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Higher-order spatial organization of the Deinococcus radiodurans chromosomes

ABSTRACT: 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.

ORGANISM(S): Deinococcus radiodurans

PROVIDER: GSE241498 | GEO | 2025/01/29

REPOSITORIES: GEO

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Project description:Bacterial cells lacking pyrroloquinoline quinone (PQQ) were sensitive to gamma radiation as compared to wild type cells. Deinococcus radiodurans genome encode for five putative PQQ binding STK domain-containing proteins. The comparison of gamma radiation response of all five-deletion mutants with wild type suggested that dr2518 mutant was hypersensitive to gamma radiation as compared to wild type and other mutants. DR2518 is an auto kinase. Hence, the effect of dr2518 mutation on cellular response of Deinococcus radiodurans R1, to DNA damage and subsequently to its genome functions under both normal and post irradiation growth condition was further examined. Transcriptome analysis of dr2518 mutant grown under normal conditions and post-irradiated cells was done and compared with wild type cells. Mutant lacking dr2518 become extremely sensitive to gamma radiation and complete arrest in DSB repair. These cells were therefore checked for gene expression profile in native growth and gamma irradiated growth conditions All the genes subjected to microarray analysis are as described in the genome sequence of bacterium available at ftp://ftp.ncbi.nih.gov/genomes/bacteria/Deinococcus_radiodurans. Oligonucleotides designed to represent the respective predicted ORFs of Deinococcus radiodurans ((NC_001263, NC_001264, NC_000958, NC_000959) are synthesized and purified by hydrophobic column on HPLC. The oligonucleotides are deposited on to poly-L-Lysine slide in triplicate. Microarrays were scanned using Gene Pix 4000B and hybridization signals were quantified using GenePix Pro 5.1. Prior to channel normalization, microarray outputs were filtered to remove spots of poor signal quality by excluding those data points with a mean intensity by less that 2 standard deviation above background in both channels. Normalization of data and its statistical analysis were carried out in the R computing environment using linear models for microarray data package (Limma). Using this tool, the global LOESS normalization was carried out for each microarray. The 3- replicate spots per gene in each array were used to maximize the robustness of differential expression measurements of each gene via the âlmFitâ function within Limma. Two biological replicates were analysed for global gene expression profile in dr2518 mutant against wild type cells.

			Action	DRS
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	GSE241498_MAT_scn_UV.txt.gz	Txt
	GSE241498_MAT_scn_WT.txt.gz	Txt
	GSE241498_MAT_scn_dr0199.txt.gz	Txt
	GSE241498_RAW.tar	Raw

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Higher-order spatial organization of the Deinococcus radiodurans chromosomes

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