Bioinformatic Analysis Of Tandem Repeats And Non-Coding RNA In Deinococcus Radiodurans

Deinococcus radiodurans belonging to the family Deinococcaceae is extremely resistant to ionizing radiation, ultraviolet radiation and reactive oxygen species. Little is known about how this species use adapations to allow cells to avoid the potentially detrimental effects of DNA strand breaks and the mechanisms that limit DNA degradation and restrict the diffusion of DNA fragments that are produced following irradiation. So, it is very important to understand the repair pathways of D. radiodurans. It is currently difficult to predict which mechanism is the most effective way to radioresistance. There also are lots of reasearch on the DNA repair pathways, including base excision repair (BER), direct reversal of damage (DR), nucleotide excision repair (NER), mismatch repair (MMR), recombination repair (RR), SOS and so on. Here, we provided a new perspective to further understand the mechanisms of DNA damage and repair pathways by analyzing the potential functions of the tandem repeats and non-coding RNA located in the genome of D. radiodurans based on bioinformatic method.Tandem repeats (SSRs, a class of tandem repeats consisting of simple motifs of 1-6 nucleotides) are exist commonly in eukaryotes, prokaryotic, and bacteria. Numerous lines of evidences have demostrated that tandem repeats may be involved in chromatin organization, regulation of gene activity, DNA replication and recombination, cell cycle, mismatch repair (MMR) system, adaptation to environmental changes, etc.. Comparative genomics on tandem repeats distribution is facilitated to further understand the history of genome evolution as well as the gene function of different species. Distribution of Tandem repeats in D. radiodurans, D. geothermalis, Thermus thermophilus, Kineococcus radiotolerans, Rubrobacter xylanophilus and Escherichia coli indicates that the radioresistances of these bacteria are linear-correlated with thier tandem repeats densities. Also, we found that different amino acid repeats in D. radiodurans may play importany role in DNA replication and recombination, cell cycle, mismatch repair (MMR) system.Non-coding (ncRNA) RNAs are involved in a variety of processes such as transcriptional regulation, RNA processing and modification, mRNA translation, protein transportation and stability. 28 ncRNA families were found in the intergenic regions of the genome of D. radiodurans Rl using computer biology method based on the conserved secondary structure of RNA. Among these families, IRE is the largest class family, followed by Histone3, tRNA, SECIS. DicF, ctRNA_pGAl and tmRNA are only discovered in bacteria. The comparison of ncRNA between D. radiodurans and other organisms is helpful to the analysis of the biological function and the further study of DNA damage and repair mechanisms in this organism.