Higher-order spatial organization of the Deinococcus radiodurans chromosomes
Radiation-resistant Deinococcus radiodurans is an extreme microorganism capable of withstanding high levels of ionizing radiation and chemical mutagens. It possesses remarkable DNA repair capabilities and serves as a model organism for studying stress resistance mechanisms. However, our understanding of the relationship between the biological characteristics of this species and its chromosomal 3D structure remains limited. In this study, we employed chromosome conformation capture and sequencing (3C-seq) technology to determine the 3D genome structure of D. radiodurans and to further investigate the changes of chromosome conformation induced by ultraviolet irradiation. We observed that the overall chromatin folding structure of the cells became much looser after UV irradiation, with smaller chromosomal interaction domains (CIDs) merging to form larger CIDs. Integrating transcriptomic data analysis, we found that the majority of upregulated differentially expressed genes were significantly enriched near specific CID boundaries. Additionally, we comprehensively elucidated that Dr_ebfC as a nuclear-associated protein, serves as a global regulatory factor in gene expression processes and may modulate transcriptional regulation by altering chromosomal structure, thereby influencing the physiological state of the bacterium. Overall, our study provides insights into the chromosomal conformational changes of D. radiodurans under different conditions, offering valuable resources for further understanding the molecular mechanisms underlying its extreme resistance. Overall design: Chromosome conformation capture of Deinococcus radiodurans wt cells, UV irradiated cells and a deletion mutant (dr_0199)