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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

Venn Diagram.Genomic comparison of R. opacus R7 and Rhodococcus sp. BCP1 with other Rhodococcus strains, including R. jostii RHA1, R. opacus PD630, R. opacus B4, R. pyridinivorans SB4094. Each strain is represented by a colored oval. Number of predicted protein coding genes (CDSs) shared by all strains (i.e., the core genome) is in the centre. Overlapping regions show the number of CDSs conserved only within the specified genomes. Numbers in non-overlapping portions of each oval show the number of CDSs unique to each strain. The total number of protein coding genes within each genome is listed below the strain name.
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pone.0139467.g001: Venn Diagram.Genomic comparison of R. opacus R7 and Rhodococcus sp. BCP1 with other Rhodococcus strains, including R. jostii RHA1, R. opacus PD630, R. opacus B4, R. pyridinivorans SB4094. Each strain is represented by a colored oval. Number of predicted protein coding genes (CDSs) shared by all strains (i.e., the core genome) is in the centre. Overlapping regions show the number of CDSs conserved only within the specified genomes. Numbers in non-overlapping portions of each oval show the number of CDSs unique to each strain. The total number of protein coding genes within each genome is listed below the strain name.

Mentions: The percentage of the regions of each Rhodococcus strain shared amongst all the genomes under analysis, ranged between 37% and 50% values, indicating a high level of genetic variability amongst Rhodococcus genus strains. The genomic diversity in this group of bacteria is represented in the diagram of Venn shown in Fig 1. The core genome identified for the Rhodococcus strains under analysis contains 644 predicted protein coding genes, that represent around the 50% of the predicted proteome of each strain. The most shared regions identified in Rhodococcus sp. BCP1 and R. opacus R7 are located on the chromosomes; this result suggests that these regions could be characteristic of the Rhodococcus genus.


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)

Venn Diagram.Genomic comparison of R. opacus R7 and Rhodococcus sp. BCP1 with other Rhodococcus strains, including R. jostii RHA1, R. opacus PD630, R. opacus B4, R. pyridinivorans SB4094. Each strain is represented by a colored oval. Number of predicted protein coding genes (CDSs) shared by all strains (i.e., the core genome) is in the centre. Overlapping regions show the number of CDSs conserved only within the specified genomes. Numbers in non-overlapping portions of each oval show the number of CDSs unique to each strain. The total number of protein coding genes within each genome is listed below the strain name.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139467.g001: Venn Diagram.Genomic comparison of R. opacus R7 and Rhodococcus sp. BCP1 with other Rhodococcus strains, including R. jostii RHA1, R. opacus PD630, R. opacus B4, R. pyridinivorans SB4094. Each strain is represented by a colored oval. Number of predicted protein coding genes (CDSs) shared by all strains (i.e., the core genome) is in the centre. Overlapping regions show the number of CDSs conserved only within the specified genomes. Numbers in non-overlapping portions of each oval show the number of CDSs unique to each strain. The total number of protein coding genes within each genome is listed below the strain name.
Mentions: The percentage of the regions of each Rhodococcus strain shared amongst all the genomes under analysis, ranged between 37% and 50% values, indicating a high level of genetic variability amongst Rhodococcus genus strains. The genomic diversity in this group of bacteria is represented in the diagram of Venn shown in Fig 1. The core genome identified for the Rhodococcus strains under analysis contains 644 predicted protein coding genes, that represent around the 50% of the predicted proteome of each strain. The most shared regions identified in Rhodococcus sp. BCP1 and R. opacus R7 are located on the chromosomes; this result suggests that these regions could be characteristic of the Rhodococcus genus.

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