{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:35:25Z","timestamp":1791160525173,"version":"4.1.0"},"reference-count":47,"publisher":"American Society for Microbiology","issue":"16","license":[{"start":{"date-parts":[[2002,8,15]],"date-time":"2002-08-15T00:00:00Z","timestamp":1029369600000},"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":[[2002,8,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    We present the complete genome sequence of\n                    <jats:italic>Yersinia pestis<\/jats:italic>\n                    KIM, the etiologic agent of bubonic and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to those of\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    K-12. The KIM genome sequence was compared with that of\n                    <jats:italic>Y. pestis<\/jats:italic>\n                    CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome rearrangement for strains so closely related. The differences appear to result from multiple inversions of genome segments at insertion sequences, in a manner consistent with present knowledge of replication and recombination. There are few differences attributable to horizontal transfer. The KIM and\n                    <jats:italic>E. coli<\/jats:italic>\n                    K-12 genome proteins were also compared, exposing surprising amounts of locally colinear \u201cbackbone,\u201d or synteny, that is not discernible at the nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with conserved housekeeping functions. However, a number of\n                    <jats:italic>E. coli<\/jats:italic>\n                    pathways and transport systems and at least one global regulator were not found, reflecting differences in lifestyle between them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae.\n                  <\/jats:p>","DOI":"10.1128\/jb.184.16.4601-4611.2002","type":"journal-article","created":{"date-parts":[[2002,10,1]],"date-time":"2002-10-01T15:36:19Z","timestamp":1033486579000},"page":"4601-4611","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":454,"title":["Genome Sequence of\n                    <i>Yersinia pestis<\/i>\n                    KIM"],"prefix":"10.1128","volume":"184","author":[{"given":"Wen","family":"Deng","sequence":"first","affiliation":[{"name":"Laboratory of Genetics"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerie","family":"Burland","sequence":"additional","affiliation":[{"name":"Laboratory of 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J.","family":"Rose","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bob","family":"Mau","sequence":"additional","affiliation":[{"name":"Department of Animal Health and Biomedical Sciences"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiguo","family":"Zhou","sequence":"additional","affiliation":[{"name":"Genome Center"},{"name":"Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David C.","family":"Schwartz","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics"},{"name":"Genome Center"},{"name":"Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaqueline D.","family":"Fetherston","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Kentucky, Lexington, Kentucky, 40536-0084"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luther E.","family":"Lindler","sequence":"additional","affiliation":[{"name":"Department of Bacterial Diseases, Division of Communicable Diseases and Immunology, Walter Reed Army Institute of Research, Washington, District of Columbia 20307-5100"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert R.","family":"Brubaker","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory V.","family":"Plano","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Miami School of Medicine, Miami, Florida 33176"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan C.","family":"Straley","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Kentucky, Lexington, Kentucky, 40536-0084"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathleen A.","family":"McDonough","sequence":"additional","affiliation":[{"name":"David Axelrod Institute, Wadsworth Center, Albany, New York 12201-2002"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew L.","family":"Nilles","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202-9037"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyl S.","family":"Matson","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 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Zurth, C. Morelli, G. Torrea, A. Guiyoule, and E. Carniel. 1999. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA96:14043-14048.","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.183.20.5927-5936.2001"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.277.5331.1453"},{"key":"e_1_3_2_6_2","unstructured":"Brubaker R. R. 2000. Yersinia pestis and bubonic plague. In S. F. M. Dworkin E. D. Rosenberg K.-H. Schleifer and E. Stackelbrandt (ed.) The prokaryotes an evolving electronic resource for the microbiological community. Springer Verlag New York N.Y."},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.67.9.4851-4861.1999"},{"key":"e_1_3_2_8_2","doi-asserted-by":"crossref","first-page":"3385","DOI":"10.1093\/nar\/21.15.3385","volume":"21","year":"1993","unstructured":"Burland, V., D. L. Daniels, G. Plunkett III, and F. R. Blattner. 1993. Genome sequencing on both strands: the Janus strategy. Nucleic Acids Res.21:3385-3390.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_9_2","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1006\/geno.1993.1230","volume":"16","year":"1993","unstructured":"Burland, V., G. Plunkett III, D. L. Daniels, and F. R. Blattner. 1993. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. 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