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

Wang X, Chen M, Xiao J, Hao L, Crowley DE, Zhang Z, Yu J, Huang N, Huo M, Wu J - PLoS ONE (2015)

Bottom Line: Many genes were associated with xenobiotic biodegradation and metal resistance functions.The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3.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.

View Article: PubMed Central - PubMed

Affiliation: School of Environment Sciences, Key Laboratory of Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China.

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.

No MeSH data available.


Related in: MedlinePlus

Rooted phylogenetic tree based on 16S rRNA gene sequence similarity of the genus Cupriavidus.Cluster analysis was based upon the neighbour-joining method with Ralstonia pickettii 12D as the outlier. The scale bar represents 5‰ sequence divergence. Numbers at branch-points are percentages of 1000 bootstrap resamplings that support the tree topology.
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pone.0132881.g002: Rooted phylogenetic tree based on 16S rRNA gene sequence similarity of the genus Cupriavidus.Cluster analysis was based upon the neighbour-joining method with Ralstonia pickettii 12D as the outlier. The scale bar represents 5‰ sequence divergence. Numbers at branch-points are percentages of 1000 bootstrap resamplings that support the tree topology.

Mentions: Phylogenetic analyses based on 16S rRNA gene sequences suggested C. gilardii CR3 fit firmly into the genus Cupriavidus strain. The result indicated that its closest relative was C. necator HPC (L) (Fig 2). The relationship between the CR3 and HPC (L) strains was also shown in their genome composition analysis. As shown in Table 2, other Cupriavidus genome sizes [4–7, 11, 17] range from 5.49 Mb to 8.55 Mb, and the smallest genome is HPC (L); CR3 comes second. Whereas, GC content of all these other members of Cupriavidus varies from 63.53% to 67.54%, and the highest GC content genome is HPC (L). And strain CR3 has the GC content at 67.55%. Gene number in other genomes ranges from 4,990 to 7,915, and the fewest gene number genomes is HPC (L). And strain CR3 contained only 4,572 genes. Both results of GC content and gene number indicate the close relationship between CR3 and HPC (L). Moreover, the CR3 genome was composed of only two chromosomes, while other finished genomes are composed of two chromosomes and at least one plasmid.


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

Wang X, Chen M, Xiao J, Hao L, Crowley DE, Zhang Z, Yu J, Huang N, Huo M, Wu J - PLoS ONE (2015)

Rooted phylogenetic tree based on 16S rRNA gene sequence similarity of the genus Cupriavidus.Cluster analysis was based upon the neighbour-joining method with Ralstonia pickettii 12D as the outlier. The scale bar represents 5‰ sequence divergence. Numbers at branch-points are percentages of 1000 bootstrap resamplings that support the tree topology.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4547698&req=5

pone.0132881.g002: Rooted phylogenetic tree based on 16S rRNA gene sequence similarity of the genus Cupriavidus.Cluster analysis was based upon the neighbour-joining method with Ralstonia pickettii 12D as the outlier. The scale bar represents 5‰ sequence divergence. Numbers at branch-points are percentages of 1000 bootstrap resamplings that support the tree topology.
Mentions: Phylogenetic analyses based on 16S rRNA gene sequences suggested C. gilardii CR3 fit firmly into the genus Cupriavidus strain. The result indicated that its closest relative was C. necator HPC (L) (Fig 2). The relationship between the CR3 and HPC (L) strains was also shown in their genome composition analysis. As shown in Table 2, other Cupriavidus genome sizes [4–7, 11, 17] range from 5.49 Mb to 8.55 Mb, and the smallest genome is HPC (L); CR3 comes second. Whereas, GC content of all these other members of Cupriavidus varies from 63.53% to 67.54%, and the highest GC content genome is HPC (L). And strain CR3 has the GC content at 67.55%. Gene number in other genomes ranges from 4,990 to 7,915, and the fewest gene number genomes is HPC (L). And strain CR3 contained only 4,572 genes. Both results of GC content and gene number indicate the close relationship between CR3 and HPC (L). Moreover, the CR3 genome was composed of only two chromosomes, while other finished genomes are composed of two chromosomes and at least one plasmid.

Bottom Line: Many genes were associated with xenobiotic biodegradation and metal resistance functions.The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3.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.

View Article: PubMed Central - PubMed

Affiliation: School of Environment Sciences, Key Laboratory of Wetland Ecology and Vegetation Restoration of National Environmental Protection, Northeast Normal University, Changchun, China.

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.

No MeSH data available.


Related in: MedlinePlus