Transcriptome Data Mining Of Deinococcus Radiodurans And Function Analysis Of Oxidative Stress Related Genes

Deinococcus radiodurans is an extreme bacterium well known for its tolerance to ionizing radiation and oxidants. Functional macromolecules such as DNA, protein and plasma structure were susceptible to those stresses. The detailed mechanisms involved in the tolerance are still under investigation. Previous global analysis of the transcriptome with microarrays revealed an efficient DNA repair and ROS scavenging system contributed to its survival under irradiation or ROS stress.However, microarray techniques mainly depends on the well annotation of reference genome and work at a limited dynamics. In order to dig out more information, we applied the SOLiDTM system to investigate the whole transcriptome of Deinococcus radiodurans under normal condition and in response to hydrogen peroxide. The whole transcriptome profile suggested additional genes that might involve in ROS stress which had not been reported.sRNAs were also known as regulatory RNAs including regulatory leader sequences in the mRNA and the non-coding RNAs. It is becoming increasingly apparent that ncRNAs play important function in bacteria. Few sRNAs were annotated in Deinococcus radiodurans, except for FMN, T-box. and Y-RNA etc. according to the Rfam database. RNA-seq are readily to discover sRNAs. and we performed global search of noncoding RNAs in the genome of Deinococcus radiodurans for further function analysis.Some transcripts that did not match the genome annotation were observed, which lead to the discovery of new open reading frames. These "missing" information might be due to the inaccuracy and incompleteness in the early genome sequencing. RNA-seq data help to pick out these region for further conservation and function analysis.One of the newly discovered ORF encoded a Fur family homolog and was further designed as DrPerR. Re-sequencing of this region uncovered an omission of guanine at Chromosome I2,340,150led to a frameshift. The drperR gene disruption strain showed increasing resistance to hydrogen peroxide along with increasing catalases activity in cell extraction. EMSA assay with the purified protein and RT-PCR results indicated that DrPerR functions as a repressor of katE and dps-1. De-repressing dps under H2O2stress by DrPerR also link it to the regulation of metal ions hemostasis. Thus, DrPerR might function as a PerR-like protein which is involved in ROS response and defense. These results help to understand the complicated regulatory network in D. radiodurans against ROS stress.Our study demonstrated the importance of genome data mining using Deep sequencing and also provided implications on how to utilize the data.