The complete genome sequence of the nitrile biocatalyst Rhodococcus rhodochrous ATCC BAA-870

• Published in: BMC genomics Vol. 21; no. 1; pp. 1 - 19
• Main Authors: Frederick, Joni, Hennessy, Fritha, Horn, Uli, de la Torre Cortés, Pilar, van den Broek, Marcel, Strych, Ulrich, Willson, Richard, Hefer, Charles A, Daran, Jean-Marc G, Sewell, Trevor, Otten, Linda G, Brady, Dean
• Format: Journal Article
• Language: English
• Published: BioMed Central Ltd 02.01.2020; BMC
• Subjects: Actinomycetes; Amides; Bacteria; Base sequence; Biotechnology; Chemical plants; DNA sequencing; Enantiomers; Enzymes; Genes; Genetic aspects; Genomes; Genomics; Hydrolysis; Ligases; Lipase; Metabolites; Microbiological research; Nitriles; Oxidases; Oxidoreductases; Peptides; Proteases; South Africa
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-019-6405-7

Rhodococci 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. The 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. The 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.