{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T13:18:54Z","timestamp":1770297534433,"version":"3.49.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Toxin-antitoxin systems (TAS) are abundant, diverse, horizontally mobile gene modules that encode powerful resistance mechanisms in prokaryotes. We use the comparative-genomic approach to predict a new TAS that consists of a two-gene cassette encoding uncharacterized HicA and HicB proteins. Numerous bacterial and archaeal genomes encode from one to eight HicAB modules which appear to be highly prone to horizontal gene transfer. The HicB protein (COG1598\/COG4226) has a partially degraded RNAse H fold, whereas HicA (COG1724) contains a double-stranded RNA-binding domain. The stable combination of these two domains suggests a link to RNA metabolism, possibly, via an RNA interference-type mechanism. In most HicB proteins, the RNAse H-like domain is fused to a DNA-binding domain, either of the ribbon-helix-helix or of the helix-turn-helix class; in other TAS, proteins containing these DNA-binding domains function as antitoxins. Thus, the HicAB module is predicted to be a novel TAS whose mechanism involves RNA-binding and, possibly, cleavage.<\/jats:p>\n               <jats:p>Contact: \u00a0koonin@ncbi.nlm.nih.gov<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl418","type":"journal-article","created":{"date-parts":[[2006,8,9]],"date-time":"2006-08-09T03:27:36Z","timestamp":1155094056000},"page":"2581-2584","source":"Crossref","is-referenced-by-count":105,"title":["The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria"],"prefix":"10.1093","volume":"22","author":[{"given":"Kira S.","family":"Makarova","sequence":"first","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 1 \u00a0 1 \u00a0 \u00a0 Bethesda, MD 20894, USA"}]},{"given":"Nick V.","family":"Grishin","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas 2 \u00a0 2 \u00a0 \u00a0 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA"}]},{"given":"Eugene V.","family":"Koonin","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 1 \u00a0 1 \u00a0 \u00a0 Bethesda, MD 20894, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,8,8]]},"reference":[{"key":"2023012408425859900_b1","doi-asserted-by":"crossref","first-page":"R81","DOI":"10.1186\/gb-2003-4-12-r81","article-title":"New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system","volume":"4","author":"Anantharaman","year":"2003","journal-title":"Genome Biol."},{"key":"2023012408425859900_b2","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012408425859900_b3","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1016\/j.tibs.2005.10.004","article-title":"Toxin-antitoxin modules as bacterial metabolic stress managers","volume":"30","author":"Buts","year":"2005","journal-title":"Trends Biochem. Sci."},{"key":"2023012408425859900_b4","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.cell.2005.06.023","article-title":"RNAi: the nuts and bolts of the RISC machine","volume":"122","author":"Filipowicz","year":"2005","journal-title":"Cell"},{"key":"2023012408425859900_b5","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/nrmicro1147","article-title":"Prokaryotic toxin-antitoxin stress response loci","volume":"3","author":"Gerdes","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"2023012408425859900_b6","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0065-227X(04)80166-7","article-title":"Structure and function of the shufflon in plasmid R64","volume":"38","author":"Gyohda","year":"2004","journal-title":"Adv. Biophys."},{"key":"2023012408425859900_b7","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1002\/prot.20692","article-title":"Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8","volume":"61","author":"Hattori","year":"2005","journal-title":"Proteins"},{"key":"2023012408425859900_b8","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.1126\/science.1088157","article-title":"Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest","volume":"301","author":"Hayes","year":"2003","journal-title":"Science"},{"key":"2023012408425859900_b9","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1006\/jmbi.2000.3873","article-title":"Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI","volume":"300","author":"Ichiyanagi","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2023012408425859900_b10","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/347306a0","article-title":"Three-dimensional structure of ribonuclease H from E.coli","volume":"347","author":"Katayanagi","year":"1990","journal-title":"Nature"},{"key":"2023012408425859900_b11","doi-asserted-by":"crossref","first-page":"4693","DOI":"10.1128\/JB.180.17.4693-4703.1998","article-title":"Evolution of the major pilus gene cluster of Haemophilus influenzae","volume":"180","author":"Mhlanga-Mutangadura","year":"1998","journal-title":"J. Bacteriol"},{"key":"2023012408425859900_b12","first-page":"295","article-title":"Occurrence of mazEF-like antitoxin\/toxin systems in bacteria","volume":"1","author":"Mittenhuber","year":"1999","journal-title":"J. Mol. Microbiol. Biotechnol."},{"key":"2023012408425859900_b13","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1093\/nar\/gki201","article-title":"Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes","volume":"33","author":"Pandey","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408425859900_b14","doi-asserted-by":"crossref","first-page":"14385","DOI":"10.1073\/pnas.0405913101","article-title":"Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity","volume":"101","author":"Rand","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012408425859900_b15","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.tibs.2004.12.007","article-title":"siRNA and miRNA: an insight into RISCs","volume":"30","author":"Tang","year":"2005","journal-title":"Trends Biochem. Sci."},{"key":"2023012408425859900_b16","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/21\/2581\/48839048\/bioinformatics_22_21_2581.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/21\/2581\/48839048\/bioinformatics_22_21_2581.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:04:08Z","timestamp":1674551048000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/21\/2581\/250435"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,8,8]]},"references-count":16,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2006,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl418","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,11,1]]},"published":{"date-parts":[[2006,8,8]]}}}