Diversity And Organisation Of Genes Involved In The Upper Pathway Of Pahs Degradation

Most bacteria degrade PAHs through a similar upper pathway under aerobic condition. A similar set of enzymes(pah ABCDEF) responsible for catalizing the reactions in the pathway is present in all the well-studied PAHs degraders. Until now, the diversity of genes encoding these enzymes lacks comprehensive and in-depth investigation. In this work, all available pah ABCDEF sequences as well as the corresponding genomes in Genbank are collected, the diversity of individual gene is studied and compared, and the way in which these genes are organised in the genome are compared, several new type of genes involved in PAHs degradation are predicted.Aromatics ring hydroxylating dioxygense(Arh A) can be classified into four major class, PAHs ring hydroxylating dioxygense(pah A) belongs to the IVth class of Arh A, which containing one oxygenase component and two electron transfer components(ETCs): reductase and redoxin. Based on the phylogenetic relationship of the oxygenase component, pah A can be classified into two major groups, each from PAHs degrading Proteobacteria or Actinobacteria, separately. Highly similar oxygenase sequences generally come from bacteria with close relationship. Various types of ETCs are present in pah A, however pah A with similar oxygenase component usually comprise same type of ETCs. There is a tight relationship between the oxygenase and ETCs during the evolution process of pah A.The diversity of pah BCDEF genes vary with one another. There are several different origins for pah BCF genes, these genes are closely related to the counterpart genes involved in the degradation of other aromatic hydrocarbons in their phylogenetic trees. Both pah D and pah E genes have a single origin and their phylogenetic trees contain no counterpart genes in other aromatics degradation process. pah D gene is presented in PAHs degrading Proteobacteria but not Actinobacteria, pah E genes is presented in all PAHs degraders, which suggests pah E gene can serve as a promising biomarker in PAHs degradation process. If two PAHs degraders contains highly similar pah X gene, they generally contains highly similar pah Y genes(X, Y can be ABCDEF), however two pah X genes with same origin can not promise pah Y genes with same origin.pah ABCDEF genes are generally distributed in a region of 10 s kb in the genomes of PAHs degraders, these genes can be organised into various types of gene clusters related to PAHs degradation. PAHs degraders with highly similar pah X genes generally contain the same gene clusters and vice versa. Clear signals of horizontal gene transfer are revealed through whole genome comparison and the comparion of PAHs degrading gene clusters, in these cases all pah ABCDEF genes are transferred as a whole.Two new groups of pah A genes are predicted by ultilizing pah E genes as biomarker gene. The first group is from PAHs degraders belonging to α-Proteobacteria, these pah A are tightly related to Arh A typically involved in biphenyl and toluene degradation, two members in this group have been demonstrated to be involvled in PAHs degradation. Another new type of pah A is from Burkholderiales, the pah BCDE genes in these strains are tightly related to the typical PAHs degrading Burkholderiales in the phylogenetic trees, however, pah A is more closely related to pah A belonging to PAHs degrading Actinobacteria.