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

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dc.contributor.authorFrederick, Joni
dc.contributor.authorHennessy, Fritha
dc.contributor.authorHorn, Uli
dc.contributor.authorde la Torre Cortés, Pilar
dc.contributor.authorvan den Broek, Marcel
dc.contributor.authorStrych, Ulrich
dc.contributor.authorWillson, Richard
dc.contributor.authorHefer, Charles A
dc.contributor.authorDaran, Jean-Marc G
dc.contributor.authorSewell, Trevor
dc.contributor.authorOtten, Linda G
dc.contributor.authorBrady, Dean
dc.date.accessioned2020-01-08T09:27:31Z
dc.date.available2020-01-08T09:27:31Z
dc.date.issued2020-01-02
dc.date.updated2020-01-05T04:13:39Z
dc.description.abstractAbstract Background 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. Results 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. 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. Conclusions 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.
dc.identifier.apacitationFrederick, J., Hennessy, F., Horn, U., de la Torre Cortés, P., van den Broek, M., Strych, U., ... Brady, D. (2020). The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. http://hdl.handle.net/11427/30717en_ZA
dc.identifier.chicagocitationFrederick, Joni, Fritha Hennessy, Uli Horn, Pilar de la Torre Cortés, Marcel van den Broek, Ulrich Strych, Richard Willson, et al "The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870." (2020) http://hdl.handle.net/11427/30717en_ZA
dc.identifier.citationBMC Genomics. 2020 Jan 02;21(1):3
dc.identifier.ris TY - Journal Article AU - Frederick, Joni AU - Hennessy, Fritha AU - Horn, Uli AU - de la Torre Cortés, Pilar AU - van den Broek, Marcel AU - Strych, Ulrich AU - Willson, Richard AU - Hefer, Charles A AU - Daran, Jean-Marc G AU - Sewell, Trevor AU - Otten, Linda G AU - Brady, Dean AB - Abstract Background 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. Results 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. 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. Conclusions 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. DA - 2020-01-02 DB - OpenUCT DP - University of Cape Town LK - https://open.uct.ac.za PY - 2020 T1 - The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870 TI - The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870 UR - http://hdl.handle.net/11427/30717 ER - en_ZA
dc.identifier.urihttps://doi.org/10.1186/s12864-019-6405-7
dc.identifier.urihttp://hdl.handle.net/11427/30717
dc.identifier.vancouvercitationFrederick J, Hennessy F, Horn U, de la Torre Cortés P, van den Broek M, Strych U, et al. The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. 2020; http://hdl.handle.net/11427/30717.en_ZA
dc.language.rfc3066en
dc.rights.holderThe Author(s).
dc.titleThe complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870
dc.typeJournal Article
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