{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T08:55:55Z","timestamp":1791276955431,"version":"4.1.0"},"reference-count":50,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2004,3,17]],"date-time":"2004-03-17T00:00:00Z","timestamp":1079481600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["enviromicro-journals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Environmental Microbiology"],"published-print":{"date-parts":[[2004,7]]},"abstract":"<jats:title>Summary<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Ralstonia eutropha<\/jats:italic>\n                    JMP134 (pJP4) is a useful model for the study of bacterial degradation of substituted aromatic pollutants. Several key degrading capabilities, encoded by\n                    <jats:italic>tfd<\/jats:italic>\n                    genes, are located in the 88\u2003kb, self\u2010transmissible, IncP\u20101 \u03b2 plasmid pJP4. The complete sequence of the 87\u2003688 nucleotides of pJP4, encoding 83 open reading frames (ORFs), is reported. Most of the coding sequence corresponds to a well\u2010conserved IncP\u20101 \u03b2 backbone and the previously reported\n                    <jats:italic>tfd<\/jats:italic>\n                    genes. In addition, we found hypothetical proteins putatively involved in the transport of aromatic compounds and short\u2010chain fatty acid oxidation. ORFs related to mobile elements, including the Tn\n                    <jats:italic>501<\/jats:italic>\n                    \u2010encoded mercury resistance determinants, an IS\n                    <jats:italic>1071<\/jats:italic>\n                    \u2010based composite transposon and a cryptic class II transposon, are also present in pJP4. These mobile elements are inefficient in transposition and are located in two regions of pJP4 that are rich in remnants of lateral gene transfer events. pJP4 plasmid was able to capture chromosomal genes and form hybrid plasmids with the IncP\u20101 \u03b1 plasmid RP4. These observations are integrated into a model for the evolution of pJP4, which reveals mechanisms of bacterial adaptation to degrade pollutants.\n                  <\/jats:p>","DOI":"10.1111\/j.1462-2920.2004.00596.x","type":"journal-article","created":{"date-parts":[[2004,6,4]],"date-time":"2004-06-04T09:08:51Z","timestamp":1086340131000},"page":"655-668","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":134,"title":["Genetic organization of the catabolic plasmid pJP4 from\n                    <i>Ralstonia eutropha<\/i>\n                    JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways"],"prefix":"10.1111","volume":"6","author":[{"given":"N.","family":"Trefault","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R.","family":"De la Iglesia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. M.","family":"Molina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Manzano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T.","family":"Ledger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"P\u00e9rez\u2010Pantoja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. A.","family":"S\u00e1nchez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Stuardo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B.","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2004,3,17]]},"reference":[{"key":"e_1_2_5_2_1","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-148-9-2883"},{"key":"e_1_2_5_3_1","first-page":"376","article-title":"XL1\u2010Blue: a high efficiency plasmid transforming recA Escherichia coli strain with beta\u2010galactosidase selection","volume":"5","author":"Bullock W.O.","year":"1987","journal-title":"Biotechniques"},{"key":"e_1_2_5_4_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.172.12.6818-6825.1990"},{"key":"e_1_2_5_5_1","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-147-8-2141"},{"key":"e_1_2_5_6_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.145.2.681-686.1981"},{"key":"e_1_2_5_7_1","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1128\/jb.161.1.85-90.1985","article-title":"Transposon mutagenesis and cloning analysis of the pathways for degradation of 2,4\u2010dichlorophenoxyacetic acid and 3\u2010chlorobenzoate in Alcaligenes eutrophus JMP134 (pJP4)","volume":"161","author":"Don R.H.","year":"1985","journal-title":"J Bacteriol"},{"key":"e_1_2_5_8_1","doi-asserted-by":"publisher","DOI":"10.1023\/A:1001755928637"},{"key":"e_1_2_5_9_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.22.6301-6315.2002"},{"key":"e_1_2_5_10_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.82.6.1638"},{"key":"e_1_2_5_11_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-2920.2002.00305.x"},{"key":"e_1_2_5_12_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.181.10.3310-3316.1999"},{"key":"e_1_2_5_13_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.68.2.968-972.2002"},{"key":"e_1_2_5_14_1","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.26260-0"},{"key":"e_1_2_5_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.1999.tb00632.x"},{"key":"e_1_2_5_16_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.6.1976-1986.2003"},{"key":"e_1_2_5_17_1","doi-asserted-by":"publisher","DOI":"10.1128\/jb.145.3.1365-1373.1981"},{"key":"e_1_2_5_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/s007920100202"},{"key":"e_1_2_5_19_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.15.4165-4172.2000"},{"key":"e_1_2_5_20_1","doi-asserted-by":"publisher","DOI":"10.1007\/s004380050862"},{"key":"e_1_2_5_21_1","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-148-11-3431"},{"key":"e_1_2_5_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(97)00460-5"},{"key":"e_1_2_5_23_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2006.05539.x"},{"key":"e_1_2_5_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)01400-6"},{"key":"e_1_2_5_25_1","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1988.tb02971.x"},{"key":"e_1_2_5_26_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.183.19.5684-5697.2001"},{"key":"e_1_2_5_27_1","doi-asserted-by":"publisher","DOI":"10.1128\/mr.56.4.677-694.1992"},{"key":"e_1_2_5_28_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00329837"},{"key":"e_1_2_5_29_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.3.1564-1572.2003"},{"key":"e_1_2_5_30_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.4.1602-1608.2000"},{"key":"e_1_2_5_31_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.5.1534-1542.2003"},{"key":"e_1_2_5_32_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.15.4054-4064.2002"},{"key":"e_1_2_5_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0147-619X(02)00018-5"},{"key":"e_1_2_5_34_1","doi-asserted-by":"publisher","DOI":"10.1128\/jb.176.15.4635-4641.1994"},{"key":"e_1_2_5_35_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.52.1.287"},{"key":"e_1_2_5_36_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.181.5.1585-1602.1999"},{"key":"e_1_2_5_37_1","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.26570-0"},{"key":"e_1_2_5_38_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.183.18.5268-5278.2001"},{"key":"e_1_2_5_39_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00428881"},{"key":"e_1_2_5_40_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.68.5.2307-2315.2002"},{"key":"e_1_2_5_41_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.22.6741-6745.2003"},{"key":"e_1_2_5_42_1","doi-asserted-by":"publisher","DOI":"10.1128\/jb.175.6.1674-1681.1993"},{"key":"e_1_2_5_43_1","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-145-12-3321"},{"key":"e_1_2_5_44_1","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1007\/s00438-002-0785-z","article-title":"The 79,370\u2010bp conjugative plasmid pB4 consists of an IncP\u20101 \u03b2 backbone loaded with a chromate resistance transposon, the strA\u2010strB streptomycin resistance gene pair, the oxacillinase gene bla\n                  NPS\u20101, and a tripartite antibiotic efflux system of the resistance\u2010nodulation\u2010division family","volume":"268","author":"Tauch A.","year":"2003","journal-title":"Mol Gen Genomics"},{"key":"e_1_2_5_45_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1998.2060"},{"key":"e_1_2_5_46_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-7799(98)01295-5"},{"key":"e_1_2_5_47_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.67.4.1508-1516.2001"},{"key":"e_1_2_5_48_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2002.tb11250.x"},{"key":"e_1_2_5_49_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(00)00329-2"},{"key":"e_1_2_5_50_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00696468"},{"key":"e_1_2_5_51_1","doi-asserted-by":"publisher","DOI":"10.1006\/plas.1997.1332"}],"container-title":["Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Fj.1462-2920.2004.00596.x","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/j.1462-2920.2004.00596.x","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:39:09Z","timestamp":1761863949000},"score":1,"resource":{"primary":{"URL":"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/10.1111\/j.1462-2920.2004.00596.x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,3,17]]},"references-count":50,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2004,7]]}},"alternative-id":["10.1111\/j.1462-2920.2004.00596.x"],"URL":"https:\/\/doi.org\/10.1111\/j.1462-2920.2004.00596.x","archive":["Portico"],"relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.1019681.222518","asserted-by":"object"}]},"ISSN":["1462-2912","1462-2920"],"issn-type":[{"value":"1462-2912","type":"print"},{"value":"1462-2920","type":"electronic"}],"subject":[],"published":{"date-parts":[[2004,3,17]]},"assertion":[{"value":"2004-03-17","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}