In Silico Analysis of the Endonuclease III Protein Family Identifies Key Residues and Processes During Evolution

Abstract

DNA repair refers to a collection of processes by which a cell identifies and corrects damage to genomic DNA molecules. DNA repair processes significantly overcome DNA damage and restore the normal nucleotide sequence and DNA structure. This study focuses on the evolution of the endonuclease III gene/protein family, which plays a key role in the base excision repair pathway. We analyzed 463 homologs of the endonuclease III protein and compared them with the corresponding gene and 16S/18S rRNA sequences to understand the evolutionary processes of this protein family. The sequence analysis and comparison reveal consensus sequence motifs within the ENDO3c and iron–sulfur cluster loop domains that are functionally and structurally important. On the basis of phylogenetic analysis, we propose an evolutionary model of the endonuclease III protein family. Horizontal gene transfer was identified as the key event among bacteria, archaea, and eukaryotic organisms that occurred during the evolution of the endonuclease III gene family among bacteria, archaea, and eukaryotic organisms. This analysis may be exploited to achieve a better prediction of the endonuclease III family gene/protein in unannotated organisms or families of organisms that are completely sequenced as well as in those for which sequencing is ongoing.