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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 xenobiotic compounds (Scatter Plot).A three diagonal lines represented the mean (μA), standard deviation (σA) and double standard deviation (2σA) of the difference activity (ΔA) of the two genomes overlapped. It highlighted regions of specificity for the genomes of the two strains on the tails of the gaussian distribution: R. opacus R7 specific compounds are in regions where ΔA <-σA (red points) and Rhodococcus sp. BCP1 specific compounds are on the other extreme points: ΔA > +σA (green points). Numbers in the plot represent the tested chemicals reported in the Table 8.
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pone.0139467.g007: Phenotype Microarray PM with xenobiotic compounds (Scatter Plot).A three diagonal lines represented the mean (μA), standard deviation (σA) and double standard deviation (2σA) of the difference activity (ΔA) of the two genomes overlapped. It highlighted regions of specificity for the genomes of the two strains on the tails of the gaussian distribution: R. opacus R7 specific compounds are in regions where ΔA <-σA (red points) and Rhodococcus sp. BCP1 specific compounds are on the other extreme points: ΔA > +σA (green points). Numbers in the plot represent the tested chemicals reported in the Table 8.

Mentions: R. opacus R7 and Rhodococcus sp. BCP1 metabolic activity was tested on 41 organic/xenobiotic compounds supplied as sole carbon and energy source. The tested substrates belong to four chemical categories including: 1) aliphatic hydrocarbons and cycloalkanes, 2) BTEX and other aromatic compounds, 3) polycyclic aromatics (PAHs), 4) naphthenic acids and other carboxylic acids. Phenotype Microarray analysis was conducted following both the tetrazolium-based metabolic activity and the growth measured as OD590 increment over 72 h. Both strains were able to grow on several hydrocarbons and their putative metabolic intermediates (Fig 7) (S6 Table). Based on the growth results in presence of several linear- and cycloalkanes, Rhodococcus sp. BCP1 showed a general high activity on all n-alkanes tested ranging from n-hexane to n-hexatriacontane; while R. opacus R7 had a preferential activity on n-dodecane, n-tetradecane, n-hexadecane and n-eicosane. These data confirmed previous works on BCP1 and R7 strains reported by Cappelletti et al., 2011 and by Zampolli et al., 2014 [29, 25]. Moreover, results showed that R7 strain was not able to grow in presence of odd-alkanes, except for n-heptadecane. Both the two strains evidenced activity on cyclohexane and cyclohexanone; however these substrates were preferentially utilized by BCP1 strain. In addition, high level of activity was revealed for both R7 and BCP1 strains on fuel oil, a mixture of different alkanes, including prystane and phytane.


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 xenobiotic compounds (Scatter Plot).A three diagonal lines represented the mean (μA), standard deviation (σA) and double standard deviation (2σA) of the difference activity (ΔA) of the two genomes overlapped. It highlighted regions of specificity for the genomes of the two strains on the tails of the gaussian distribution: R. opacus R7 specific compounds are in regions where ΔA <-σA (red points) and Rhodococcus sp. BCP1 specific compounds are on the other extreme points: ΔA > +σA (green points). Numbers in the plot represent the tested chemicals reported in the Table 8.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139467.g007: Phenotype Microarray PM with xenobiotic compounds (Scatter Plot).A three diagonal lines represented the mean (μA), standard deviation (σA) and double standard deviation (2σA) of the difference activity (ΔA) of the two genomes overlapped. It highlighted regions of specificity for the genomes of the two strains on the tails of the gaussian distribution: R. opacus R7 specific compounds are in regions where ΔA <-σA (red points) and Rhodococcus sp. BCP1 specific compounds are on the other extreme points: ΔA > +σA (green points). Numbers in the plot represent the tested chemicals reported in the Table 8.
Mentions: R. opacus R7 and Rhodococcus sp. BCP1 metabolic activity was tested on 41 organic/xenobiotic compounds supplied as sole carbon and energy source. The tested substrates belong to four chemical categories including: 1) aliphatic hydrocarbons and cycloalkanes, 2) BTEX and other aromatic compounds, 3) polycyclic aromatics (PAHs), 4) naphthenic acids and other carboxylic acids. Phenotype Microarray analysis was conducted following both the tetrazolium-based metabolic activity and the growth measured as OD590 increment over 72 h. Both strains were able to grow on several hydrocarbons and their putative metabolic intermediates (Fig 7) (S6 Table). Based on the growth results in presence of several linear- and cycloalkanes, Rhodococcus sp. BCP1 showed a general high activity on all n-alkanes tested ranging from n-hexane to n-hexatriacontane; while R. opacus R7 had a preferential activity on n-dodecane, n-tetradecane, n-hexadecane and n-eicosane. These data confirmed previous works on BCP1 and R7 strains reported by Cappelletti et al., 2011 and by Zampolli et al., 2014 [29, 25]. Moreover, results showed that R7 strain was not able to grow in presence of odd-alkanes, except for n-heptadecane. Both the two strains evidenced activity on cyclohexane and cyclohexanone; however these substrates were preferentially utilized by BCP1 strain. In addition, high level of activity was revealed for both R7 and BCP1 strains on fuel oil, a mixture of different alkanes, including prystane and phytane.

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