Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3

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...

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Bibliographic Details
Published in:PloS one 2015-08, Vol.10 (8), p.e0132881
Main Authors: Wang, Xiaoyu, Chen, Meili, Xiao, Jingfa, Hao, Lirui, Crowley, David E, Zhang, Zhewen, Yu, Jun, Huang, Ning, Huo, Mingxin, Wu, Jiayan
Format: Article
Language:English
Subjects:
Acid resistance
Acids
Alcaligenes
Aromatic compounds
Aromatic hydrocarbons
Asphalt
Bacteria
Bacterial genetics
Biodegradation
Biodegradation, Environmental
Carbon sources
Carboxylic Acids - metabolism
Chromosomes
Chromosomes, Bacterial - genetics
Cupriavidus - drug effects
Cupriavidus - genetics
Cupriavidus - metabolism
Cupriavidus metallidurans
Cyclohexanecarboxylic acid
Deoxyribonucleic acid
Detoxification
DNA
DNA repair
E coli
Ecology
Efflux
Environmental protection
Escherichia coli
Fatty acids
Fission products
Gene sequencing
Genes
Genes, Bacterial
Genetic aspects
Genome, Bacterial - genetics
Genomes
Genomic analysis
Genomics
Heavy metals
Hydrocarbon-degrading bacteria
Hydrocarbons
Laboratories
Metal concentrations
Metals, Heavy - pharmacology
Microbial metabolism
Microbial Sensitivity Tests
Naphthenic acid
Naphthenic acids
Nucleotide sequence
Oxidation
Pathways
Physiological aspects
Plasmids
Proteins
Reduction (metal working)
Silver
Substrates
tRNA
Vegetation
Volatile compounds
Wetlands
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0132881