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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 polycyclic aromatic hydrocarbon degradations.Comparative organization of genetic determinants for naphthalene and biphenyl (as reference compounds of PAH and putative intermediates) in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S11, S12 and S13 Tables) and their orientation are shown by arrow. (A) nar gene cluster; (B) gen gene cluster; (C) bph gene cluster organization. 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.g009: Comparison of gene clusters from R7 and BCP1 genomes correlated to polycyclic aromatic hydrocarbon degradations.Comparative organization of genetic determinants for naphthalene and biphenyl (as reference compounds of PAH and putative intermediates) in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S11, S12 and S13 Tables) and their orientation are shown by arrow. (A) nar gene cluster; (B) gen gene cluster; (C) bph gene cluster organization. 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: In a previous work, genes involved in naphthalene (nar gene cluster) and salicylate (gen gene cluster) degradation were found in R. opacus R7 [24]. The whole genome sequence analysis pointed out that nar gene cluster is located in pPDG4 plasmid in R7 strain and that the same cluster was found in pBMC2 in Rhodococcus sp. BCP1 (Fig 9 Panel A); this genomic region identified in pBMC2 is the same identified as akb gene cluster in BCP1. In S11 Table, protein identities are reported. The whole genome sequence analysis revealed the presence of orf7 within the cluster, as in R7 strain, while any of the other six CDSs identified in R7 were found in BCP1 strain. An homologous nar gene cluster was not found in the reference strain R. jostii RHA1. The lower naphthalene catabolic pathway was previously investigated in R7 and it was hypothesized that the gen gene cluster was located far from the nar region as no amplification of the middle region was obtained. Genome sequence analysis confirmed these data (Fig 9 Panel B). Moreover, two copies of the gene clusters involved in naphthalene lower pathway were found in R7: one in the pPDG4 plasmid distant 12.4 kb from nar gene cluster; the other in the pPDG1 plasmid, but lacking of genL gene. Comparison of this cluster with genome sequence of BCP1 revealed that some genes involved in gentisate oxidation were found: genH and genI genes were found in the chromosome with high protein identity (around 80%), followed by genL gene that showed a protein identity of 48% with the homologous genes of R7. Instead, genes involved in salicylate degradation, genA, B, C were found in different regions of the BCP1 chromosome showing a lower amino acid identity as reported in S12 Table. This could be the reason of the low activity level shown by BCP1 during the growth on salicylic acid.


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 polycyclic aromatic hydrocarbon degradations.Comparative organization of genetic determinants for naphthalene and biphenyl (as reference compounds of PAH and putative intermediates) in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S11, S12 and S13 Tables) and their orientation are shown by arrow. (A) nar gene cluster; (B) gen gene cluster; (C) bph gene cluster organization. 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.g009: Comparison of gene clusters from R7 and BCP1 genomes correlated to polycyclic aromatic hydrocarbon degradations.Comparative organization of genetic determinants for naphthalene and biphenyl (as reference compounds of PAH and putative intermediates) in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S11, S12 and S13 Tables) and their orientation are shown by arrow. (A) nar gene cluster; (B) gen gene cluster; (C) bph gene cluster organization. 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: In a previous work, genes involved in naphthalene (nar gene cluster) and salicylate (gen gene cluster) degradation were found in R. opacus R7 [24]. The whole genome sequence analysis pointed out that nar gene cluster is located in pPDG4 plasmid in R7 strain and that the same cluster was found in pBMC2 in Rhodococcus sp. BCP1 (Fig 9 Panel A); this genomic region identified in pBMC2 is the same identified as akb gene cluster in BCP1. In S11 Table, protein identities are reported. The whole genome sequence analysis revealed the presence of orf7 within the cluster, as in R7 strain, while any of the other six CDSs identified in R7 were found in BCP1 strain. An homologous nar gene cluster was not found in the reference strain R. jostii RHA1. The lower naphthalene catabolic pathway was previously investigated in R7 and it was hypothesized that the gen gene cluster was located far from the nar region as no amplification of the middle region was obtained. Genome sequence analysis confirmed these data (Fig 9 Panel B). Moreover, two copies of the gene clusters involved in naphthalene lower pathway were found in R7: one in the pPDG4 plasmid distant 12.4 kb from nar gene cluster; the other in the pPDG1 plasmid, but lacking of genL gene. Comparison of this cluster with genome sequence of BCP1 revealed that some genes involved in gentisate oxidation were found: genH and genI genes were found in the chromosome with high protein identity (around 80%), followed by genL gene that showed a protein identity of 48% with the homologous genes of R7. Instead, genes involved in salicylate degradation, genA, B, C were found in different regions of the BCP1 chromosome showing a lower amino acid identity as reported in S12 Table. This could be the reason of the low activity level shown by BCP1 during the growth on salicylic acid.

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