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Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance.

Orro A, Cappelletti M, D'Ursi P, Milanesi L, Di Canito A, Zampolli J, Collina E, Decorosi F, Viti C, Fedi S, Presentato A, Zannoni D, Di Gennaro P - PLoS ONE (2015)

Bottom Line: Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1.According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work.Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biomedical Technology, CNR, Segrate, Milano, Italy.

ABSTRACT
In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

No MeSH data available.


Related in: MedlinePlus

PhylogeneticTree.Phylogenetic analysis of R. opacus R7 and Rhodococcus sp. BCP1 based on sequence alignments with reference strains of Rhodococcus genus. The tree was constructed based on concatemer sequences of four marker genes of the 28 strains: 16S rRNA gene, secY gene, rpoC gene and rpsA gene.
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pone.0139467.g002: PhylogeneticTree.Phylogenetic analysis of R. opacus R7 and Rhodococcus sp. BCP1 based on sequence alignments with reference strains of Rhodococcus genus. The tree was constructed based on concatemer sequences of four marker genes of the 28 strains: 16S rRNA gene, secY gene, rpoC gene and rpsA gene.

Mentions: To develop a framework for resolving the phylogeny of the two Rhodococcus strains, we constructed a multi-locus sequence analysis (MLSA) maximum likelihood (ML) tree based on four marker genes (16SrRNA, secY, rpoC and rpsA) that were previously identified as conserved and informative for the bacteria classification [35]. The phylogenetic tree based on sequence alignments with reference strains of Rhodococcus genus show the distinctly defined phylogenetic positions of Rhodococcus sp. BCP1 and R. opacus R7 (Fig 2). This is the first taxonomical study of R. opacus R7 that correlates R7 strain to Rhodococcus opacus and Rhodococcus wratislaviensis species in a clade that also includes R. jostii RHA1. Rhodococcus sp. BCP1 clusters with R. aetherivorans strains in a clade including also R. ruber species. These results on BCP1 are in line with previous phylogenetic analyses based on Rhodococcus 16S rDNA genes and 1-alkane monooxygenase (AlkB) protein sequences reported by Táncsics et al., 2015 [42]. In conclusion, Rhodococcus sp. BCP1 can be taxonomically related to R. aetherivorans species. The importance of this taxonomic definition is related to the fact that BCP1 strain genome is the first complete genome available in database for R. aetherivorans species.


Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance.

Orro A, Cappelletti M, D'Ursi P, Milanesi L, Di Canito A, Zampolli J, Collina E, Decorosi F, Viti C, Fedi S, Presentato A, Zannoni D, Di Gennaro P - PLoS ONE (2015)

PhylogeneticTree.Phylogenetic analysis of R. opacus R7 and Rhodococcus sp. BCP1 based on sequence alignments with reference strains of Rhodococcus genus. The tree was constructed based on concatemer sequences of four marker genes of the 28 strains: 16S rRNA gene, secY gene, rpoC gene and rpsA gene.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591350&req=5

pone.0139467.g002: PhylogeneticTree.Phylogenetic analysis of R. opacus R7 and Rhodococcus sp. BCP1 based on sequence alignments with reference strains of Rhodococcus genus. The tree was constructed based on concatemer sequences of four marker genes of the 28 strains: 16S rRNA gene, secY gene, rpoC gene and rpsA gene.
Mentions: To develop a framework for resolving the phylogeny of the two Rhodococcus strains, we constructed a multi-locus sequence analysis (MLSA) maximum likelihood (ML) tree based on four marker genes (16SrRNA, secY, rpoC and rpsA) that were previously identified as conserved and informative for the bacteria classification [35]. The phylogenetic tree based on sequence alignments with reference strains of Rhodococcus genus show the distinctly defined phylogenetic positions of Rhodococcus sp. BCP1 and R. opacus R7 (Fig 2). This is the first taxonomical study of R. opacus R7 that correlates R7 strain to Rhodococcus opacus and Rhodococcus wratislaviensis species in a clade that also includes R. jostii RHA1. Rhodococcus sp. BCP1 clusters with R. aetherivorans strains in a clade including also R. ruber species. These results on BCP1 are in line with previous phylogenetic analyses based on Rhodococcus 16S rDNA genes and 1-alkane monooxygenase (AlkB) protein sequences reported by Táncsics et al., 2015 [42]. In conclusion, Rhodococcus sp. BCP1 can be taxonomically related to R. aetherivorans species. The importance of this taxonomic definition is related to the fact that BCP1 strain genome is the first complete genome available in database for R. aetherivorans species.

Bottom Line: Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1.According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work.Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biomedical Technology, CNR, Segrate, Milano, Italy.

ABSTRACT
In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

No MeSH data available.


Related in: MedlinePlus