Table 1.
Accession Number of the main genes of R. opacus R7 and Rhodococcus sp. BCP1 strains discussed in this paper.
Table 2.
Number of functions in each of the RAST category.
Table 3.
Numbers of metabolic pathways deriving from metabolic reconstruction of R. opacus R7 and Rhodococcus sp. BCP1 genomes.
Table 4.
Similarity scores for Rhodococcus genomes under analysis.
Values in the matrix represent the percent of bases shared in regions longer than 300 bp.
Table 5.
Numbers of similar regions that maintain the same order in each pair of genomes respect the total number of similar regions in R7 and BCP1 strains.
Fig 1.
Genomic comparison of R. opacus R7 and Rhodococcus sp. BCP1 with other Rhodococcus strains, including R. jostii RHA1, R. opacus PD630, R. opacus B4, R. pyridinivorans SB4094. Each strain is represented by a colored oval. Number of predicted protein coding genes (CDSs) shared by all strains (i.e., the core genome) is in the centre. Overlapping regions show the number of CDSs conserved only within the specified genomes. Numbers in non-overlapping portions of each oval show the number of CDSs unique to each strain. The total number of protein coding genes within each genome is listed below the strain name.
Table 6.
Unique regions larger than 4 kb identified in R7 and BCP1 strains.
Table 7.
Uniqueness characteristics of the six compared Rhodococcus spp. strains.
Fig 2.
Phylogenetic analysis of R. opacus R7 and Rhodococcus sp. BCP1 based on sequence alignments with reference strains of Rhodococcus genus. The tree was constructed based on concatemer sequences of four marker genes of the 28 strains: 16S rRNA gene, secY gene, rpoC gene and rpsA gene.
Fig 3.
Phenotype Microarray PM with different carbohydrates as carbon sources.
Metabolic differences among R. opacus R7 and Rhodococcus sp. BCP1 in presence of carbohydrates (AI, AII). 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.
Fig 4.
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.
Fig 5.
Phenotype Microarray PM with different Nitrogen sources.
Metabolic differences among R. opacus R7 and Rhodococcus sp. BCP1 in presence of different Nitrogen sources (AI, AII, AIII). 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.
Fig 6.
Phenotype Microarray PM with different Phosphorous and Sulphur Sources.
Metabolic differences among R. opacus R7 and Rhodococcus sp. BCP1 in presence of different Phosphorous Sources (AI, AII) and Sulphur sources (B). 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.
Fig 7.
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.
Table 8.
List of the xenobiotic compounds tested in phenotype microarray analysis and EC the numbers of the enzymes identified in R7 and BCP1 genomes and predicted to be involved in their metabolisms by DuctApe software.
Fig 8.
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.
Fig 9.
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.
Fig 10.
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.
Fig 11.
Comparison of gene clusters from R7 and BCP1 genomes correlated to xenobiotic peripheral pathways.
Comparative organization of genetic determinants for xenobiotic peripheral pathways in R. opacus R7 and Rhodococcus sp. BCP1 with R. jostii RHA1 as reference strain. Predicted genes (listed in S15, S16, S17 and S18 Tables) and their orientation are shown by arrow. (A) cat gene cluster; (B) pca gene cluster; (C) paa gene cluster; (D) hmg 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.