Abstract
Pseudomonas aeruginosa DN1, isolated from petroleum-contaminated soil, showed excellent degradation ability toward diverse polycyclic aromatic hydrocarbons (PAHs). Many studies have been done to improve its degradation ability. However, the molecular mechanisms of PAHs degradation in DN1 strain are unclear. In this study, the whole genome of DN1 strain was sequenced and analyzed. Its genome contains 6,641,902 bp and encodes 6,684 putative open reading frames (ORFs), which has the largest genome in almost all the comparative Pseudomonas strains. Results of gene annotation showed that this strain harbored over 100 candidate genes involved in PAHs degradation, including those encoding 25 dioxygenases, four ring-hydroxylating dioxygenases, five ring-cleaving dioxygenases, and various catabolic enzymes, transcriptional regulators, and transporters in the degradation pathways. In addition, gene knockout experiments revealed that the disruption of some key PAHs degradation genes in DN1 strain, such as catA, pcaG, pcaH, and rhdA, did not completely inhibit fluoranthene degradation, even though their degradative rate reduced to some extent. Three intermediate metabolites, including 9-hydroxyfluorene, 1-acenaphthenone, and 1, 8-naphthalic anhydride, were identified as the dominating intermediates in presence of 50 μg/mL fluoranthene as the sole carbon source according to gas chromatography mass spectrometry analysis. Taken together, the genomic and metabolic analysis indicated that the fluoranthene degradation by DN1 strain was initiated by dioxygenation at the C-1, 2-, C-2, 3-, and C-7, 8- positions. These results provide new insights into the genomic plasticity and environmental adaptation of DN1 strain.
Highlights
Polycyclic aromatic hydrocarbons (PAHs) are characterized as hazardous organic pollutants comprising two or more fused benzene rings in linear, angular and clustered arrangements, and their distribution in the environment and possible human exposure is a public concern (Seeger et al, 2010; Kumar et al, 2011)
As described in our previously report, the genome of P. aeruginosa DN1 consisted of a single circular chromosome of 6,641,902,251 base pairs and a plasmid of 317,349 bp (Dong et al, 2017)
The genome of DN1 strain harbors over 100 candidate genes potentially involved in polycyclic aromatic hydrocarbons (PAHs) metabolism, as well as 198 genes associated with two-component systems, including genes encoding 76 histidine kinases and response regulators
Summary
Polycyclic aromatic hydrocarbons (PAHs) are characterized as hazardous organic pollutants comprising two or more fused benzene rings in linear, angular and clustered arrangements, and their distribution in the environment and possible human exposure is a public concern (Seeger et al, 2010; Kumar et al, 2011). Genes Involved in Fluoranthene Biodegradation is given to restore the contaminated sites with PAHs (Kanaly and Harayama, 2000; Yan et al, 2004). Great advances have been made in many aspects of PAHs biodegradation, there remain practical constrains in efficiently implementing bioremediation technology due to the complex nature of the contaminated sites and the lack of valuable information concerning the environment adaption and pollutant degradation performance of microbes (Kanaly and Harayama, 2000; Fuchs et al, 2011; Kweon et al, 2011; Cao et al, 2015). Implementation of more genome sequencing projects is of great help to understand the genetic basis for versatile metabolic potential and environmental adaption (Feng et al, 2007; Jin et al, 2011; Shetty et al, 2015)
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