- The complete genome sequence of the nitrile biocatalyst Rhodococcus rhodochrous ATCC BAA-870. - 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. - rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using. - 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 draft sequence of the R. - ATCC BAA-870. - rhodo- chrous ATCC BAA-870 [33], was isolated through en- richment culturing of soil samples from South Africa on nitrile nitrogen sources. - rhodochrous ATCC BAA-870 was ori- ginally sequenced in 2009 by Solexa Illumina with. - rhodo- chrous ATCC BAA-870 is deposited at NCBI GenBank, with Bioproject accession number PRJNA487734, and Biosample accession number SAMN09909133.. - rhodochrous ATCC BAA-870 The R. - rhodochrous ATCC BAA-870 genome encodes four 16S rRNA genes, consistent with the average 16S gene count statistics of Rhodococcus genomes. - Of the four 16S rRNA genes found in R. - rhodochrous ATCC BAA-870, two pairs are identical (i.e. - rhodochrous ATCC BAA-870 to other similar species using 16S rRNA multiple sequence align- ment and phylogeny in ClustalO and ClustalW respect- ively [45–47] (Fig. - Nucleotide BLAST results of the two different R. - rhodochrous ATCC BAA-870 16S rRNA genes show closest sequence identities to Rhodococcus sp. - rhodochrous ATCC BAA-870 to its closest matched strains based on 16S rRNA alignment (R. - rhodochrous ATCC BAA- 870 cannot be distinguished from the other strains based on GC content. - rhodochrous ATCC BAA-870 and R. - rhodochrous ATCC BAA-870 was submitted to the Bacterial Annota- tion System web server, BASys, for automated, in-depth annotation [51]. - rhodochrous ATCC BAA-870 with a total genome length of 5.9 Mbp, in which 7548 genes were identified and annotated (Fig. - 4), showing the importance of the bioinformatics tool used. - rhodochrous ATCC BAA-870 16S rRNA genes and other closely matched genes from rhodococcal species. - rhodochrous ATCC BAA-870 contains four copies of the 16S rRNA gene (labelled RNA_1 to RNA_4) and are indicated with an asterisk. - The average GC content of the R. - rhodochrous ATCC BAA-870 chromosome and plasmid is 68.2 and 63.8%, respectively. - rhodochrous ATCC BAA-870 associ- ated with translation, ribosomal structure and biogenesis (protein biosynthesis). - 3 Protein function breakdown of Rhodococcus rhodochrous ATCC BAA-870 based on BASys annotation COG classifications. - 2 BASys bacterial annotation summary view of the Rhodococcus rhodochrous ATCC BAA-870 genome. - rhodochrous ATCC BAA-870 gen- ome, made up of 52 tRNA genes encoding natural amino acids, 2 pseudogenes, one tRNA with mismatched isotype and one + 9 Selenocysteine tRNA.. - Of the membrane proteins in R. - rhodochrous ATCC BAA-870, 47% constitute single- pass, inner or peripheral membrane proteins, while 41%. - Nu- merous components of the ubiquitous transporter fam- ilies, the ATP-Binding Cassette (ABC) superfamily and the Major Facilitator Superfamily (MFS), are present in Rhodococcus strain BAA-870. - rhodochrous ATCC BAA-870 has 81 members of the MFS, mostly from the phthalate permease and sugar transporter families. - rhodochrous ATCC BAA-870 include at least 122 members of the ABC superfamily, which in- cludes both uptake and efflux transport systems. - rhodochrous ATCC BAA-870. - rho- dochrous ATCC BAA-870. - Analysis of the R. - rhodochrous ATCC BAA-870 genome suggests that at least four major path- ways exist for the catabolism of central aromatic inter- mediates. - rhodochrous ATCC BAA-870 there are 14 cyto- chrome P450 genes and 87 oxygenase genes. - 4 RAST annotation summary of the Rhodococcus rhodochrous ATCC BAA-870 genome. - rhodochrous ATCC BAA-870, 26% of annotated genes belong to an identified functional role, or subsystem. - rhodochrous ATCC BAA-870 was isolated from a nitrile enrichment culture [33], we were very interested in its nitrile degrading enzymes. - rhodochrous ATCC BAA-870 is supported by the presence of at least 227 genes linked to secondary metabolite biosynthesis, transport and catabolism. - rhodochrous BAA- 870 include ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyri- midinecarboxylic acid), butyrolactone, betalactone, and. - rhodochrous ATCC BAA-870 plasmid, four of an unknown type, and the other two with low similarity to enterobactin and lipo- polysaccharide biosynthetic clusters.. - Some of the examples of annotated R. - rhodochrous ATCC BAA-870 plasmid encodes a lactone ring-opening en- zyme, monoterpene epsilon-lactone hydrolase.. - rhodochrous ATCC BAA-870 genome has two PKS genes, one regulator of PKS expression, one exporter of polyketide antibiotics, as well as three polyketide cyclase/dehydrases involved in polyketide biosynthesis. - rhodochrous ATCC BAA-870 con- tains 4 probable siderophore-binding lipoproteins, 3 probable siderophore transport system permeases, and two probable siderophore transport system ATP- binding proteins. - rhodo- chrous ATCC BAA-870 genome, according to analysis by CRISPRCasFinder [72]. - rhodochrous ATCC BAA-870 genome, including a ruvC gene, and HNH endonuclease and nuclease genes.. - rhodo- chrous ATCC BAA-870 which may have been obtained through horizontal mobility. - rhodochrous ATCC BAA-870 genome contains 31 transposase genes found in the genomic regions identified by IslandViewer, one of which is from the IS30 family, a ubiquitous mobile in- sertion element in prokaryotic genomes [74]. - Size and content of the genome. - rhodochrous ATCC BAA-870 was outlined and compared to other rhodococcal. - rhodochrous ATCC BAA- 870 chromosome and plasmid is 68.2 and 63.8%, re- spectively. - rhodochrous ATCC BAA- 870 has a 90.6% coding ratio, which is in line with its smaller total size. - rhodochrous ATCC BAA-870 combines this with multiple transport systems (44% of total COG annotated genes), highlight- ing the metabolic versatility of this Rhodococcus, which facilitates the use of whole cells in biotechnological applications.. - rhodochrous ATCC BAA-870 the dominant portion of annotated enzymes are involved in oxidation and reduction. - rhodochrous ATCC BAA-870 reflects a fundamental aspect of rhodo- coccal physiology. - rhodochrous ATCC BAA-870 are catabolic and which are involved in secondary metabolism, their abundance is consistent with a potential ability to degrade an exceptional range of aromatic compounds (oxygenases catalyse the hydrox- ylation and cleavage of these compounds). - rhodochrous ATCC BAA-870 has 87 oxygenase genes while the PCB degrading R. - rhodochrous ATCC BAA-870 encodes several monooxy- genases. - rhodochrous ATCC BAA-870 has effective osmoregulation and enzyme protection capabilities. - Like strain ATCC BAA-870, R. - rhodo- chrous ATCC BAA-870 may host a significant potential source of molecules with immunosuppressing, antifun- gal, antibiotic and siderophore activities [115].. - rhodo- chrous ATCC BAA-870 (Table 2). - rhodochrous ATCC BAA-870 2 (pl) 1 (pl) 4 (pl) 7 (chr). - ATCC BAA-870 contains several nitrile converting enzymes which is in line with previous activity assays using this Rhodococcus strain [34, 35]. - rhodochrous ATCC BAA- 870, they are found on a plasmid. - rhodochrous ATCC BAA-870 the nitrile hydratase is expressed constitutively, explaining why this strain is an excep- tional nitrile biocatalyst [37]. - rhodochrous ATCC BAA-870 expresses an enantioselective aliphatic nitrilase encoded on the plas- mid, which is induced by dimethylformamide [37].. - rhodochrous ATCC BAA-870 has adapted its genome recently in response to the selective pressure of routine culturing in nitrile media in the laboratory. - based on matching BLASTs of the flanking regions.. - rhodochrous ATCC BAA-870 CRISPR up- stream and downstream regions (based on a 270- and 718 nucleotide length BLAST, respectively) showed significant, but not matching, alignment with several other Rhodococcus strains. - The region upstream of the BAA-870 CRISPR showed a maximum 95% iden- tity with that from R. - rhodochrous ATCC BAA-870 could also have arisen from bacteriophage infection during its evolutionary history.. - rhodochrous ATCC BAA- 870 is one of 353 Rhodococcus genomes that are se- quenced to date, but it is only the 4th sequence that. - Therefore, the sequence of the R. - rhodochrous ATCC BAA-870 genome will facilitate the further ex- ploitation of rhodococci for biotechnology applica- tions, as well as enable further characterisation of a biotechnologically relevant organism. - rhodochrous ATCC BAA-870 was submitted to the Bacterial An- notation System web server, BASys, for automated, in-depth annotation of the chromosomal and plasmid sequences [51]. - BAA-870 genome. - Whole genome distance statistics between Rhodococcus rhodochrous ATCC BAA-870 and two closely matched strains. - Rhodococcus rhodochrous ATCC BAA-870 protein function breakdown based on BASys annotation COG classifications.. - FH: annotation of the preliminary genome and contribution to the manuscript preparation. - rhodochrous ATCC BAA 870 is deposited at NCBI GenBank, with Bioproject accession number PRJNA487734, and Biosample accession number SAMN09909133.. - Biodegradation potential of the genus Rhodococcus. - Core genome and plasmidome of the quorum-quenching bacterium. - Analysis of the 7.6-kb cryptic plasmid pNC500 from Rhodococcus rhodochrous B-276 and construction of Rhodococcus – E. - Enantioselective hydrolysis of β -hydroxy nitriles using the whole cell biocatalyst Rhodococcus rhodochrous ATCC BAA-870. - Enantioselective biocatalytic hydrolysis of β -aminonitriles to β -amino-amides using Rhodococcus rhodochrous ATCC BAA-870. - Sizing of the Rhodococcus sp. - Functional organization of the inverted repeats of IS30. - Environmental genome shotgun sequencing of the Sargasso sea. - Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. - Gene cloning, overexpression, and characterization of the nitrilase from Rhodococcus rhodochrous tg1-A6 in E. - PHASTER: a better, faster version of the PHAST phage search tool
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