Genome and phenotype microarray analyses of rhodococcus sp. BCP1 and rhodococcus opacus R7: Genetic determinants and metabolic abilities with environmental relevance

6533b853fe1ef96bd12ac0ab

RESEARCH PRODUCT

Genome and phenotype microarray analyses of rhodococcus sp. BCP1 and rhodococcus opacus R7: Genetic determinants and metabolic abilities with environmental relevance

Francesca Decorosi Patrizia Di Gennaro Davide Zannoni Alessandra Di Canito Luciano Milanesi Alessandro Orro Stefano Fedi Elena Collina Pasqualina D'ursi Alessandro Presentato Jessica Zampolli Carlo Viti Martina Cappelletti

subject

AROMATIC-COMPOUNDS; GENUS RHODOCOCCUS; HIGH-THROUGHPUT; PATHWAY; DEGRADATION; BIODEGRADATION; EQUI; PERFORMANCE; CATABOLISM Genomics Rhodococcus Gene prediction Bacterial Protein lcsh:Medicine Biology Genome Xenobiotics Rhodococcus opacus Bacterial Proteins Rhodococcus lcsh:Science Gene Phylogeny Genetics Comparative genomics Multidisciplinary lcsh:R Metabolic Networks and Pathway Phenotype microarray High-Throughput Nucleotide Sequencing Rhodococcus sp. BCP1 Rhodococcus opacus R7 Genome analysis Gene Expression Regulation Bacterial Genomics Sequence Analysis DNA biology.organism_classification BIO/19 - MICROBIOLOGIA GENERALE Biodegradation Environmental Phenotype Proteome Genomic lcsh:Q Phenotype Microarray Rhodococcus Metabolic Networks and Pathways Rhodococcu hydrocarbon degradation Research Article

description

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, includ- ing 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. More- over, 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 multi- ple 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 Rhodo- coccus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

year	journal	country	edition	language
2015-01-01

10.1371/journal.pone.0139467 http://hdl.handle.net/10281/100176