Recombination of a 3-chlorobenzoate catabolic plasmid from Alcaligenes eutrophus NH9 mediated by direct repeat elements.

Alcaligenes eutrophus NH9 was isolated from soil. This strain can utilize 3-chlorobenzoate (3-CB) as a sole source of carbon and energy. Most of the 3-CB-negative segregants had lost one of the plasmids present in the parent strain. The genes for catabolism of 3-CB were located within a 9.2-kb SacI fragment of this plasmid (pENH91). The genes were found to hybridize with genes for components of the modified ortho cleavage pathway from Pseudomonas putida. In one of the 3-CB-negative segregants, the plasmid had undergone the deletion of a segment with a size of about 12.5 kb that covered the catabolic genes. The deletion event seemed to be the result of reciprocal recombination between two highly homologous sequences with sizes of 2.5 kb that were present as a direct repeat at the two ends of the region that included the catabolic genes. Nucleotide sequence analysis of homologous fragments revealed a structure that resembled an insertion sequence and relatedness to IS21. During repeated subculturing of NH9 on liquid media with 3-CB, the culture was taken over by a derivative strain (designated NH9A) in which the degradative plasmid carried a duplicate copy of the 12.5-kb region that contained the catabolic genes. The duplication of these genes seemed again to have been mediated by recombination between the direct repeat sequences.