{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T18:49:58Z","timestamp":1790880598243,"version":"4.1.0"},"reference-count":57,"publisher":"Microbiology Society","issue":"10","funder":[{"name":"National Science Foundation","award":["DEB-0841999"],"award-info":[{"award-number":["DEB-0841999"]}]},{"name":"Technology Development Program for Agriculture and Forestry (TDPAF) of the Ministry for Agriculture, Forestry and Fisheries"},{"name":"21C Frontier Microbial Genomics and Application Center Program","award":["MG05-0104-4-0"],"award-info":[{"award-number":["MG05-0104-4-0"]}]},{"name":"MOST\/KOSEF"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,1]]},"abstract":"<jats:p>\n                  <jats:italic>Polaromonas naphthalenivorans<\/jats:italic> strain CJ2 metabolizes naphthalene via the gentisate pathway and has recently been shown to carry a third copy of gentisate 1,2-dioxygenase (GDO), encoded by <jats:italic>nagI3,<\/jats:italic> within a previously uncharacterized naphthalene catabolic gene cluster. The role of this cluster (especially <jats:italic>nagI3<\/jats:italic>) in naphthalene metabolism of strain CJ2 was investigated by documenting patterns in regulation, transcription and enzyme activity. Transcriptional analysis of wild-type cells showed the third cluster to be polycistronic and that <jats:italic>nagI3<\/jats:italic> was expressed at a relatively high level. Individual knockout mutants of all three <jats:italic>nagI<\/jats:italic> genes were constructed and their influence on both GDO activity and cell growth was evaluated. Of the three knockout strains, CJ2\u0394<jats:italic>nagI3<\/jats:italic> showed severely diminished GDO activity and grew slowest on aromatic substrates. These observations are consistent with the hypothesis that <jats:italic>nagI3<\/jats:italic> may prevent toxic intracellular levels of gentisate from accumulating in CJ2 cells. All three <jats:italic>nagI<\/jats:italic> genes from strain CJ2 were cloned into <jats:italic>Escherichia coli<\/jats:italic>: the <jats:italic>nagI2<\/jats:italic> and <jats:italic>nagI3<\/jats:italic> genes were successfully overexpressed. The subunit mass of the GDOs were ~36\u201339 kDa, and their structures were deduced to be dimeric. The <jats:italic>K<\/jats:italic>\n                  <jats:sub>m<\/jats:sub> values of NagI2 and NagI3 were 31 and 10 \u00b5M, respectively, indicating that the higher affinity of NagI3 for gentisate may protect the wild-type cells from gentisate toxicity. These results provide clues for explaining why the third gene cluster, particularly the <jats:italic>nagI3<\/jats:italic> gene, is important in strain CJ2. The organization of genes in the third gene cluster matched that of clusters in <jats:italic>Polaromonas<\/jats:italic> sp. JS666 and <jats:italic>Leptothrix cholodnii<\/jats:italic> SP-6. While horizontal gene transfer (HGT) is one hypothesis for explaining this genetic motif, gene duplication within the ancestral lineage is equally valid. The HGT hypothesis was discounted by noting that the <jats:italic>nagI3<\/jats:italic> allele of strain CJ2 did not share high sequence identity with its homologues in <jats:italic>Polaromonas<\/jats:italic> sp. JS666 and <jats:italic>L. cholodnii<\/jats:italic> SP-6.<\/jats:p>","DOI":"10.1099\/mic.0.049387-0","type":"journal-article","created":{"date-parts":[[2011,7,8]],"date-time":"2011-07-08T14:45:07Z","timestamp":1310136307000},"page":"2891-2903","source":"Crossref","is-referenced-by-count":25,"title":["Gentisate 1,2-dioxygenase, in the third naphthalene catabolic gene cluster of Polaromonas naphthalenivorans CJ2, has a role in naphthalene degradation"],"prefix":"10.1099","volume":"157","author":[{"given":"Hyo Jung","family":"Lee","sequence":"first","affiliation":[{"name":"Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeong Myeong","family":"Kim","sequence":"additional","affiliation":[{"name":"Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Se Hee","family":"Lee","sequence":"additional","affiliation":[{"name":"Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minjeong","family":"Park","sequence":"additional","affiliation":[{"name":"Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kangseok","family":"Lee","sequence":"additional","affiliation":[{"name":"Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugene L.","family":"Madsen","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Che Ok","family":"Jeon","sequence":"additional","affiliation":[{"name":"Schools of Biological Sciences and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"r1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2006.05334.x"},{"key":"r2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"r3","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genet-102108-134805"},{"key":"r4","first-page":"253","article-title":"The degradation of aromatic compounds by the meta and gentisate pathway: Biochemistry and regulation","volume-title":"Microbial Degradation of Aromatic Compounds","author":"Bayly","year":"1984"},{"key":"r5","doi-asserted-by":"publisher","DOI":"10.1016\/0003-2697(76)90527-3"},{"key":"r6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0606924103"},{"key":"r7","first-page":"17","article-title":"An outline of reaction sequences used for the bacterial degradation of phenolic compounds","volume-title":"Degradation of Synthetic Organic Molecules in the Biosphere","author":"Chapman","year":"1972"},{"key":"r8","doi-asserted-by":"publisher","DOI":"10.1110\/ps.035881.108"},{"key":"r9","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1128\/JB.121.3.794-799.1975","article-title":"Purification and properties of gentisate 1,2-dioxygenase from Moraxella osloensis","volume":"121","author":"Crawford","year":"1975","journal-title":"J Bacteriol"},{"key":"r10","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn180"},{"key":"r11","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1128\/AEM.65.3.946-950.1999","article-title":"Purification and characterization of gentisate 1,2-dioxygenases from Pseudomonas alcaligenes NCIB 9867 and Pseudomonas putida NCIB 9869","volume":"65","author":"Feng","year":"1999","journal-title":"Appl Environ Microbiol"},{"key":"r12","doi-asserted-by":"crossref","first-page":"2522","DOI":"10.1128\/JB.180.9.2522-2530.1998","article-title":"A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2","volume":"180","author":"Fuenmayor","year":"1998","journal-title":"J Bacteriol"},{"key":"r13","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2004.02.007"},{"key":"r14","doi-asserted-by":"publisher","DOI":"10.1139\/m88-121"},{"key":"r15","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.1128\/AEM.58.6.1874-1877.1992","article-title":"Naphthalene degradation via salicylate and gentisate by Rhodococcus sp. strain B4","volume":"58","author":"Grund","year":"1992","journal-title":"Appl Environ Microbiol"},{"key":"r16","doi-asserted-by":"publisher","DOI":"10.1271\/bbb.60444"},{"key":"r17","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.7.3088-3092.2000"},{"key":"r18","doi-asserted-by":"publisher","DOI":"10.1099\/00207713-46-3-822"},{"key":"r19","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1735529100"},{"key":"r20","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.02636-0"},{"key":"r21","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.72.2.1086-1095.2006"},{"key":"r22","doi-asserted-by":"crossref","first-page":"4047","DOI":"10.1128\/AEM.63.10.4047-4052.1997","article-title":"Multiple pathways for toluene degradation in Burkholderia sp. strain JS150","volume":"63","author":"Johnson","year":"1997","journal-title":"Appl Environ Microbiol"},{"key":"r23","doi-asserted-by":"publisher","DOI":"10.1128\/JB.185.19.5847-5853.2003"},{"key":"r24","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(96)00778-0"},{"key":"r25","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemosphere.2004.11.003"},{"key":"r26","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2009.06905.x"},{"key":"r27","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.4.1754-1764.2005"},{"key":"r28","doi-asserted-by":"publisher","DOI":"10.1016\/0006-3002(59)90239-2"},{"key":"r29","doi-asserted-by":"publisher","DOI":"10.1002\/jobm.201000291"},{"key":"r30","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2006.00477.x"},{"key":"r31","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.7.3624-3632.2005"},{"key":"r32","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1128\/AEM.61.2.549-555.1995","article-title":"Multiple genes encoding 2,3-dihydroxybiphenyl 1,2-dioxygenase in the Gram-positive polychlorinated biphenyl-degrading bacterium Rhodococcus erythropolis TA421, isolated from a termite ecosystem","volume":"61","author":"Maeda","year":"1995","journal-title":"Appl Environ Microbiol"},{"key":"r33","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00197-08"},{"key":"r34","doi-asserted-by":"publisher","DOI":"10.1007\/BF00329933"},{"key":"r35","doi-asserted-by":"crossref","first-page":"3788","DOI":"10.1128\/AEM.61.11.3788-3795.1995","article-title":"Recombination of a 3-chlorobenzoate catabolic plasmid from Alcaligenes eutrophus NH9 mediated by direct repeat elements","volume":"61","author":"Ogawa","year":"1995","journal-title":"Appl Environ Microbiol"},{"key":"r36","first-page":"1733","article-title":"Salicylic acid metabolism through a gentisate pathway by Pseudomonas sp. TA-2","volume":"55","author":"Ohmoto","year":"1991","journal-title":"Agric Biol Chem"},{"key":"r37","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-003-1420-6"},{"key":"r38","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00782-07"},{"key":"r39","first-page":"41","article-title":"Protection of Polaromonas naphthalenivorans CJ2 from naphthalene toxicity by extracellular polysaccharide capsules","volume":"50","author":"Park","year":"2007b","journal-title":"J Appl Biol Chem"},{"key":"r40","doi-asserted-by":"publisher","DOI":"10.1021\/tx980143n"},{"key":"r41","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.2007\/010728-0"},{"key":"r42","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.56.012302.161038"},{"key":"r43","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1128\/JB.170.4.1907-1912.1988","article-title":"Variation in the ability of Pseudomonas sp. strain B13 cultures to utilize meta-chlorobenzoate is associated with tandem amplification and deamplification of DNA","volume":"170","author":"Rangnekar","year":"1988","journal-title":"J Bacteriol"},{"key":"r44","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2003.03342.x"},{"key":"r45","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2004.03.031"},{"key":"r46","doi-asserted-by":"publisher","DOI":"10.1007\/BF00408897"},{"key":"r47","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.72.4.2765-2774.2006"},{"key":"r48","author":"Sambrook","year":"2001","journal-title":"Molecular cloning: a laboratory manual"},{"key":"r49","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(94)90324-7"},{"key":"r50","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1128\/JB.166.1.9-14.1986","article-title":"Identification of the nahR gene product and nucleotide sequences required for its activation of the sal operon","volume":"166","author":"Schell","year":"1986","journal-title":"J Bacteriol"},{"key":"r51","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-2920.2001.00176.x"},{"key":"r52","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1128\/MMBR.59.2.201-222.1995","article-title":"Mechanisms of membrane toxicity of hydrocarbons","volume":"59","author":"Sikkema","year":"1995","journal-title":"Microbiol Rev"},{"key":"r53","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1099\/00221287-43-2-159","article-title":"The aerobic pseudomonads: a taxonomic study","volume":"43","author":"Stanier","year":"1966","journal-title":"J Gen Microbiol"},{"key":"r54","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2004.00624.x"},{"key":"r55","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M106890200"},{"key":"r56","doi-asserted-by":"publisher","DOI":"10.1080\/10409230600817422"},{"key":"r57","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2009.01947.x"}],"container-title":["Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/micro\/10.1099\/mic.0.049387-0?crawler=true","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,19]],"date-time":"2020-11-19T11:52:59Z","timestamp":1605786779000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/micro\/10.1099\/mic.0.049387-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,1]]},"references-count":57,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2011,10,1]]}},"URL":"https:\/\/doi.org\/10.1099\/mic.0.049387-0","relation":{},"ISSN":["1350-0872","1465-2080"],"issn-type":[{"value":"1350-0872","type":"print"},{"value":"1465-2080","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,1]]}}}