Exploring the Resilience of Deinococcus radiodurans: An Integrated Analysis of Genomic Diversity and Gene Regulation

Deinococcus radiodurans, a Gram-positive extremophilic bacterium, is widely recognized for its remarkable tolerance to ionizing radiation and oxidative stress, making it a prominent organism for DNA repair studies. Members of the Deinococcus genus can be isolated from various environments, both nutrient-rich and nutrient-poor, showcasing the notable versatility of the genus, especially the species D. radiodurans. Despite its important characteristics and potential for bioremediation of radiation-contaminated areas, the underlying genomic diversity behind its remarkable resistance remains poorly understood. Previous studies have identified species-specific genes, some of which are expressed in response to extreme radiation or desiccation. However, the lack of homology with other genes in other organisms suggests they belong to a unique gene pool within the species.
This work aimed to conduct a comparative genomics analysis of 15 genomes of D. radiodurans available in the GenBank database using Computational Biology tools such as Prokka and Roary. Additionally, a genetic analysis of the promoter sequences was performed to contextualize the potential biological roles of these unique genes, by comparing them with conserved sequences in other Gram-positive bacteria and extremophiles, searching for regions responsive to different Sigma factors of RNA polymerase. These analyses provide insights into the regulatory sequences governing responses to diverse stimuli and stresses, aiming to identify novel functions in extremophilic biology with potential biotechnological applications. Furthermore, the investigation of core genes and accessory compartments revealed that the pangenome includes 2,787 genes common to all 15 lineages and 928 accessory genes. Among the core genes, 1,509 (54.14%) were annotated as hypothetical proteins, while in the accessory compartments (shell and cloud), 709 (71.83%) were identified as hypothetical proteins. Functional analysis of the core genome showed 19.48% and 10.55% of unknown functions related to amino acid transport and metabolism, respectively, indicating the need for further studies on gene function and its adaptability to adverse conditions, such as high radiation doses. In the accessory genes, proteins related to replication, recombination, and repair predominated, which are closely related to the remarkable resistance and adaptation of D. radiodurans to radiation and other stresses. Additionally, a high percentage (13.84%) of genes with unknown functions was observed in both the core and accessory compartments. Furthermore, the analysis of the bioremediation/biosurfactants-related genes revealed a significant number of genes involved in the degradation of aromatic compounds, such as benzene and xylenes, which are highly toxic and can cause harmful effects on ecosystems in soil and water. This finding suggests the potential of D. radiodurans to play a role in bioremediation by utilizing these compounds as substrates or producing biosurfactants. We believe that these comprehensive studies will have significant implications for future biotechnological applications and the development of protection and remediation strategies for contaminated environments.