title: Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.
abstract: Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals.
authors: School of Environment Sciences, Key Laboratory of Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China.
authors: Xiaoyu
authors: X
authors: Wang
authors: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors: Meili
authors: M
authors: Chen
authors: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors: Jingfa
authors: J
authors: Xiao
authors: School of Environment Sciences, Key Laboratory of Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China.
authors: Lirui
authors: L
authors: Hao
authors: Department of Environmental Sciences, University of California Riverside, Riverside, California, United States of America.
authors: David E
authors: DE
authors: Crowley
authors: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors: Zhewen
authors: Z
authors: Zhang
authors: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors: Jun
authors: J
authors: Yu
authors: School of Environment Sciences, Key Laboratory of Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China.
authors: Ning
authors: N
authors: Huang
authors: School of Environment Sciences, Key Laboratory of Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China.
authors: Mingxin
authors: M
authors: Huo
authors: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors: Jiayan
authors: J
authors: Wu
mesh_terms: D001673:Biodegradation, Environmental; D002264:Carboxylic Acids / Q000378:metabolism*; D002876:Chromosomes, Bacterial / Q000235:genetics; D049921:Cupriavidus / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D019216:Metals, Heavy / Q000494:pharmacology*; D008826:Microbial Sensitivity Tests
chemical_list: D002264:Carboxylic Acids; D019216:Metals, Heavy; C046170:naphthenic acid