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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 aliphatic and aromatic hydrocarbon degradations.Comparative organization of genetic determinants for the tested aliphatic and aromatic hydrocarbons in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S7, S8, S9, S10 Tables) and their orientation are shown by arrow. (A) alk gene cluster; (B) prm and smo gene cluster (smo gene cluster was organized in smoA encoding a methane monooxygenase component A, smoB encoding a methane monooxygenase component B, smoD and smoC encoding a methane monooxygenase regulatory protein and a methane monooxygenase component C, respectively); (C) akb gene cluster; (D) dsz 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.g008: Comparison of gene clusters from R7 and BCP1 genomes correlated to aliphatic and aromatic hydrocarbon degradations.Comparative organization of genetic determinants for the tested aliphatic and aromatic hydrocarbons in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S7, S8, S9, S10 Tables) and their orientation are shown by arrow. (A) alk gene cluster; (B) prm and smo gene cluster (smo gene cluster was organized in smoA encoding a methane monooxygenase component A, smoB encoding a methane monooxygenase component B, smoD and smoC encoding a methane monooxygenase regulatory protein and a methane monooxygenase component C, respectively); (C) akb gene cluster; (D) dsz 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: The presence of catabolic genes involved in the growth on short-, medium- and long-chain n-alkanes was previously investigated in both R. opacus R7 and Rhodococcus sp. BCP1 strains [25, 28, 29]. Compared with these studies, the presence of only one copy of the alkB gene was confirmed in R. opacus R7, while in Rhodococcus sp. BCP1, two copies of this gene (alkB1 and alkB2) were found within the chromosome (Fig 8 Panel A). One alkB gene in each strain was organized in a cluster associated in an operon with four consecutive coding sequences (CDSs): alkB coding for an alkane monooxygenase, rubA and rubB coding for two rubredoxins, and rubred coding for a rubredoxin reductase, and, in addition, the tetR gene coding for a regulator. In BCP1 genome, an additional 1161-bp alkB gene (alkB2) was identified. This gene was not organized in operon with rubA/B and rubred genes but was associated with genes coding for a putative esterase and a long-chain-fatty-acid-CoA ligase (EC 6.2.1.3), involved in the fatty acid β-oxidation. The alkB2 gene product showed a limited similarity (57% amino acid identity) with alkB1 gene product of BCP1. The gene products of alkB1 cluster of BCP1 showed high similarity (S7 Table) with those coded by alkB cluster of R7 and with the ones of the most known bacteria belonging to the Rhodococcus genus such as R. jostii RAH1 or R. opacus PD630 [14, 16].


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 aliphatic and aromatic hydrocarbon degradations.Comparative organization of genetic determinants for the tested aliphatic and aromatic hydrocarbons in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S7, S8, S9, S10 Tables) and their orientation are shown by arrow. (A) alk gene cluster; (B) prm and smo gene cluster (smo gene cluster was organized in smoA encoding a methane monooxygenase component A, smoB encoding a methane monooxygenase component B, smoD and smoC encoding a methane monooxygenase regulatory protein and a methane monooxygenase component C, respectively); (C) akb gene cluster; (D) dsz 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

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

pone.0139467.g008: Comparison of gene clusters from R7 and BCP1 genomes correlated to aliphatic and aromatic hydrocarbon degradations.Comparative organization of genetic determinants for the tested aliphatic and aromatic hydrocarbons in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S7, S8, S9, S10 Tables) and their orientation are shown by arrow. (A) alk gene cluster; (B) prm and smo gene cluster (smo gene cluster was organized in smoA encoding a methane monooxygenase component A, smoB encoding a methane monooxygenase component B, smoD and smoC encoding a methane monooxygenase regulatory protein and a methane monooxygenase component C, respectively); (C) akb gene cluster; (D) dsz 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: The presence of catabolic genes involved in the growth on short-, medium- and long-chain n-alkanes was previously investigated in both R. opacus R7 and Rhodococcus sp. BCP1 strains [25, 28, 29]. Compared with these studies, the presence of only one copy of the alkB gene was confirmed in R. opacus R7, while in Rhodococcus sp. BCP1, two copies of this gene (alkB1 and alkB2) were found within the chromosome (Fig 8 Panel A). One alkB gene in each strain was organized in a cluster associated in an operon with four consecutive coding sequences (CDSs): alkB coding for an alkane monooxygenase, rubA and rubB coding for two rubredoxins, and rubred coding for a rubredoxin reductase, and, in addition, the tetR gene coding for a regulator. In BCP1 genome, an additional 1161-bp alkB gene (alkB2) was identified. This gene was not organized in operon with rubA/B and rubred genes but was associated with genes coding for a putative esterase and a long-chain-fatty-acid-CoA ligase (EC 6.2.1.3), involved in the fatty acid β-oxidation. The alkB2 gene product showed a limited similarity (57% amino acid identity) with alkB1 gene product of BCP1. The gene products of alkB1 cluster of BCP1 showed high similarity (S7 Table) with those coded by alkB cluster of R7 and with the ones of the most known bacteria belonging to the Rhodococcus genus such as R. jostii RAH1 or R. opacus PD630 [14, 16].

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