Exploring of Radiation Resistance from Bacterium Deinococcus radiodurans R1 by Amino Acid Compositions of Proteins: View from Comparative Whole Protein Sequences
Date Issued
2004
Date
2004
Author(s)
Chang, Chia-Wen
DOI
zh-TW
Abstract
The Bacterium Deinococcus radiodurans 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 R1 whole genome carries 3,195 predicted genes, consists of two chromosomes, one megaplasmid, and one plasmid. This combination of factors has positioned D. radiodurans R1 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 R1 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 R1 remain unanswered.
In this study, two protein databases including the radiation resistant bacterium: Deinococcus radiodurans R1 and mesophilic radiation sensitive bacterium: Escherichia 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. The analysis was consisted by several programs in four steps, including Step 1: “PROTEIN LOADER” loaded the FASTA format proteins into the database; Step 2: SADPC (Semi-Automatic Distributed Protein Comparison); Step 3: SPVAW (Significant Protein Viewer and Writer) and Step 4: MSPS (Most Significant Protein Search, Analysis and Output tool). From the protein database comparison results, our target is to find the candidate proteins in D. radiodurans R1 and E. coli K-12 that are with similar compositions, 3-dimensional structure or characteristics, but with different resistance to radiation.
The results in this study indicated that programs developed from this study were helpful for biologists to analyze their data. More works such as artificial selection of candidate proteins were in process. In preliminary results, 997 candidate proteins were selected from thousands genes of D. radiodurans R1 and E. coli K-12. Duplicated and hypothetical proteins will be reduced and the target numbers of candidate proteins were under 300. In vitro radiation resistant tests of proteins will be preformed after gene cloning, expression and purification. The final goal is to figure out the radiation resistant mechanisms of microbes from the view of proteins.
Subjects
胺基酸
資料庫
蛋白質
抗輻射奇異球菌
protein
Deinococcus radiodurans R1
Amino Acid
database
Type
thesis
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