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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

Comparison of gene clusters from R7 and BCP1 genomes correlated to xenobiotic peripheral pathways.Comparative organization of genetic determinants for xenobiotic peripheral pathways in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S15, S16, S17 and S18 Tables) and their orientation are shown by arrow. (A) cat gene cluster; (B) pca gene cluster; (C) paa gene cluster; (D) hmg gene cluster. When not specified, it means that genes were located on chromosome. Genes with unknown or hypothetical functions were reported as HP. Double slash indicates a distances between two genes more than 1 kb within the same plasmid or chromosome.
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pone.0139467.g011: Comparison of gene clusters from R7 and BCP1 genomes correlated to xenobiotic peripheral pathways.Comparative organization of genetic determinants for xenobiotic peripheral pathways in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S15, S16, S17 and S18 Tables) and their orientation are shown by arrow. (A) cat gene cluster; (B) pca gene cluster; (C) paa gene cluster; (D) hmg gene cluster. When not specified, it means that genes were located on chromosome. Genes with unknown or hypothetical functions were reported as HP. Double slash indicates a distances between two genes more than 1 kb within the same plasmid or chromosome.

Mentions: Considering the aromatic compounds that R7 and BCP1 can metabolize, four different peripheral pathways for the catabolism of several xenobiotics can be predicted, which include catechol (cat genes), protocatechuate (pca genes), phenylacetate (paa genes) and homogentisate (hmg genes) pathways. Genes responsable for such catabolic pathways have been reported in several bacteria [52], in particular in R. jostii RHA1. We performed a sequence comparison analysis to identify the genes predicted to be involved in these pathways in R. opacus R7 and in R. sp. BCP1. R7 genome contains several genes potentially involved in catechol catabolism. It shows six catechol 1,2-dioxygenases (five on the chromosome and one on pPDG2 plasmid), and three catechol 2,3-dioxygenases (one on the chromosome, one on pPDG2 and one on pPDG5 plasmid). BCP1 genome presents only two catechol 1,2-dioxygenases and one catechol 2,3-dioxygenase on the chromosome. These aspects might be explained on the basis of the significant difference of their genome size. Two catechol dioxygenase genes, amongst those identified on R7 chromosome, were organized in cluster (Fig 11 Panel A). The first cat gene cluster presented catA (catA1), coding for a catechol 1,2-dioxygenase, catB (catB1) coding for a muconate cycloisomerase and catC coding for a muconolactone isomerase. The same gene cluster was identified in RHA1 and, compared to R7, it showed high protein identity (96–99%). The second cat gene cluster identified in R7 lacked of catC gene; moreover, CatA2 (catA2) and CatB2 (catB2) were not found homologous to RHA1 genes (S15 Table). Rhodococcus sp. BCP1 presented only one copy of cat gene cluster with the same organization of RHA1 and R7; BCP1 cat genes showed high similarity (70–90%) with those of RHA1 and R7 strains as reported in table (S15 Table).


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)

Comparison of gene clusters from R7 and BCP1 genomes correlated to xenobiotic peripheral pathways.Comparative organization of genetic determinants for xenobiotic peripheral pathways in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S15, S16, S17 and S18 Tables) and their orientation are shown by arrow. (A) cat gene cluster; (B) pca gene cluster; (C) paa gene cluster; (D) hmg gene cluster. When not specified, it means that genes were located on chromosome. Genes with unknown or hypothetical functions were reported as HP. Double slash indicates a distances between two genes more than 1 kb within the same plasmid or chromosome.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139467.g011: Comparison of gene clusters from R7 and BCP1 genomes correlated to xenobiotic peripheral pathways.Comparative organization of genetic determinants for xenobiotic peripheral pathways in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S15, S16, S17 and S18 Tables) and their orientation are shown by arrow. (A) cat gene cluster; (B) pca gene cluster; (C) paa gene cluster; (D) hmg gene cluster. When not specified, it means that genes were located on chromosome. Genes with unknown or hypothetical functions were reported as HP. Double slash indicates a distances between two genes more than 1 kb within the same plasmid or chromosome.
Mentions: Considering the aromatic compounds that R7 and BCP1 can metabolize, four different peripheral pathways for the catabolism of several xenobiotics can be predicted, which include catechol (cat genes), protocatechuate (pca genes), phenylacetate (paa genes) and homogentisate (hmg genes) pathways. Genes responsable for such catabolic pathways have been reported in several bacteria [52], in particular in R. jostii RHA1. We performed a sequence comparison analysis to identify the genes predicted to be involved in these pathways in R. opacus R7 and in R. sp. BCP1. R7 genome contains several genes potentially involved in catechol catabolism. It shows six catechol 1,2-dioxygenases (five on the chromosome and one on pPDG2 plasmid), and three catechol 2,3-dioxygenases (one on the chromosome, one on pPDG2 and one on pPDG5 plasmid). BCP1 genome presents only two catechol 1,2-dioxygenases and one catechol 2,3-dioxygenase on the chromosome. These aspects might be explained on the basis of the significant difference of their genome size. Two catechol dioxygenase genes, amongst those identified on R7 chromosome, were organized in cluster (Fig 11 Panel A). The first cat gene cluster presented catA (catA1), coding for a catechol 1,2-dioxygenase, catB (catB1) coding for a muconate cycloisomerase and catC coding for a muconolactone isomerase. The same gene cluster was identified in RHA1 and, compared to R7, it showed high protein identity (96–99%). The second cat gene cluster identified in R7 lacked of catC gene; moreover, CatA2 (catA2) and CatB2 (catB2) were not found homologous to RHA1 genes (S15 Table). Rhodococcus sp. BCP1 presented only one copy of cat gene cluster with the same organization of RHA1 and R7; BCP1 cat genes showed high similarity (70–90%) with those of RHA1 and R7 strains as reported in table (S15 Table).

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