{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:52:58Z","timestamp":1791247978075,"version":"4.1.0"},"reference-count":57,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2003,2,1]],"date-time":"2003-02-01T00:00:00Z","timestamp":1044057600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2003,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            A partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmRNA gene (\n            <jats:italic>ssrA<\/jats:italic>\n            ) than for any type of tRNA gene. Horizontal gene transfer, a major avenue of bacterial evolution, was assessed by focusing on elements using this single attachment locus. Diverse elements use\n            <jats:italic>ssrA<\/jats:italic>\n            ; among enterobacteria alone, at least four different integrase subfamilies have independently evolved specificity for\n            <jats:italic>ssrA<\/jats:italic>\n            , and almost every strain analyzed presents a unique set of integrated elements. Even elements using essentially the same integrase can be very diverse, as is a group with an\n            <jats:italic>ssrA<\/jats:italic>\n            -specific integrase of the P4 subfamily. This same integrase appears to promote damage routinely at attachment sites, which may be adaptive. Elements in arrays can recombine; one such event mediated by invertible DNA segments within neighboring elements likely explains the monophasic nature of\n            <jats:italic>Salmonella enterica<\/jats:italic>\n            serovar Typhi. One of a limited set of conserved sequences occurs at the attachment site of each enterobacterial element, apparently serving as a transcriptional terminator for\n            <jats:italic>ssrA<\/jats:italic>\n            . Elements were usually found integrated into tRNA-like sequence at the 3\u2032 end of\n            <jats:italic>ssrA<\/jats:italic>\n            , at subsites corresponding to those used in tRNA genes; an exception was found at the non-tRNA-like 3\u2032 end produced by\n            <jats:italic>ssrA<\/jats:italic>\n            gene permutation in cyanobacteria, suggesting that, during the evolution of new site specificity by integrases, tropism toward a conserved 3\u2032 end of an RNA gene may be as strong as toward a tRNA-like sequence. The proximity of\n            <jats:italic>ssrA<\/jats:italic>\n            and\n            <jats:italic>smpB<\/jats:italic>\n            , which act in concert, was also surveyed.\n          <\/jats:p>","DOI":"10.1128\/jb.185.3.1059-1070.2003","type":"journal-article","created":{"date-parts":[[2003,1,18]],"date-time":"2003-01-18T00:04:17Z","timestamp":1042848257000},"page":"1059-1070","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":53,"title":["Traffic at the tmRNA Gene"],"prefix":"10.1128","volume":"185","author":[{"given":"Kelly P.","family":"Williams","sequence":"first","affiliation":[{"name":"Department of Biology, Indiana University, Bloomington, Indiana 47405"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.181.23.7385-7389.1999"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(02)08713-5"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.180.8.2220-2223.1998"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.62.5.1623-1630.1994"},{"key":"e_1_3_2_6_2","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1099\/00221287-137-3-601","volume":"137","year":"1991","unstructured":"Beltran, P., S. A. Plock, N. H. Smith, T. S. Whittam, D. C. Old, and R. K. Selander. 1991. Reference collection of strains of the Salmonella typhimurium complex from natural populations. J. Gen. Microbiol.137:601-606.","journal-title":"J. Gen. Microbiol."},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.67.3.1277-1286.1999"},{"key":"e_1_3_2_8_2","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1099\/00221287-139-6-1125","volume":"139","year":"1993","unstructured":"Boyd, E. F., F. S. Wang, P. Beltran, S. A. Plock, K. Nelson, and R. K. Selander. 1993. Salmonella reference collection B (SARB): strains of 37 serovars of subspecies I. J. Gen. Microbiol.139:1125-1132.","journal-title":"J. Gen. Microbiol."},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.62.3.804-808.1996"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.174.23.7495-7499.1992"},{"key":"e_1_3_2_11_2","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1093\/nar\/29.3.644","volume":"29","year":"2001","unstructured":"Chopin, A., A. Bolotin, A. Sorokin, S. D. Ehrlich, and M. C. Chopin. 2001. Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations. Nucleic Acids Res.29:644-651.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_12_2","doi-asserted-by":"crossref","first-page":"4240","DOI":"10.1093\/emboj\/cdf427","volume":"21","year":"2002","unstructured":"Davis, B. M., H. H. Kimsey, A. V. Kane, and M. K. Waldor. 2002. A satellite phage-encoded antirepressor induces repressor aggregation and cholera toxin gene transfer. EMBO J.21:4240-4249.","journal-title":"EMBO J."},{"key":"e_1_3_2_13_2","doi-asserted-by":"crossref","first-page":"8572","DOI":"10.1073\/pnas.140109997","volume":"97","year":"2000","unstructured":"Davis, B. M., and M. K. Waldor. 2000. CTX\u03c6 contains a hybrid genome derived from tandemly integrated elements. Proc. Natl. Acad. Sci. USA97:8572-8577.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_14_2","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/S0966-842X(01)02293-4","volume":"10","year":"2002","unstructured":"Edwards, R. A., G. J. Olsen, and S. R. Maloy. 2002. Comparative genomics of closely related salmonellae. Trends Microbiol.10:94-99.","journal-title":"Trends Microbiol."},{"key":"e_1_3_2_15_2","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/S1369-5274(00)00125-9","volume":"3","year":"2000","unstructured":"Eisen, J. A. 2000. Assessing evolutionary relationships among microbes from whole-genome analysis. Curr. Opin. Microbiol.3:475-480.","journal-title":"Curr. Opin. Microbiol."},{"key":"e_1_3_2_16_2","unstructured":"Felsenstein J. 1995. PHYLIP (Phylogeny Inference Package) version 3.57c. Department of Genetics University of Washington Seattle."},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.40.6.2074-2078.2002"},{"key":"e_1_3_2_18_2","doi-asserted-by":"crossref","first-page":"2018","DOI":"10.1093\/nar\/30.9.2018","volume":"30","year":"2002","unstructured":"Gaudin, C., X. Zhou, K. P. Williams, and B. Felden. 2002. Two-piece tmRNA in cyanobacteria and its structural analysis. Nucleic Acids Res.30:2018-2024.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_19_2","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1016\/S1369-5274(98)80106-9","volume":"1","year":"1998","unstructured":"Golden, J. W., and H. S. Yoon. 1998. Heterocyst formation in Anabaena. Curr. Opin. Microbiol.1:623-629.","journal-title":"Curr. Opin. Microbiol."},{"key":"e_1_3_2_20_2","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1016\/S0092-8674(00)81442-7","volume":"93","year":"1998","unstructured":"Hardt, W. D., L. M. Chen, K. E. Schuebel, X. R. Bustelo, and J. E. Galan. 1998. S. typhimurium encodes an activator of Rho GTPases that induces membrane ruffling and nuclear responses in host cells. Cell93:815-826.","journal-title":"Cell"},{"key":"e_1_3_2_21_2","doi-asserted-by":"crossref","first-page":"6859","DOI":"10.1016\/S0021-9258(19)50506-3","volume":"267","year":"1992","unstructured":"Hauser, M. A., and J. J. Scocca. 1992. Site-specific integration of the Haemophilus influenzae bacteriophage HP1. Identification of the points of recombinational strand exchange and the limits of the host attachment site. J. Biol. Chem.267:6859-6864.","journal-title":"J. Biol. Chem."},{"key":"e_1_3_2_22_2","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1016\/S0966-842X(00)01863-1","volume":"8","year":"2000","unstructured":"Hendrix, R. W., J. G. Lawrence, G. F. Hatfull, and S. Casjens. 2000. The origins and ongoing evolution of viruses. Trends Microbiol.8:504-508.","journal-title":"Trends Microbiol."},{"key":"e_1_3_2_23_2","doi-asserted-by":"crossref","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","volume":"89","year":"1992","unstructured":"Henikoff, S., and J. G. Henikoff. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA89:10915-10919.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_24_2","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/S0968-0004(99)01428-0","volume":"24","year":"1999","unstructured":"Hou, Y. M. 1999. Transfer RNAs and pathogenicity islands. Trends Biochem. Sci.24:295-298.","journal-title":"Trends Biochem. Sci."},{"key":"e_1_3_2_25_2","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1016\/S0092-8674(85)80059-3","volume":"41","year":"1985","unstructured":"Johnson, R. C., and M. I. Simon. 1985. Hin-mediated site-specific recombination requires two 26 bp recombination sites and a 60-bp recombinational enhancer. Cell41:781-791.","journal-title":"Cell"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.6.1558-1563.2000"},{"key":"e_1_3_2_27_2","doi-asserted-by":"crossref","first-page":"3134","DOI":"10.1073\/pnas.95.6.3134","volume":"95","year":"1998","unstructured":"Karaolis, D. K., J. A. Johnson, C. C. Bailey, E. C. Boedeker, J. B. Kaper, and P. R. Reeves. 1998. A Vibrio cholerae pathogenicity island associated with epidemic and pandemic strains. Proc. Natl. Acad. Sci. USA95:3134-3139.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_28_2","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1038\/75843","volume":"7","year":"2000","unstructured":"Karzai, A. W., E. D. Roche, and R. T. Sauer. 2000. The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat. Struct. Biol.7:449-455.","journal-title":"Nat. Struct. Biol."},{"key":"e_1_3_2_29_2","doi-asserted-by":"crossref","first-page":"3793","DOI":"10.1093\/emboj\/18.13.3793","volume":"18","year":"1999","unstructured":"Karzai, A. W., M. M. Susskind, and R. T. Sauer. 1999. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J.18:3793-3799.","journal-title":"EMBO J."},{"key":"e_1_3_2_30_2","doi-asserted-by":"crossref","first-page":"7778","DOI":"10.1073\/pnas.97.14.7778","volume":"97","year":"2000","unstructured":"Keiler, K. C., L. Shapiro, and K. P. Williams. 2000. tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Proc. Natl. Acad. Sci. USA97:7778-7783.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.176.7.2068-2081.1994"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(00)04403-2"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.17.4891-4905.2002"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.57.3.683-702.1993"},{"key":"e_1_3_2_35_2","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1046\/j.1365-2958.1997.2591616.x","volume":"23","year":"1997","unstructured":"McShan, W. M., Y. F. Tang, and J. J. Ferretti. 1997. Bacteriophage T12 of Streptococcus pyogenes integrates into the gene encoding a serine tRNA. Mol. Microbiol.23:719-728.","journal-title":"Mol. Microbiol."},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.1.315-324.2001"},{"key":"e_1_3_2_37_2","doi-asserted-by":"crossref","first-page":"9845","DOI":"10.1073\/pnas.96.17.9845","volume":"96","year":"1999","unstructured":"Mirold, S., W. Rabsch, M. Rohde, S. Stender, H. Tschape, H. Russmann, E. Igwe, and W. D. Hardt. 1999. Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain. Proc. Natl. Acad. Sci. USA96:9845-9850.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_38_2","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1126\/science.1058543","volume":"292","year":"2001","unstructured":"Ochman, H., and N. A. Moran. 2001. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science292:1096-1099.","journal-title":"Science"},{"key":"e_1_3_2_39_2","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1126\/science.290.5490.347","volume":"290","year":"2000","unstructured":"Ogata, H., S. Audic, V. Barbe, F. Artiguenave, P. E. Fournier, D. Raoult, and J. M. Claverie. 2000. Selfish DNA in protein-coding genes of Rickettsia. Science290:347-350.","journal-title":"Science"},{"key":"e_1_3_2_40_2","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1126\/science.291.5502.252","volume":"291","year":"2001","unstructured":"Ogata, H., S. Audic, and J. M. Claverie. 2001. Selfish DNA and the origin of genes. Science291:252-253.","journal-title":"Science"},{"key":"e_1_3_2_41_2","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/S0966-842X(01)02173-4","volume":"9","year":"2001","unstructured":"Ohnishi, M., K. Kurokawa, and T. Hayashi. 2001. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol.9:481-485.","journal-title":"Trends Microbiol."},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/35101607"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.178.18.5533-5536.1996"},{"key":"e_1_3_2_44_2","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/35054089","volume":"409","year":"2001","unstructured":"Perna, N. T., G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157.:H7. Nature409:529-533.","journal-title":"Nature"},{"key":"e_1_3_2_45_2","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1006\/viro.1998.9263","volume":"248","year":"1998","unstructured":"Portelli, R., I. B. Dodd, Q. Xue, and J. B. Egan. 1998. The late-expressed region of the temperate coliphage 186 genome. Virology248:117-130.","journal-title":"Virology"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.176.7.2082-2089.1994"},{"key":"e_1_3_2_47_2","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1146\/annurev.mi.32.100178.002511","volume":"32","year":"1978","unstructured":"Riley, M., and A. Anilionis. 1978. Evolution of the bacterial genome. Annu. Rev. Microbiol.32:519-560.","journal-title":"Annu. Rev. Microbiol."},{"key":"e_1_3_2_48_2","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1111\/j.1365-2958.1994.tb01023.x","volume":"12","year":"1994","unstructured":"Sandmeier, H. 1994. Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres. Mol. Microbiol.12:343-350.","journal-title":"Mol. Microbiol."},{"key":"e_1_3_2_49_2","doi-asserted-by":"crossref","first-page":"20798","DOI":"10.1016\/S0021-9258(17)32063-X","volume":"269","year":"1994","unstructured":"Smith-Mungo, L., I. T. Chan, and A. Landy. 1994. Structure of the P22 att site: conservation and divergence in the lambda motif of recombinogenic complexes. J. Biol. Chem.269:20798-20805.","journal-title":"J. Biol. Chem."},{"key":"e_1_3_2_50_2","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1007\/s004380050535","volume":"255","year":"1997","unstructured":"Steiner, K., and H. Malke. 1997. Primary structure requirements for in vivo activity and bidirectional function of the transcription terminator shared by the oppositely oriented skc\/rel-orf1 genes of Streptococcus equisimilis H46A. Mol. Gen. Genet.255:611-618.","journal-title":"Mol. Gen. Genet."},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.42.2.385-413.1978"},{"key":"e_1_3_2_52_2","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1038\/286218a0","volume":"286","year":"1980","unstructured":"van de Putte, P., S. Cramer, and M. Giphart-Gassler. 1980. Invertible DNA determines host specificity of bacteriophage mu. Nature286:218-222.","journal-title":"Nature"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.179.21.6551-6559.1997"},{"key":"e_1_3_2_54_2","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1101\/gad.901001","volume":"15","year":"2001","unstructured":"Wassarman, K. M., F. Repoila, C. Rosenow, G. Storz, and S. Gottesman. 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev.15:1637-1651.","journal-title":"Genes Dev."},{"key":"e_1_3_2_55_2","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1093\/nar\/30.9.2025","volume":"30","year":"2002","unstructured":"Williams, K. P. 2002. Descent of a split RNA. Nucleic Acids Res.30:2025-2030.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_56_2","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1093\/nar\/30.4.866","volume":"30","year":"2002","unstructured":"Williams, K. P. 2002. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res.30:866-875.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_57_2","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1093\/nar\/26.1.163","volume":"26","year":"1998","unstructured":"Williams, K. P., and D. P. Bartel. 1998. The tmRNA Website. Nucleic Acids Res.26:163-165.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_58_2","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1046\/j.1365-2958.1996.00116.x","volume":"22","year":"1996","unstructured":"Wood, M. W., R. Rosqvist, P. B. Mullan, M. H. Edwards, and E. E. Galyov. 1996. SopE, a secreted protein of Salmonella dublin, is translocated into the target eukaryotic cell via a sip-dependent mechanism and promotes bacterial entry. Mol. Microbiol.22:327-338.","journal-title":"Mol. Microbiol."}],"container-title":["Journal of Bacteriology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JB.185.3.1059-1070.2003","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JB.185.3.1059-1070.2003","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T18:12:56Z","timestamp":1627582376000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JB.185.3.1059-1070.2003"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,2]]},"references-count":57,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2003,2]]}},"alternative-id":["10.1128\/JB.185.3.1059-1070.2003"],"URL":"https:\/\/doi.org\/10.1128\/jb.185.3.1059-1070.2003","relation":{},"ISSN":["0021-9193","1098-5530"],"issn-type":[{"value":"0021-9193","type":"print"},{"value":"1098-5530","type":"electronic"}],"subject":[],"published":{"date-parts":[[2003,2]]},"assertion":[{"value":"2002-01-31","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2002-10-16","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-12-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}