Abstract
The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.
Highlights
The genus Rhodococcus comprises Gram-p ositive actinobacteria that are widely distributed in the environment, including in soil and water from tropical, desert and artic habitats [1,2,3]
Garrido-Sanz et al, Microbial Genomics 2020;6 including hydrocarbon-p olluted soils [10], results from the presence of multiple catabolic pathways predominantly encoded by extrachromosomal replicons [11, 12], which allow rhodococci to degrade a wide range of chemical structures, including aliphatic hydrocarbons, polycyclic aromatic hydrocarbons (PAHs) and halogenated compounds such as polychlorinated biphenyls (PCBs), nitroaromatics, heterocyclic compounds and herbicides [8, 10, 13, 14]
The telomeres of the linear replicons of WAY2 are typical actinobacterial invertrons, with terminal inverted repeats (TIRs) and the central GCTXCGC motif, as described elsewhere [54, 55]. These telomeres are similar to those found in other linear replicons in rhodococci, such as R. jostii RHA1 and Rhodococcus opacus strains B4 and 1CP (File S2)
Summary
The genus Rhodococcus comprises Gram-p ositive actinobacteria that are widely distributed in the environment, including in soil and water from tropical, desert and artic habitats [1,2,3]. Dioxygenase systems have been extensively studied in this genus because of their involvement in the degradation of several toxic aromatic compounds, including the bph, etb and nah gene clusters encoding, among others, the ring-hydroxylating dioxygenases that initiate the degradation of biphenyl and PCB congeners, ethylbenzene and naphthalene, respectively, in many strains [11, 14, 23,24,25].
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