N4-cytosine DNA methylation is involved in the maintenance of genomic stability in Deinococcus radiodurans

Purpose: DNA methylation has a global impact on gene expressionMethods: Gene expression profiles of D. radiodurans R1 wild type and ΔM.DraR1 strains were generated by deep sequencing using Illumina HiSeqTM2500.Results: RNA-seq was used for differential expression gene analysis between wild-type and ΔM.DraR1 strains. A total of 1158 genes (766 upregulated genes and 392 downregulated genes) were differentially expressed in ΔM.DraR1 strain. GO enrichment analysis revealed that upregulated unigenes were significantly enriched in twelve subcategories. The majority of unigenes in the biological process category were associated with macromolecule metabolic processes. Interestingly, a number of unigenes were also associated with DNA recombination. Within the molecular function category, most unigenes were assigned to nucleic acid, DNA binding and hydrolase, and nucleoside triphosphatase activity. The KEGG enrichment analytical scatter diagram showed that the major pathways affected in the deletion strain belonged to ABC transport, two-component systems, DNA replication, homologous recombination, and protein export pathways. The majority of DNA damage response genes, such as ddrA, ddrB, ddrO, ddrG, ddrJ, ddrK, ddrD and pprA, were significantly upregulated. Several genes involved in DNA recombinational repair pathway including recA, recO, rexD, and ruvB were also significantly upregulated. Putative competence genes, including those encoding prepilin peptidase, CRP and CinA, were upregulated in the mutant strain. This gene expression pattern of the ΔM.DraR1 strain resembled that of D. radiodurans during recovery after exposure to acute radiation, indicating that the absence of N4-cytosine DNA methylation may result in intracellular stress.Conclusion: Absence of N4-cytosine DNA Methylation in D. radiodurans Leads to Expression Changes of Proteins Involved in DNA Damage Response