{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T11:43:07Z","timestamp":1790854987988,"version":"4.1.0"},"reference-count":57,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2006,2,1]],"date-time":"2006-02-01T00:00:00Z","timestamp":1138752000000},"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":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2006,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            <jats:italic>Polaromonas naphthalenivorans<\/jats:italic>\n            CJ2, found to be responsible for the degradation of naphthalene in situ at a coal tar waste-contaminated site (C.-O. Jeon et al., Proc. Natl. Acad. Sci. USA 100:13591-13596, 2003), is able to grow on mineral salts agar media with naphthalene as the sole carbon source. Beginning from a 484-bp\n            <jats:italic>nagAc<\/jats:italic>\n            -like region, we used a genome walking strategy to sequence genes encoding the entire naphthalene degradation pathway andadditional flanking regions. We found that the naphthalene catabolic genes in\n            <jats:italic>P. naphthalenivorans<\/jats:italic>\n            CJ2 were divided into one large and one small gene cluster, separated by an unknown distance. The large gene cluster (\n            <jats:italic>nagRAaGHAbAcAdBFCQEDJI\u2032ORF1tnpA<\/jats:italic>\n            ) is bounded by a LysR-type regulator (\n            <jats:italic>nagR<\/jats:italic>\n            ). The small cluster (\n            <jats:italic>nagR2ORF2I\"KL<\/jats:italic>\n            ) is bounded by a MarR-type regulator (\n            <jats:italic>nagR2<\/jats:italic>\n            ). The catabolic genes of\n            <jats:italic>P. naphthalenivorans<\/jats:italic>\n            CJ2 were homologous to many of those of\n            <jats:italic>Ralstonia<\/jats:italic>\n            U2, which uses the gentisate pathway to convert naphthalene to central metabolites. However, three open reading frames (\n            <jats:italic>nagY<\/jats:italic>\n            ,\n            <jats:italic>nagM<\/jats:italic>\n            , and\n            <jats:italic>nagN<\/jats:italic>\n            ), present in\n            <jats:italic>Ralstonia<\/jats:italic>\n            U2, were absent. Also,\n            <jats:italic>P. naphthalenivorans<\/jats:italic>\n            carries two copies of gentisate dioxygenase (\n            <jats:italic>nagI<\/jats:italic>\n            ) with 77.4% DNA sequence identity to one another and 82% amino acid identity to their homologue in\n            <jats:italic>Ralstonia<\/jats:italic>\n            sp. strain U2. Investigation of the operons using reverse transcription PCR showed that each cluster was controlled independently by its respective promoter. Insertional inactivation and lacZ reporter assays showed that\n            <jats:italic>nagR2<\/jats:italic>\n            is a negative regulator and that expression of the small cluster is not induced by naphthalene, salicylate, or gentisate. Association of two putative\n            <jats:italic>Azoarcus<\/jats:italic>\n            -related transposases with the large cluster and one\n            <jats:italic>Azoarcus<\/jats:italic>\n            -related putative salicylate 5-hydroxylase gene (\n            <jats:italic>ORF2<\/jats:italic>\n            ) in the small cluster suggests that mobile genetic elements were likely involved in creating the novel arrangement of catabolic and regulatory genes in\n            <jats:italic>P. naphthalenivorans<\/jats:italic>\n            .\n          <\/jats:p>","DOI":"10.1128\/aem.72.2.1086-1095.2006","type":"journal-article","created":{"date-parts":[[2006,2,3]],"date-time":"2006-02-03T21:18:24Z","timestamp":1139001504000},"page":"1086-1095","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":83,"title":["The Naphthalene Catabolic (\n            <i>nag<\/i>\n            ) Genes of\n            <i>Polaromonas naphthalenivorans<\/i>\n            CJ2: Evolutionary Implications for Two Gene Clusters and Novel Regulatory Control"],"prefix":"10.1128","volume":"72","author":[{"given":"Che Ok","family":"Jeon","sequence":"first","affiliation":[{"name":"Department of Microbiology, Cornell University, Ithaca, New York 14853-8101"},{"name":"Division of Environmental Biotechnology, EBNCRC &amp; PMBBRC, Gyeongsang National University, 900 Gazwa-dong, JinJu, GyeongNam 660-701, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minjeong","family":"Park","sequence":"additional","affiliation":[{"name":"Division of Environmental Biotechnology, EBNCRC &amp; PMBBRC, Gyeongsang National University, 900 Gazwa-dong, JinJu, GyeongNam 660-701, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyun-Su","family":"Ro","sequence":"additional","affiliation":[{"name":"Division of Environmental Biotechnology, EBNCRC &amp; PMBBRC, Gyeongsang National University, 900 Gazwa-dong, JinJu, GyeongNam 660-701, Korea"},{"name":"Department of Microbiology and Research Institute of Life Science, Gyeongsang National University, 900 Gazwa-dong, JinJu, GyeongNam 660-701, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Woojun","family":"Park","sequence":"additional","affiliation":[{"name":"Division of Environmental Science and Ecological Engineering, Korea University 1, Anam-DongGa, Seungbuk-Ku, Seoul 136-701, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugene L.","family":"Madsen","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Cornell University, Ithaca, New York 14853-8101"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_2_3_2","first-page":"2769","volume":"234","year":"1988","unstructured":"Assinder, S. 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