title: Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance.
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.
authors.affiliation: Institute of Biomedical Technology, CNR, Segrate, Milano, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Orro
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
authors.forename: Martina
authors.initials: M
authors.lastname: Cappelletti
authors.affiliation: Institute of Biomedical Technology, CNR, Segrate, Milano, Italy.
authors.forename: Pasqualina
authors.initials: P
authors.lastname: D'Ursi
authors.affiliation: Institute of Biomedical Technology, CNR, Segrate, Milano, Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Milanesi
authors.affiliation: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Di Canito
authors.affiliation: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy; Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy.
authors.forename: Jessica
authors.initials: J
authors.lastname: Zampolli
authors.affiliation: Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Collina
authors.affiliation: Department of Agrifood Production and Environmental Sciences, University of Firenze, Firenze, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Decorosi
authors.affiliation: Department of Agrifood Production and Environmental Sciences, University of Firenze, Firenze, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Viti
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Fedi
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Presentato
authors.affiliation: Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Zannoni
authors.affiliation: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.
authors.forename: Patrizia
authors.initials: P
authors.lastname: Di Gennaro
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001673:Biodegradation, Environmental / Q000187:drug effects*; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D012240:Rhodococcus / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods; D015262:Xenobiotics / Q000494:pharmacology
chemical_list: D001426:Bacterial Proteins; D015262:Xenobiotics