Evolution end classification oftfdgene clusters mediating bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D)

Abstract

Thetfd(tfdIandtfdII) are gene clusters originally discovered in plasmid pJP4 which is involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusterstcbandclc. Although great efforts have been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches revealed that alltfdclusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed:tfdI,tfdII,tfdIIIandtfdIV(A,B,C). Horizontal gene transfer betweenBurkholderialesandSphingomonadalesprovided phenomenal linkage betweentfdI,tfdII,tfdIIIandtfdIVtype clusters and their mosaic nature. It is hypothesized that the evolution oftfdgene clusters proceeded within first (tcb,clcandtfdI), second (tfdIIandtfdIII) and third (tfdIV(A,B,C)) evolutionary lineages in each of which the genes were clustered in specific combinations. Their clusterization has been discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements have also been proposed to explain the structural variations across members of clusterstfdIIandtfdIII, respectively. Taking everything into account, these findings reconstructing the phylogeny oftfdclusters, have delineated their evolutionary trajectories, and allowed the contribution of various evolutionary processes to be assessed.