Abstract
BackgroundRhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst.ResultsThe genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase.Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci.ConclusionsThe sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.
Highlights
Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics
R. jostii RHA1 was isolated in Japan from soil contaminated with the toxic insecticide lindane (γ-hexachlorocyclohexane) [11] and was found to degrade a range of polychlorinated biphenyls (PCBs) [12]
A more recently performed paired-end Illumina library combined with the mate-pair library reduced this to only 6 scaffolds (5.88 megabase pairs (Mbp))
Summary
Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus is arguably the most industrially important actinomycetes genus [1] owing to its wide-ranging applications as a biocatalyst used in the synthesis of pharmaceuticals [2], in bioactive steroid production [3], fossil fuel desulphurization [4], and the production of kilotons (2020) 21:3 wall composition changes, becoming more resistant to many solvents and more stable under industrially relevant conditions like high substrate concentration and relatively high concentrations of both watermiscible and -immiscible solvents. This results in a longer lifetime of the whole cell biocatalyst and subsequent higher productivity. One sequencing effort to improve prokaryotic systematics has been implemented by the University of Northumbria, which showed that full genome sequencing provides a robust basis for the classification and identification of rhodococci that have agricultural, industrial and medical/ veterinary significance [13]
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