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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

Phenotype Microarray PM with different carboxylic acids-alcohols, amines, amides, esters, fatty acids and polymers-amino acids as carbon sources.Metabolic differences among R. opacus R7 and Rhodococcus sp. BCP1 in presence of carboxylic acids (BI, BII), of alcohols, amines, amides, esters, fatty acids, polymers (C), and amino acids (D). Based on activity values of phenotype microarray analysis, threshold values were established for every plates. Determined thresholds were high (green), upper middle (light green), lower middle (orange) and low (red) for high, upper middle, lower middle and low activity, respectively.
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pone.0139467.g004: Phenotype Microarray PM with different carboxylic acids-alcohols, amines, amides, esters, fatty acids and polymers-amino acids as carbon sources.Metabolic differences among R. opacus R7 and Rhodococcus sp. BCP1 in presence of carboxylic acids (BI, BII), of alcohols, amines, amides, esters, fatty acids, polymers (C), and amino acids (D). Based on activity values of phenotype microarray analysis, threshold values were established for every plates. Determined thresholds were high (green), upper middle (light green), lower middle (orange) and low (red) for high, upper middle, lower middle and low activity, respectively.

Mentions: The 190 carbon sources were divided in different chemical categories, including carbohydrates, carboxylic acids, nitrogen containing compounds, alcohols, amides, amines, esters, fatty acids, polymers (S3 Table). R7 and BCP1 strains were metabolically active on the following monosaccharides: α-D-glucose, D-fructose, D-ribose, L-rhamnose, L-lyxose and 2-deoxy-D-ribose. Both the strains could oxidize the three disaccharides composed by glucose and fructose monomers (sucrose, palatinose and turanose) as well as the trisaccharide D-melezitose (formed by D-turanose and D-glucose). They showed high metabolic activity on the sugar alcohols D-sorbitol, D-mannitol and D-arabitol. Amongst the carbon sources utilized, R7 generally showed higher activities compared to BCP1 (69% of the carbon sources utilized by R7 gave high activity level vs 41% for BCP1) (Fig 3 Panel AI, AII). Both the strains could utilize a wide range of carboxylic acids (Fig 4 Panel BI, BII). Several short-chain carboxylate compounds (C2-C6) were oxidized by R7 and BCP1 strains including acetic and propionic acids as well as other common intermediates in central metabolism such as pyruvic, succinic, and citric acids. They both oxidized and grew on gluconic acid that is degraded by the pentose phosphate pathway. Carboxylate metabolism also included the C10 dicarboxylate sebacic acid whose metabolism involves the β-oxidation pathway. β-oxidation could also explain the activity on Tween 40 and Tween 80 compounds by BCP1 and R7 (Fig 4 Panel C). Tween 20 did not support growth of the two Rhodococcus spp. probably because of the toxicity resulting from the hydrolytic process of this compound [16]. Interestingly, the utilization of Tween compounds is considered diagnostic of the substrate specificity of bacteria toward the use of hydrocarbons as a source of carbon and energy [43]. The complexity of fatty acids β-oxidation pathway present in BCP1 and R7 genomes is consistent with the number of genes coding for each of the oxidation steps (S4 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)

Phenotype Microarray PM with different carboxylic acids-alcohols, amines, amides, esters, fatty acids and polymers-amino acids as carbon sources.Metabolic differences among R. opacus R7 and Rhodococcus sp. BCP1 in presence of carboxylic acids (BI, BII), of alcohols, amines, amides, esters, fatty acids, polymers (C), and amino acids (D). Based on activity values of phenotype microarray analysis, threshold values were established for every plates. Determined thresholds were high (green), upper middle (light green), lower middle (orange) and low (red) for high, upper middle, lower middle and low activity, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139467.g004: Phenotype Microarray PM with different carboxylic acids-alcohols, amines, amides, esters, fatty acids and polymers-amino acids as carbon sources.Metabolic differences among R. opacus R7 and Rhodococcus sp. BCP1 in presence of carboxylic acids (BI, BII), of alcohols, amines, amides, esters, fatty acids, polymers (C), and amino acids (D). Based on activity values of phenotype microarray analysis, threshold values were established for every plates. Determined thresholds were high (green), upper middle (light green), lower middle (orange) and low (red) for high, upper middle, lower middle and low activity, respectively.
Mentions: The 190 carbon sources were divided in different chemical categories, including carbohydrates, carboxylic acids, nitrogen containing compounds, alcohols, amides, amines, esters, fatty acids, polymers (S3 Table). R7 and BCP1 strains were metabolically active on the following monosaccharides: α-D-glucose, D-fructose, D-ribose, L-rhamnose, L-lyxose and 2-deoxy-D-ribose. Both the strains could oxidize the three disaccharides composed by glucose and fructose monomers (sucrose, palatinose and turanose) as well as the trisaccharide D-melezitose (formed by D-turanose and D-glucose). They showed high metabolic activity on the sugar alcohols D-sorbitol, D-mannitol and D-arabitol. Amongst the carbon sources utilized, R7 generally showed higher activities compared to BCP1 (69% of the carbon sources utilized by R7 gave high activity level vs 41% for BCP1) (Fig 3 Panel AI, AII). Both the strains could utilize a wide range of carboxylic acids (Fig 4 Panel BI, BII). Several short-chain carboxylate compounds (C2-C6) were oxidized by R7 and BCP1 strains including acetic and propionic acids as well as other common intermediates in central metabolism such as pyruvic, succinic, and citric acids. They both oxidized and grew on gluconic acid that is degraded by the pentose phosphate pathway. Carboxylate metabolism also included the C10 dicarboxylate sebacic acid whose metabolism involves the β-oxidation pathway. β-oxidation could also explain the activity on Tween 40 and Tween 80 compounds by BCP1 and R7 (Fig 4 Panel C). Tween 20 did not support growth of the two Rhodococcus spp. probably because of the toxicity resulting from the hydrolytic process of this compound [16]. Interestingly, the utilization of Tween compounds is considered diagnostic of the substrate specificity of bacteria toward the use of hydrocarbons as a source of carbon and energy [43]. The complexity of fatty acids β-oxidation pathway present in BCP1 and R7 genomes is consistent with the number of genes coding for each of the oxidation steps (S4 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