DNA sequence of the Acinetobacter calcoaceticus catechol 1,2-dioxygenase I structural gene catA: evidence for evolutionary divergence of intradiol dioxygenases by acquisition of DNA sequence repetitions

Abstract

The DNA sequence of a 1.6-kilobase-pair SalI-KpnI Acinetobacter calcoaceticus restriction fragment carrying catA, the structural gene for catechol 1,2-dioxygenase I, was determined. The 933-nucleotide gene encodes a protein product with a deduced molecular weight of 34,351. The similarly sized Pseudomonas clcA gene encodes catechol 1,2-dioxygenase II, an enzyme with relatively broad substrate specificity and relatively low catalytic efficiency. Comparison of the catA and clcA sequences demonstrated their common ancestry and suggested that acquisitions of direct and inverted sequence repetitions of 6 to 10 base pairs were frequent events in their evolutionary divergence. The catechol 1,2-dioxygenases proved to be evolutionarily homologous with the alpha and beta subunits of Pseudomonas protocatechuate 3,4-dioxygenase, and analysis of conserved residues in the intradiol dioxygenases revealed conserved histidyl and tyrosyl residues that are probably involved in the ligation of ferric ion in their active sites.

Sequence analysis of the Pseudomonas sp. strain P51 tcb gene cluster, which encodes metabolism of chlorinated catechols: evidence for specialization of catechol 1,2-dioxygenases for chlorinated substrates

“…In contrast, the TfdC enzyme shows a higher rate of conversion with 3,5-DCC as a substrate, which is in agreement with the findings of Pieper et al (22). In A. eutrophus JMP134, 3,5-DCC occurs as an intermediate in the conversion of 2,4-dichlorophenoxyacetic acid by enzymes of the tfd pathway (5), indicating that this pathway is specialized for conversion of 3,5-DCC (22 (10,13,17). The data presented here reinforce the hypothesis that the intradiol dioxygenases have a common ancestor.…”

“…The cycloisomerase gene appeared to have the highest degree of sequence conservation among the different genes of the clusters, followed by the catechol 1,2-dioxygenase gene. The overall organization of the chlorocatechol gene clusters is different from the organization of the cat genes in P. putida (1) and Acinetobacter calcoaceticus (17). In these cases, the catA gene encoding the catechol 1,2-dioxygenase is separated from catB, which encodes muconate-lactonizing enzyme.…”

“…4A). The DNA sequences of structural genes tcbC, cicA, and tfdC provide examples of three relatively recently evolved genes sharing close homology but otherwise differing subtly and as such may reflect mechanisms that are acting on sequence conservation and divergence (13,17).…”

Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases

“…In contrast, genes for such isofunctional enzymes have diverged substantially, as indicated by differences in G+C content of about 15% (9,20,27). Such differences in G+C content may be attributed in part to directional pressure exerted by mutations within divergent cell lines (32).…”

“…Many bacterial species, exemplified by Acinetobacter calcoaceticus, carry chromosomal genes for enzymes that convert catechol to citric acid cycle intermediates via 3-ketoadipate (20,21,23,31). These enzymes do not act effectively upon methylsubstituted substrates.…”