and occurs within the 5' end of most mRNAs (PubMed:19210620).
CC Ribosome-binding confers the sequence specificity and reading frame-
CC dependence (PubMed:19210620). When overexpressed in liquid media YafQ
CC partially inhibits protein synthesis, with a reduction in growth rate
CC and colony growth rate. This effect is counteracted by coexpression
CC with cognate antitoxin DinJ (PubMed:17263853). YafQ and DinJ together
CC bind their own promoter, and repress its expression (PubMed:24898247).
CC {ECO:0000269|PubMed:17263853, ECO:0000269|PubMed:19210620,
CC ECO:0000269|PubMed:24898247}.
CC -!- FUNCTION: Cell death governed by the MazE-MazF and DinJ-YafQ TA systems
CC seems to play a role in biofilm formation (PubMed:19707553).
CC {ECO:0000269|PubMed:19707553}.
CC -!- SUBUNIT: Monomer in the absence of antitoxin (PubMed:24898247). Forms a
CC heterotetramer with antitoxin DinJ, with 2 YafQ-DinJ dimers associated
CC via the N-terminus of the DinJ antitoxins (YafQ-(DinJ)2-YafQ)
CC (PubMed:17263853, PubMed:24898247). In this complex the toxin activity
CC is inhibited. Binds the 70S ribosome via the 50S ribosomal subunit
CC (PubMed:19210620). {ECO:0000269|PubMed:17263853,
CC ECO:0000269|PubMed:19210620, ECO:0000269|PubMed:24898247}.
CC -!- DEVELOPMENTAL STAGE: May function as a drug tolerance determinant in
CC biofilm, but not stationary phase planktonic cells.
CC {ECO:0000269|PubMed:19707553}.
CC -!- INDUCTION: By the DNA damaging agent mitomycin C.
CC {ECO:0000269|PubMed:19210620}.
CC -!- DISRUPTION PHENOTYPE: Cells missing yafQ show increased biofilm
CC sensitivity to the antibiotics cefazolin (a beta-lactam inhibitor) and
CC tobramycin (a protein synthesis inhibitor). There is no difference in
CC antibiotic sensitivity in stationary phase planktonic cells
CC (PubMed:19307375). {ECO:0000269|PubMed:19307375,
CC ECO:0000269|PubMed:19707553}.
CC -!- SIMILARITY: Belongs to the RelE toxin family. YafQ subfamily.
CC {ECO:0000305}.
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DR EMBL; D38582; BAA07587.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73329.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA77895.1; -; Genomic_DNA.
DR PIR; B64747; B64747.
DR RefSeq; NP_414760.1; NC_000913.3.
DR RefSeq; WP_000615983.1; NZ_SSZK01000029.1.
DR PDB; 4Q2U; X-ray; 1.80 A; B/D/F/H/J/L/N/P=2-92.
DR PDBsum; 4Q2U; -.
DR AlphaFoldDB; Q47149; -.
DR SMR; Q47149; -.
DR BioGRID; 4259771; 15.
DR BioGRID; 849310; 1.
DR ComplexPortal; CPX-1079; DinJ-YafQ toxin-antitoxin complex.
DR DIP; DIP-11221N; -.
DR IntAct; Q47149; 4.
DR STRING; 511145.b0225; -.
DR PaxDb; Q47149; -.
DR PRIDE; Q47149; -.
DR EnsemblBacteria; AAC73329; AAC73329; b0225.
DR EnsemblBacteria; BAA77895; BAA77895; BAA77895.
DR GeneID; 944911; -.
DR KEGG; ecj:JW0215; -.
DR KEGG; eco:b0225; -.
DR PATRIC; fig|1411691.4.peg.2058; -.
DR EchoBASE; EB2948; -.
DR eggNOG; COG3041; Bacteria.
DR HOGENOM; CLU_161929_4_1_6; -.
DR InParanoid; Q47149; -.
DR OMA; DHRECHV; -.
DR PhylomeDB; Q47149; -.
DR BioCyc; EcoCyc:G6109-MON; -.
DR BioCyc; MetaCyc:G6109-MON; -.
DR PRO; PR:Q47149; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR CollecTF; EXPREG_00000de0; -.
DR GO; GO:0110001; C:toxin-antitoxin complex; IPI:ComplexPortal.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:EcoCyc.
DR GO; GO:0016892; F:endoribonuclease activity, producing 3'-phosphomonoesters; IDA:EcoCyc.
DR GO; GO:0043022; F:ribosome binding; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006402; P:mRNA catabolic process; IDA:EcoCyc.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:ComplexPortal.
DR GO; GO:0040008; P:regulation of growth; IC:ComplexPortal.
DR GO; GO:0046677; P:response to antibiotic; IMP:EcoCyc.
DR GO; GO:0044010; P:single-species biofilm formation; IDA:ComplexPortal.
DR GO; GO:0006415; P:translational termination; IDA:EcoCyc.
DR Gene3D; 3.30.2310.20; -; 1.
DR InterPro; IPR007712; RelE/ParE_toxin.
DR InterPro; IPR035093; RelE/ParE_toxin_dom_sf.
DR InterPro; IPR004386; Toxin_YafQ-like.
DR PANTHER; PTHR40588; PTHR40588; 1.
DR Pfam; PF15738; YafQ_toxin; 1.
DR PIRSF; PIRSF006156; YafQ; 1.
DR SUPFAM; SSF143011; SSF143011; 1.
DR TIGRFAMs; TIGR02385; RelE_StbE; 1.
DR TIGRFAMs; TIGR00053; TIGR00053; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Endonuclease; Hydrolase; Nuclease;
KW Reference proteome; Repressor; RNA-binding; Toxin-antitoxin system;
KW Transcription; Transcription regulation.
FT CHAIN 1..92
FT /note="mRNA interferase toxin YafQ"
FT /id="PRO_0000168540"
FT ACT_SITE 87
FT /note="Proton donor"
FT /evidence="ECO:0000305"
FT MUTAGEN 87
FT /note="H->Q: Loss of mRNA cleavage, loss of toxic effect.
FT Still associates with the ribosome."
FT /evidence="ECO:0000269|PubMed:19210620"
FT STRAND 5..9
FT /evidence="ECO:0007829|PDB:4Q2U"
FT HELIX 10..21
FT /evidence="ECO:0007829|PDB:4Q2U"
FT HELIX 26..37
FT /evidence="ECO:0007829|PDB:4Q2U"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:4Q2U"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:4Q2U"
FT STRAND 59..65
FT /evidence="ECO:0007829|PDB:4Q2U"
FT STRAND 68..74
FT /evidence="ECO:0007829|PDB:4Q2U"
FT STRAND 76..85
FT /evidence="ECO:0007829|PDB:4Q2U"
FT HELIX 87..91
FT /evidence="ECO:0007829|PDB:4Q2U"
SQ SEQUENCE 92 AA; 10847 MW; 6EF6BD97C7F74291 CRC64;
MIQRDIEYSG QYSKDVKLAQ KRHKDMNKLK YLMTLLINNT LPLPAVYKDH PLQGSWKGYR
DAHVEPDWIL IYKLTDKLLR FERTGTHAAL FG
