YXID_BACSU
ID YXID_BACSU Reviewed; 569 AA.
AC P42296;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 28-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Toxin YxiD {ECO:0000303|PubMed:22200572};
DE AltName: Full=DNase YxiD {ECO:0000303|PubMed:34280190};
GN Name=yxiD; Synonyms=J3D; OrderedLocusNames=BSU39300;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / BGSC1A1;
RX PubMed=7704263; DOI=10.1099/13500872-141-2-337;
RA Yoshida K., Sano H., Seki S., Oda M., Fujimura M., Fujita Y.;
RT "Cloning and sequencing of a 29 kb region of the Bacillus subtilis genome
RT containing the hut and wapA loci.";
RL Microbiology 141:337-343(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP SEQUENCE REVISION TO 176; 287; 397 AND 533.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [4]
RP INCORRECT FUNCTION AS AN RNASE, FUNCTION AS A TOXIN, AND EXPRESSION IN
RP E.COLI.
RC STRAIN=168;
RX PubMed=22200572; DOI=10.1016/j.febslet.2011.12.020;
RA Holberger L.E., Garza-Sanchez F., Lamoureux J., Low D.A., Hayes C.S.;
RT "A novel family of toxin/antitoxin proteins in Bacillus species.";
RL FEBS Lett. 586:132-136(2012).
RN [5]
RP FUNCTION AS A TOXIN, FUNCTION AS A DNASE, SUBCELLULAR LOCATION, INDUCTION,
RP AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=34280190; DOI=10.1371/journal.pgen.1009682;
RA Kobayashi K.;
RT "Diverse LXG toxin and antitoxin systems specifically mediate intraspecies
RT competition in Bacillus subtilis biofilms.";
RL PLoS Genet. 17:e1009682-e1009682(2021).
CC -!- FUNCTION: Toxic component of one of 6 LXG toxin-immunity modules in
CC this strain. They promote kin selection, mediate competition in
CC biofilms, and drive spatial segregation of different strains,
CC indicating that LXG toxins may help avoid warfare between strains in
CC biofilms. Mediates intercellular competition during biofilm formation;
CC disruption of the operon disadvantages the bacteria, but overexpression
CC of the cognate immunity protein restores growth in competition with
CC wild-type. Overexpression alone in situ causes growth arrest but not
CC cell lysis, a large decrease in chromosomal DNA content and the
CC production of anucleate cells. No effect is seen on rRNA. Co-
CC overexpression with cognate immunity protein YxxD does not cause growth
CC arrest. The toxic effect is not dependent on the epsA and tapA operons
CC which are required for biofilm formation.
CC {ECO:0000269|PubMed:34280190}.
CC -!- SUBUNIT: Probably interacts with cognate immunity protein YxxD but not
CC with non-cognate immunity proteins. The interaction inhibits the toxic
CC activity of YxxD (Probable). {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305|PubMed:34280190}.
CC Note=Delivery to target cells requires the type VII secretion system
CC (T7SS) and YukE. {ECO:0000269|PubMed:34280190}.
CC -!- INDUCTION: Expressed on rich and minimal solid media likely in early
CC stationary phase; dependent on DegSU. Not expressed in liquid LB, but
CC only under conditions that promote biofilm formation.
CC {ECO:0000269|PubMed:34280190}.
CC -!- DISRUPTION PHENOTYPE: Deletion of the yxiB-yxiC-yxiD-yxxD-yxxE operon
CC has no visible growth phenotype, however it is out-competed by wild-
CC type cells. {ECO:0000269|PubMed:34280190}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the LXG family.
CC {ECO:0000303|PubMed:22200572}.
CC -!- CAUTION: Was originally thought to be an RNase; when the C-terminus
CC (residues 409-569) is expressed in E.coli it has RNase, not DNase
CC activity, and inhibits growth upon expression in E.coli. In vitro RNase
CC activity and in vivo growth inhibition are neutralized by cognate
CC immunity protein YxxD, but not by immunity proteins specific to other
CC toxins with the LXG domain. Mutation of His-548 to Ala leads to loss of
CC growth inhibition and RNase activity in E.coli.
CC {ECO:0000269|PubMed:22200572}.
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DR EMBL; D31856; BAA06649.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15966.2; -; Genomic_DNA.
DR PIR; H70076; H70076.
DR RefSeq; NP_391809.2; NC_000964.3.
DR RefSeq; WP_003244234.1; NZ_JNCM01000034.1.
DR AlphaFoldDB; P42296; -.
DR STRING; 224308.BSU39300; -.
DR PaxDb; P42296; -.
DR PRIDE; P42296; -.
DR EnsemblBacteria; CAB15966; CAB15966; BSU_39300.
DR GeneID; 937523; -.
DR KEGG; bsu:BSU39300; -.
DR PATRIC; fig|224308.179.peg.4254; -.
DR eggNOG; COG5444; Bacteria.
DR OMA; SPMEMML; -.
DR BioCyc; BSUB:BSU39300-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0004518; F:nuclease activity; IEA:UniProtKB-KW.
DR CDD; cd00085; HNHc; 1.
DR InterPro; IPR003615; HNH_nuc.
DR InterPro; IPR006829; LXG_dom.
DR InterPro; IPR027797; PT-TG_dom.
DR Pfam; PF04740; LXG; 1.
DR Pfam; PF14449; PT-TG; 1.
DR PROSITE; PS51756; LXG; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Hydrolase; Nuclease; Reference proteome; Secreted; Toxin.
FT CHAIN 1..569
FT /note="Toxin YxiD"
FT /id="PRO_0000050023"
FT DOMAIN 1..235
FT /note="LXG"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01092"
FT REGION 548..569
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 8..91
FT /evidence="ECO:0000255"
FT CONFLICT 176
FT /note="A -> G (in Ref. 1; BAA06649)"
FT /evidence="ECO:0000305"
FT CONFLICT 287
FT /note="T -> P (in Ref. 1; BAA06649)"
FT /evidence="ECO:0000305"
FT CONFLICT 397
FT /note="K -> E (in Ref. 1; BAA06649)"
FT /evidence="ECO:0000305"
FT CONFLICT 533
FT /note="E -> K (in Ref. 1; BAA06649)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 569 AA; 64326 MW; E97E4F3E910D260E CRC64;
MKTLDVHALH EGIQHTIEKL DKQKQQLEKL EKSVEHLAGM KDALKGKGGD AIRTFYEECH
KPFLLFFGIF IDEYKKVLKQ TQHAISSVES NSHGMIAEAF LSHDARHGVK HAREVTEQLT
DAVNRQTSAI DHIVSLPTVN DSFFRMETEQ AERLISDTLN KLFQFDGQQT QALEAAKSDF
QTMKKYIDQL ETMYTGPKIE ITGYKSGSIL KSQEEENINQ IFGAINPQMK QADDSPMEMM
LKKLAENEKS KVDSVVKTGD SKKVSKNIIV INGKVYNTSE HREHIKTDFS NAEVKQVVYN
DTLYNVYISG NDMKLEPVVS LSDIKVDENG YVKILETAVE LTGVYDLFKA ATGRDPVSGE
KVTGKDRVVA SINSVPFAKI AKLEKLIDIN KLINNGKKAK KASEVKNVAK DKGKIANDVS
GSANKINSDL IKKYARDIEQ RTGRELPKNQ IDKLKEALRN KEYKKMSPIE TAKHRTKFDK
VKNKVIKEWE ENTGQKWPVY KENVVSEKTG KIIRKKGDKY DAHHIIENTF GGEHEWWNMH
PAKFPNEHQA GIHGTGSPAN ELFKGGKKK
