Genomic analysis of the degradation gene clusters and the parABS system in Afipia sp. strain DD3 capable of utilizing 2,4-dichlorophenoxyacetic acid

Here, I report the complete genome of the soil bacterium Afipia strain DD3, the first representative of its genus to utilize the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) as its sole carbon source. The compact 2,4-D degradation gene cluster of strain DD3 is a set of cadABKC and tfdBFRDEC gene clusters on its chromosome. No tfdA homologs were detected in the genome. The parAB genes responsible for chromosome segregation were found to be close to a candidate chromosomal replication initiation region (oriC) in the chromosome of strain DD3, which is located approximately 180 kb away from dnaA. In 14 strains from five Alphaproteobacterial orders, including strain DD3, parAB was found to be clustered with the genes mnmEG and rsmG coding for tRNA- and rRNA-modifying enzymes. Binding sequences for ParB were found in the promoters of or within these genes, suggesting that parAB genes in Alphaproteobacteria are involved in regulating RNA metabolism during chromosome segregation.