Characteristics of phenol degradation genetic loci in the genome of bacteria Rhodococcus pyridinivorans strain 5Ap
Abstract
The growth dynamics of the bacteria Rhodococcus pyridinivorans strain 5Ap in a medium with phenol (200 mg/L) was characterised. The bacteria reach the stationary phase after 24 h of cultivation. By this time phenol is completely utilised. As a result of whole-genome sequencing, it was established that the genome of bacteria R. pyridinivorans strain 5Ap is represented by a circular chromosome with a size of 5 220 735 base pairs (number in the GenBank database CP063450.1) and three circular megaplasmids – pSID with a size of 250 428 base pairs (CP063453.1), pRh5Ap-243 with a size of 243 288 base pairs (CP063452.1) and pNAPH with a size of 207 815 base pairs (CP063451.1). A comparison of the organisation of genes of the β-ketoadipate phenol degradation pathway in the genomes of 78 bacteria of the genus Rhodococcus of groups B (subgroups B1 and B2), C and D showed that, despite the high level of synteny in general, each group has characteristic features in the structure of the studied loci. Unlike other groups, in genomes of group C bacteria the pheA2A1 and catABC operons are separated by three genes, including fadA and fadI genes, which determine the alternative possibility of phenol oxidation with the formation of succinyl-CoA (in other groups, likely, only acetyl-CoA is formed). Rhodococci of group C and subgroup B1 have an additional locus in their genome, including the pheA2, pheA1 and catA genes. The second locus in bacteria of the subgroup B1, groups C and D includes the pcaIJ and pcaHGBLRF operons, while in bacteria of the subgroup B2 it includes the pcaIJ and pcaBLRF operons, and the pcaHG operon, encoding the components of protocatechuate-3,4-dioxygenase, is located in a different chromosomal locus. The regulatory regions of the pheA2A1 and catABC operons in the bacteria R. pyridinivorans strain 5Ap are similar to the known ones and contain binding sites for both the specific regulatory proteins PheR and CatR, respectively, and for the global catabolism regulator CRP. As a result of analysis of the pcaI – pcaB intergenic region of R. pyridinivorans strain 5Ap, six potential binding sites for the protein PcaR were identified. The nature of the location of these sites may indicate a dual role of the regulatory protein PcaR: as a repressor in a state unbound to the effector and as an activator in a state bound to the effector.
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