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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 carboxylated hydrocarbon degradations.Comparative organization of genetic determinants for naphthenic acids (as reference compounds of carboxylated hydrocarbons and putative intermediates) in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S14 Table) and their orientation are shown by arrow. The following genes encode for: benK, benzoate transporter; orf1, O-antigen acetylase; iclR, transcriptional regulator IclR family; tetR, transcriptional regulator, TetR family; orf 2 and orf 3, permease; ABC transp, ABC transporter; sc-DH, probable short-chain dehydrogenase; orf4, permease. 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.g010: Comparison of gene clusters from R7 and BCP1 genomes correlated to carboxylated hydrocarbon degradations.Comparative organization of genetic determinants for naphthenic acids (as reference compounds of carboxylated hydrocarbons and putative intermediates) in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S14 Table) and their orientation are shown by arrow. The following genes encode for: benK, benzoate transporter; orf1, O-antigen acetylase; iclR, transcriptional regulator IclR family; tetR, transcriptional regulator, TetR family; orf 2 and orf 3, permease; ABC transp, ABC transporter; sc-DH, probable short-chain dehydrogenase; orf4, permease. 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 ability of the two strains to grow on these contaminants, the putative gene clusters involved in this degradation were investigated. In literature, few metabolic studies are available on the biodegradation of naphthenic acids (NAs) based on cyclohexane ring i.e. cyclohexane carboxylic acid (CHCA); while none has been focused on cyclopentane ring i.e. cyclopentane carboxylic acid (CPCA). Although no genetic information was provided in these studies [48, 49], the metabolism of CHCA was described to follow two main routes: (i) aromatization of the cycloalkane ring to produce hydroxybenzoate before ring opening [48], or (ii) activation of cycloalkane ring as CoA thioester-derivative that is further degraded through β-oxidation steps [49]. Iwaki and co-workers identified the pobA gene to have an essential role for the growth on CHCA by Corynebacterium cyclohexanicum. This gene codes for 4-hydroxybenzoate (4-HBA) 3-hydroxylase generally described to be responsible for the conversion of 4-hydroxybenzoate to protocatechuate, a common intermediate in the degradation of various aromatic compounds. Iwaki and co-workers [48] demonstrated the involvement of pobA product in CHCA catabolism by Corynebacterium strain downstream of the formation of 4-hydroxybenzoate from CHCA through several oxidation steps. One gene homologous to pobA was identified in both BCP1 and R7 genomes and its product was annotated as p-hydroxybenzoate hydroxylase in RAST server. Similarly to what found in Corynebacterium strain, pobA gene was flanked by a gene coding for an IclR-type transcriptional regulator. The genomic region including pobA in R7 included also the alkB gene cluster, TetR-like regulator and a BenK transporter and the same organization was maintained between RHA1 and R7. On the contrary, the genomic organization of BCP1 region with pobA was different from those of R7 and RHA1 and included a permease coding gene and several oxidoreductases (Fig 10).


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 carboxylated hydrocarbon degradations.Comparative organization of genetic determinants for naphthenic acids (as reference compounds of carboxylated hydrocarbons and putative intermediates) in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S14 Table) and their orientation are shown by arrow. The following genes encode for: benK, benzoate transporter; orf1, O-antigen acetylase; iclR, transcriptional regulator IclR family; tetR, transcriptional regulator, TetR family; orf 2 and orf 3, permease; ABC transp, ABC transporter; sc-DH, probable short-chain dehydrogenase; orf4, permease. 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.g010: Comparison of gene clusters from R7 and BCP1 genomes correlated to carboxylated hydrocarbon degradations.Comparative organization of genetic determinants for naphthenic acids (as reference compounds of carboxylated hydrocarbons and putative intermediates) in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S14 Table) and their orientation are shown by arrow. The following genes encode for: benK, benzoate transporter; orf1, O-antigen acetylase; iclR, transcriptional regulator IclR family; tetR, transcriptional regulator, TetR family; orf 2 and orf 3, permease; ABC transp, ABC transporter; sc-DH, probable short-chain dehydrogenase; orf4, permease. 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 ability of the two strains to grow on these contaminants, the putative gene clusters involved in this degradation were investigated. In literature, few metabolic studies are available on the biodegradation of naphthenic acids (NAs) based on cyclohexane ring i.e. cyclohexane carboxylic acid (CHCA); while none has been focused on cyclopentane ring i.e. cyclopentane carboxylic acid (CPCA). Although no genetic information was provided in these studies [48, 49], the metabolism of CHCA was described to follow two main routes: (i) aromatization of the cycloalkane ring to produce hydroxybenzoate before ring opening [48], or (ii) activation of cycloalkane ring as CoA thioester-derivative that is further degraded through β-oxidation steps [49]. Iwaki and co-workers identified the pobA gene to have an essential role for the growth on CHCA by Corynebacterium cyclohexanicum. This gene codes for 4-hydroxybenzoate (4-HBA) 3-hydroxylase generally described to be responsible for the conversion of 4-hydroxybenzoate to protocatechuate, a common intermediate in the degradation of various aromatic compounds. Iwaki and co-workers [48] demonstrated the involvement of pobA product in CHCA catabolism by Corynebacterium strain downstream of the formation of 4-hydroxybenzoate from CHCA through several oxidation steps. One gene homologous to pobA was identified in both BCP1 and R7 genomes and its product was annotated as p-hydroxybenzoate hydroxylase in RAST server. Similarly to what found in Corynebacterium strain, pobA gene was flanked by a gene coding for an IclR-type transcriptional regulator. The genomic region including pobA in R7 included also the alkB gene cluster, TetR-like regulator and a BenK transporter and the same organization was maintained between RHA1 and R7. On the contrary, the genomic organization of BCP1 region with pobA was different from those of R7 and RHA1 and included a permease coding gene and several oxidoreductases (Fig 10).

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