{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T18:44:23Z","timestamp":1788893063662,"version":"build-2803163510"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T00:00:00Z","timestamp":1750377600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100014538","name":"Indonesia Endowment Fund for Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014538","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Aims<\/jats:title>\n                  <jats:p>To identify novel brown coal-degrading bacteria, and elucidate the biochemical pathways involved in brown coal degradation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods and results<\/jats:title>\n                  <jats:p>Four bacterial isolates were identified from the surface of Indonesian brown coal, which can utilize naphthalene and 1-methylnaphthalene as carbon sources for growth. The genome sequence of the best-performing Micrococcus luteus K1 strain was determined. A novel aromatic degradation gene cluster was identified, containing several paa genes normally involved in phenylacetic acid degradation, and also containing genes found on aromatic meta-cleavage pathways. 1-Naphthoic acid was generated from 1-methylnaphthalene by M. luteus K1 whole cell biotransformation, and was also utilized as a growth substrate by M. luteus K1. Recombinant ligase PaaK from the new gene cluster was shown to activate either phenylacetic acid or 1-naphthoic acid to their respective CoA esters, consistent with 1-naphthoyl CoA being an intermediate on the pathway. From metabolite analysis and annotation of the gene cluster, a new 1-methylnaphthalene degradation pathway was proposed, via a benzene oxide-oxepin ring opening. Recombinant mono-oxygenase and extradiol catechol dioxygenase enzymes from the gene cluster were expressed, showing activities consistent with the later steps of the proposed pathway.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>A new M. luteus K1 isolate was identified as a brown coal degrader, whose genome contains an unusual aromatic degradation cluster containing paa genes. This cluster is hypothesized to be responsible for 1-methylnaphthalene degradation.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jambio\/lxaf153","type":"journal-article","created":{"date-parts":[[2025,6,28]],"date-time":"2025-06-28T00:10:18Z","timestamp":1751069418000},"source":"Crossref","is-referenced-by-count":2,"title":["Degradation of brown coal and 1-methylnaphthalene by a <i>Micrococcus luteus<\/i> isolate: investigation of a novel aromatic degradation gene cluster containing <i>paa<\/i> genes"],"prefix":"10.1093","volume":"136","author":[{"given":"Purwinda","family":"Iriani","sequence":"first","affiliation":[{"name":"University of Warwick Department of Chemistry, , Coventry CV4 7AL ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon G","family":"Allison","sequence":"additional","affiliation":[{"name":"Aberystwyth University Department of Life Sciences, , Aberystwyth, Ceredigion, SY23 3DA ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3964-4498","authenticated-orcid":false,"given":"Timothy D H","family":"Bugg","sequence":"additional","affiliation":[{"name":"University of Warwick Department of Chemistry, , Coventry CV4 7AL ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,6,20]]},"reference":[{"key":"2025070204515086800_bib1","doi-asserted-by":"publisher","first-page":"5349","DOI":"10.1073\/pnas.0709223105","article-title":"Crystal structure and functional analysis of tetracenomycin ARO\/CYC: implications for cyclization specificity of aromatic polyketides","volume":"105","author":"Ames","year":"2008","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025070204515086800_bib2","doi-asserted-by":"publisher","first-page":"2074","DOI":"10.1021\/cb300383y","article-title":"Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium","volume":"7","author":"Brown","year":"2012","journal-title":"ACS Chem Biol"},{"key":"2025070204515086800_bib3","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1039\/a815513y","article-title":"Enzymatic cleavage of aromatic rings: mechanistic aspects of the catechol dioxygenases and later enzymes of bacterial oxidative cleavage pathways","volume":"15","author":"Bugg","year":"1998","journal-title":"Nat Prod Rep"},{"key":"2025070204515086800_bib4","first-page":"258","article-title":"Overproduction, purification and properties of 2,3-dihydroxy-phenylpropionate 1,2-dioxygenase from Escherichia coli","volume":"1202","author":"Bugg","year":"1993","journal-title":"Biochem Biophys Acta"},{"key":"2025070204515086800_bib5","doi-asserted-by":"publisher","first-page":"7075","DOI":"10.1016\/S0040-4020(03)00944-X","article-title":"Dioxygenase enzymes: catalytic mechanisms and model chemistry","volume":"59","author":"Bugg","year":"2003","journal-title":"Tetrahedron"},{"key":"2025070204515086800_bib6","first-page":"2281","article-title":"The plasmid-coded metabolism of naphthalene and 2-methylnaphthalene in Pseudomonas strains: phenotypic changes correlated with structural modification of the plasmid pWW60\u20131","volume":"128","author":"Cane","year":"1982","journal-title":"J Gen Microbiology"},{"key":"2025070204515086800_bib7","doi-asserted-by":"publisher","first-page":"2141","DOI":"10.1016\/0016-7037(83)90039-X","article-title":"Polycyclic aromatic hydrocarbons in Australian coals. 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