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

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.

Complete Genome Sequence of Rhodococcus sp. Strain M8, a Platform Strain for Acrylic Monomer Production

“…Together with that, rhodococcal genomes are significantly variable in whole-genome size and the presence of genes for secondary metabolism. The quantity of complete rhodococcal genomes is too low now (five genomes [ 10 ]); therefore, this new genome is a valuable contribution to the knowledge base in this field.…”

Functional Expression and Characterization of a Panel of Cobalt and Iron-Dependent Nitrile Hydratases

“…Racemic 3-amino-3-(p-toluoyl)propanenitrile (3a) was prepared as previously published and all analytical data corresponded [20]. The corresponding amide 3b was prepared as follows: A solution of rac-3-amino-3-(p-toluoyl)propanenitrile (3a, 30 mg, 0.187 mmol) in MeOH (1 mL) was added to a suspension of Rhodococcus rhodochrous ATCC BAA-870 [25] (30 mg wet weight cells) in 50 mM Tris buffer (pH 7.6, 4 mL). The mixture was stirred vigorously on a magnetic stirrer unit for 24 h. Ethyl acetate (5 mL) was added and the mixture was vortexed well followed by centrifugation at 10,000× g for 10 min.…”