{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:43:31Z","timestamp":1760060611435,"version":"build-2065373602"},"reference-count":44,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,6]],"date-time":"2025-09-06T00:00:00Z","timestamp":1757116800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China","award":["42077212","23YFZXYC00019","UIDB\/04423\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["42077212","23YFZXYC00019","UIDB\/04423\/2020","UIDP\/04423\/2020"]}]},{"name":"Tiankai Higher Education Science and Technology Innovation Park Enterprise R&amp;D Special Project","award":["42077212","23YFZXYC00019","UIDB\/04423\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["42077212","23YFZXYC00019","UIDB\/04423\/2020","UIDP\/04423\/2020"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","award":["42077212","23YFZXYC00019","UIDB\/04423\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["42077212","23YFZXYC00019","UIDB\/04423\/2020","UIDP\/04423\/2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent organic pollutants composed of two or more fused benzene rings, posing serious threats to ecological environments and human health. Biodegradation is an efficient, economical, and sustainable approach for remediating PAHs pollution. In our previous work, we isolated and characterized a PAH-degrading bacterium, Burkholderia sp. FM-2. FM-2 demonstrated strong tolerance and efficient degradation capacity toward various PAHs, achieving 81.98% degradation of 2 mM phenanthrene within 3 days, and over 58% degradation of 2 mM fluorene, dibenzofuran, and dibenzothiophene under the same conditions. Through combined genomic and transcriptomic analyses, a putative PAH degradation gene cluster was identified in the FM-2 genome. Phylogenetic and domain architecture analyses were conducted on seven oxygenase genes within the cluster. Using AlphaFold 3, we predicted the three-dimensional structure of the downstream transport protein OmpW and proposed a potential transmembrane channel for PAHs uptake. To eliminate the phenanthrene degradation intermediate 1-hydroxy-2-naphthoic acid, a genetically engineered strain FM-2::nahG was constructed by heterologous expression of the salicylate hydroxylase gene (nahG). The modified strain completely abolished the accumulation of 1-hydroxy-2-naphthoic acid and achieved complete mineralization of phenanthrene. This study not only reveals the molecular basis of PAHs degradation in Burkholderia sp. FM-2 but also demonstrates the potential of metabolic engineering to enhance biodegradation ability, providing a promising microbial candidate for the bioremediation of PAH-polluted environments.<\/jats:p>","DOI":"10.3390\/microorganisms13092079","type":"journal-article","created":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T08:06:32Z","timestamp":1757318792000},"page":"2079","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Study and Modification of the Polycyclic Aromatic Hydrocarbon Degradation Gene Cluster in Burkholderia sp. FM-2"],"prefix":"10.3390","volume":"13","author":[{"given":"Jiajun","family":"Ma","sequence":"first","affiliation":[{"name":"Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China"}]},{"given":"Ying","family":"Zhai","sequence":"additional","affiliation":[{"name":"Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China"}]},{"given":"Yumeng","family":"Cui","sequence":"additional","affiliation":[{"name":"Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China"}]},{"given":"Guohui","family":"Gao","sequence":"additional","affiliation":[{"name":"Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China"}]},{"given":"Ming","family":"Ying","sequence":"additional","affiliation":[{"name":"Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9233-6959","authenticated-orcid":false,"given":"Yihe","family":"Zhao","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s\/n, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1328-1732","authenticated-orcid":false,"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450-208 Porto, Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s\/n, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3490-3393","authenticated-orcid":false,"given":"Lei","family":"Huang","sequence":"additional","affiliation":[{"name":"Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China"}]},{"given":"Meitong","family":"Li","sequence":"additional","affiliation":[{"name":"Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/j.envpol.2017.08.048","article-title":"Biodegradation of Polycyclic Aromatic Hydrocarbons: Using Microbial Bioelectrochemical Systems to Overcome an Impasse","volume":"231","author":"Maria","year":"2017","journal-title":"Environ. 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