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.
Highlights
The Rhodococcus genus comprises of Gram-positive, non-motile, non-sporulating, aerobic bacteria, with a high G+C content and mycolic acid-containing cell wall
RAST analysis of R7 genome sequence identified a total of 9,602 open reading frames (ORFs) and 62 RNAs genes (9 rRNAs and 53 tRNAs)
Comparing the akb gene cluster of RHA1 with R7, we found the same gene cluster divided in two parts and each part was allocated on two plasmids (Fig 8 Panel C): akbA1a, akbA2a, akbA3, akbA4, akbB genes were found on the pPDG5 plasmid; while akbCDEF genes, putatively coding for a complete meta-cleavage pathway, constituted by a meta-cleavage dioxygenase (AkbC), a metacleavage hydrolase product (AkbD), a hydratase (AkbE), and an aldolase (AkbF), were identified on the pPDG2 plasmid with high amino acid identity (S9 Table)
Summary
The Rhodococcus genus comprises of Gram-positive, non-motile, non-sporulating, aerobic bacteria, with a high G+C content and mycolic acid-containing cell wall. This genus was firstly proposed by Zopf and revised by Tsukamura [1] and Goodfellow and Alderson [2]; it nowadays contains nearly 50 recognized species (http://www.bacterio.net/rhodococcus.html) [3, 4]. Some of them have evolved for pathogenicity in humans, animals (i.e. R_equi) [6] and plants (i.e. R_fascians) [7] Thanks to their broad catabolic diversity and their tolerance to various environmental stress, Rhodococcus spp. play an important role in nutrient cycling and have potential applications in bioremediation, biotransformations, and biocatalysis [3]. Various Rhodococcus strains are efficient at removing sulphur from coal and petroleum products [9, 10]
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