Physiological Changes and Transposition of Insertion Sequences in the dps-Double-Knockout Mutant of Deinococcus geothermalis

DNA-protecting proteins (Dps) are crucial for safeguarding chromosomal DNA in starved cells during the stationary phase under stressful conditions. In previous research, the two Dps proteins in <i>Deinococcus geothermalis</i>, Dgeo_0257 (Dps3) and Dgeo_0281 (Dps1), were found to complement each other in protecting DNA from oxidative damage. This study investigates the physiological changes and transposition of insertion sequences (ISs) in a double-knockout (DK) mutant lacking both <i>dps</i> genes. Comparisons between the wild-type and mutant strains revealed significant phenotypic differences in viability under oxidative stress conditions induced by hydrogen peroxide and ferrous ions, particularly during the stationary phase. Notably, oxidative stress triggered the transposition of the IS families IS<i>701</i> and IS<i>5</i>, with IS<i>66</i> being transposed exclusively in the DK mutant into a gene encoding phytoene desaturase. Transcriptomic analysis using RNA-seq revealed substantial fold changes in gene expression across the genome. For example, the <i>dgeo</i>_1459-1460 gene cluster, which encodes a DUF421 domain-containing protein and a hypothetical protein, was highly upregulated under both oxidative and non-oxidative conditions. Interestingly, catalase, encoded by a single gene in <i>D. geothermalis</i>, was upregulated in the DK mutant during the stationary phase, with expression levels exceeding those observed in the single <i>dps</i> gene-deficient mutants. Conversely, a prominent downregulation of the Fur family regulator was detected. These findings highlight the growth phase-dependent physiological adaptation of the <i>dps</i>-DK mutant and reveal a novel IS transposition event of the IS<i>Bst12</i> group involving the IS<i>66</i> family. Therefore, this study provides new observations into the influence of DNA-protective protein deficiency on oxidative stress responses and IS transposition in <i>D. geothermalis</i>, as well as the regulatory mechanisms of the catalase induction pathway, raising the need for further investigation into the role of OxyR.