Effect of depletion of dr_0199 on gene experssion in Deinococcus radiodurans

The Dr_ebfC protein in D. radiodurans, encoded by the dr_0199 gene, was initially characterized as a NAP with DNA-protective and histone-like properties, involved in safeguarding the DNA from damage. To study the role of this protein in chromosomal organization and transcriptional regulation, we constructed dr_0199 deletion mutant in D. radiodurans. The mutant strain was viable, but compared with wild-type cells, the growth rate was moderately inhibited and the cell density during the stationary phase was lower than that of the wild-type. Through RNA-seq analysis of the mutant strain, we identified a total of 1077 differentially expressed genes, with 636 upregulated genes and 441 downregulated genes compared to the wild-type. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the upregulated genes in the mutant were mainly associated with environmental stress response, DNA recombination, regulation of metabolic activities, catalytic activities, and DNA binding processes. Notably, several DNA damage repair-related genes (e.g., ddrA, ddrB, ddrC, ddrD, pprA) regulated by PprI/DdrO proteins showed significantly increased expression levels in the mutant. This observation suggests that the absence of the Dr_ebfC protein might lead to cellular stress, implying a potential role of this NAP in DNA protection. Enrichment analysis of the downregulated genes in the mutant revealed their involvement in vital cellular processes closely related to respiration, translation, RNA metabolism, and electron transfer, corroborating the observed slow growth phenotype of the mutant. Overall design: Gene expression profiles of D. radiodurans R1 wild type and ?Dr_ebfC strains were generated by deep sequencing using MGISEQ-2000 PE150.