Characterization of the DdrD protein from the extremely radioresistant bacterium Deinococcus radiodurans

Abstract

Here, we report the in vitro and in vivo characterization of the DdrD protein from the extraordinary stress-resistant bacterium, D. radiodurans. DdrD is one of the most highly induced proteins following cellular irradiation or desiccation. We confirm that DdrD belongs to the Radiation Desiccation Response (RDR) regulon protein family whose expression is regulated by the IrrE/DdrO proteins after DNA damage. We show that DdrD is a DNA binding protein that binds to single-stranded DNA In vitro, but not to duplex DNA unless it has a 5′ single-stranded extension. In vivo, we observed no significant effect of the absence of DdrD on the survival of D. radiodurans cells after exposure to γ-rays or UV irradiation in different genetic contexts. However, genome reassembly is affected in a ∆ddrD mutant when cells recover from irradiation in the absence of nutrients. Thus, DdrD likely contributes to genome reconstitution after irradiation, but only under starvation conditions. Lastly, we show that the absence of the DdrD protein partially restores the frequency of plasmid transformation of a ∆ddrB mutant, suggesting that DdrD could also be involved in biological processes other than the response to DNA damage.

Comprehensive Temporal Protein Dynamics during Postirradiation Recovery in Deinococcus radiodurans

“…In vivo, PprA interacted with GyrA and DNA topoisomerase to preserve the integrity of the D. radiodurans genome after DNA damage [ 28 ]. Similar to other Ddr proteins, ddrD gene expression is controlled by the IrrE/DdrO protein pair, and DdrD likely contributes to cell recovery after extensive genotoxic stress [ 29 ].…”

DNA repair and oxidative stress defense systems in radiation-resistant Deinococcus murrayi

“…These genes were called ddrA, ddrB, ddrC, ddrD, and pprA. In recent years, these five genes and the encoded proteins have been characterized in several studies (Devigne et al 2019;Lim et al 2019;Bouthier de la Tour et al 2021;Rajpurohit et al 2021;Banneville et al 2022) (and references therein). All five proteins are able to bind to DNA (single-stranded and/or double-stranded), and contribute in DNA protection and repair processes.…”

cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans

“…Transcriptome analysis further provides direct evidence for this hypothesis: a considerable part of the upregulated genes in response to drought and radiation stress in D. radiodurans overlap, and there is a palindromic consensus sequence in the promoter region of these genes, named r adiation/ d esiccation r esponse m otif (RDRM) ( 20 – 22 ). These RDRM-containing genes are not only involved in the classical DNA repair processes (e.g., recA and ssb , which are also found in other bacteria) but also Deinococcus-specific genes with novel functions, such as some ddr ( D NA d amage r esponse) series genes ( 23 – 25 ). Recent studies have uncovered an elegant RDRM regulation mechanism by a transcription factor protein DdrO and metalloprotease PprI ( 26 – 28 ).…”