Phylogenetic Analysis Of Recombination Repair Enzymes In Bacteria

Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. In prokaryotes, Homologous recombinational repair of Double-stranded DNA break in bacteria are mainly initiated by two systems, RecBCD pathway in some lineages and AddAB as substitutes for RecBCD in some other lineages. Protein coevolution is the change of a protein triggered by the change of a related protein. Proteins experiencing coevolution exist simultaneously in the same species to achieve complex functions together. There were lots of methods that were used to predict protein coevolution. Particularly successful methods that predict coevolution at the protein level have been based on the detection of pairs of protein families with similar evolutionary histories.In this study, more conserved residues have been spotted in RecBCD than previous research. These residues are distributed mainly on the DNA tunnel and the interface of each subunit after which we highlight them on three dimensional structure of the complex. The distribution of residues in RecBCD may guarantee that DNA channels are smooth and the interaction between subunits is stable. In addition, the Chi recognition residues also locate in the3’-5’DNA tunnel, which guarantee that Chi recognition residues could recognize Chi sequence promptly and exactly.Through phylogenetic analyse, the evolved relation of RecBCD and AddAB have been present in our work. RecBCD and AddAB experience a series of events containing recombination, repetition, differentiation, horizontal gene transfer and coevolution. These events explain how RecBCD turned from a simple helicase to a powerful enzyme in homologous recombination. Furthermore, the Chi sequence and the recognition residues also have clearly coevolution. Although RecBCD and AddAB experience a series of events, there are many Conservative residues in crucial region, such as helicase domain, nuclease domain, DNA tunnel and interface between subunits. These Conservative residues protect structure Stabilization and functional integrity in RecBCD from evolution.