Exploring of radiation resistance from bacterium Deinococcus radiodurans R1 by amino acid compositions of proteins: View from comparative whole protein sequences

Bacteria Deinococcus radiodurans strain R1 was extremely resistant to ionizing radiation, UV light, hydrogen peroxide, and numerous other agents that damage DNA as well as being highly resistant to desiccation. It is clear that the D. radiodurans strain R1 whole genome which carries 3,195 predicted genes, consists of two chromosomes, one megaplasmid, and one plasmid. This combination of factors has positioned D. radiodurans as a promising candidate for the study of mechanisms of DNA damage and repair, as well as its exploitation for practical purposes such as cleanup and stabilization of radioactive waste sites. Radiation resistance of D. radiodurans seems very complex and is determined collectively by some features revealed by genome analysis, as well as by many more subtle structural peculiarities of proteins and DNA that are not readily inferred from the comparative sequences analysis. The fundamental questions underlying the extreme resistance phenotype of D. radiodurans remain unanswered. In this study, two protein databases including Deinococcus radiodurans R1 and E. coli K-12, were applied to whole protein sequences comparative analysis. Several computational tools developed from RDBMS (Relation Database Management System), were applied to this study. From the protein database comparison results, our target is to find the possible mechanisms by which proteins can become radiation resistant, either by a special 3-dimensional structure or by using a set of stable amino acids in the sequence.