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.

中文翻译：

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新型多氯联苯降解菌Rhodococcus sp。的生物降解和适应性潜力分析。WAY2通过其完整的基因组序列揭示。

红球菌属的完整基因组序列。WAY2（WAY2）由一个环状染色体，三个线性复制子和一个小的环状质粒组成。线性复制子包含具有中央CGTXCGC图案的典型的放线菌内向型端粒。比较16S rRNA基因的系统发育分析，以及基于基因组到基因组胚细胞距离系统发育（GBDP）算法和数字DNA-DNA杂交（dDDH）与其他红球菌类型菌株的系统发育分析，导致WAY2明显分化。可能是一个新物种。WAY2的基因组包含五个不同的bph，etb和nah基因簇，可能参与了几种芳香族化合物的降解。这些簇分布在整个线性质粒中。这些系统的环羟基化亚基与其他已知酶的高度同源性已使我们能够模拟它们可能降解的芳香族底物的范围。进一步的功能表征表明，WAY2能够以联苯，萘和二甲苯作为唯一的碳和能源生长，并且可以氧化多种芳族化合物，包括乙苯，菲，二苯并呋喃和甲苯。此外，WAY2能够共代谢23种多氯联苯同源物，与其基因组编码的五个不同的环羟基化系统一致。WAY2还可以使用各种链长的正构烷烃作为唯一碳源，这可能是由于存在于其染色体中的alkB和ladA基因拷贝所致。