Bacterial Genes of 2,4-Dichlorophenoxyacetic Acid Degradation Encoding α-Ketoglutarate-Dependent Dioxygenase Activity

The tfdA gene encodes α-ketoglutarate-dependent dioxygenase, which catalyzes the first step of the 2,4-dichlorophenoxyacetic acid (2,4-D) degradation pathway. The entire range of 2,4-D-degrading bacteria is divided into three groups based on their phylogeny, physiological and biochemical features, and isolation source. Each of these groups has its own version of the tfdA gene. The first group is the most studied and consists of fast-growing copiotrophic β- and γ-Proteobacteria isolated from anthropogenic habitats. The bacteria of this group possess the canonical sequence of this gene. Within this group, tfdA forms at least three classes (I, II, and III) of highly homologous gene families. The tfdA gene of Cupriavidus necator JMP134 was recognized as a Class I type. Class II consists of tfdA sequences belonging only to the genus Burkholderia of β-Proteobacteria, whereas Class III includes tfdA sequences belonging to the genera Delftia, Cupriavidus, Variovorax, Achromobacter, Comamonas, Rhodoferax, Halomonas, and Pseudomonas of β- and γ-Proteobacteria. The similarity of full-length nucleotide sequences between Class I and other classes was about 77–78%, and that between Class II and Class III was 93%. The second and third groups of 2,4-D-degrading bacteria are closely related to the genera Sphingomonas and Bradyrhizobium, which belong to α-Proteobacteria. tfdA-Like genes were identified only in four Sphingomonas spp. This fact and their phylogenetically distinct position make it possible to suggest that these genes evolved independently from each other through vertical gene transfer. The tfdAα gene was identified in the third group of bacteria of the genus Bradyrhizobium, which are both able and unable to degrade 2,4-D. Nevertheless, 2,4-D-degrading bacteria of the genera Bradyrhizobium and Sphingomonas have cad genes, which initiate the first step of the chlorophenoxyacetic acid degradation pathway. Based on the data on tfdAα localization in bacteria isolated from pristine ecosystems, a theory has been proposed that the tfdAα gene is ancestral for tfdA. Horizontal transfer and further adaptation to anthropogenic habitats probably led to the emergence of tfdA. However, tfdA and tfdAα may have diverged from a common ancestor, because they show a high similarity (51–57%) and separate distribution in the β-Proteobacteria, γ-Proteobacteria, and α-Proteobacteria, respectively.