Dataset Information

Differential Proteomics of pprI-Knockout Deinococcus radiodurans: A Label-Free Quantitative Analysis

ABSTRACT: Deinococcus radiodurans, renowned for its exceptional resistance to radiation, provides a robust model for elucidating cellular stress responses and DNA repair mechanisms. The global regulator PprI plays a pivotal role in maintaining this resilience by coordinating DNA damage repair, antioxidant defense, and metabolic reprogramming. This study employs label-free quantitative proteomics coupled with high-resolution mass spectrometry to systematically compare the proteomic profiles of pprI-knockout and wild-type D. radiodurans strains. Under stringent screening criteria, we identified 719 significantly upregulated and 281 significantly downregulated proteins in the knockout strain. Functional analysis revealed that PprI deletion disrupts homologous recombination (HR) repair, activates nucleotide excision repair (NER) and base excision repair (BER) as a compensatory mechanism, and impairs Mn/Fe homeostasis and carotenoid biosynthesis, leading to increased oxidative stress. Furthermore, PprI deficiency induces significant metabolic reprogramming, including impaired purine synthesis, compromised cell wall integrity,etc. These findings highlight PprI as a central orchestrator of multi-pathway synergies, providing critical insights into the molecular mechanisms underlying extreme radiation resistance.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Deinococcus Radiodurans

TISSUE(S): Cell Suspension Culture

SUBMITTER: siyu Zhu

LAB HEAD: Yongqian Zhang

PROVIDER: PXD062500 | Pride | 2025-06-30

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	HFX_BIT_LF_DR1_20231107.raw	Raw
	HFX_BIT_LF_DR2_20231107.raw	Raw
	HFX_BIT_LF_DR3_20231107.raw	Raw
	HFX_BIT_LF_DR4_20231107.raw	Raw
	HFX_BIT_LF_pprI1_20231107.raw	Raw

Items per page:

1 - 5 of 17

Publications

Unraveling the Central Role of Global Regulator PprI in <i>Deinococcus radiodurans</i> Through Label-Free Quantitative Proteomics.

Zhu Siyu S Liu Feng F Wang Hao H Zhang Yongqian Y

Proteomes 20250523 2

<h4>Background</h4><i>Deinococcus radiodurans</i>, renowned for its exceptional resistance to radiation, provides a robust model for elucidating cellular stress responses and DNA repair mechanisms. Previous studies have established PprI as a key regulator contributing to radiation resistance through its involvement in DNA damage repair pathways, oxidative stress response, and metabolic regulation.<h4>Methods</h4>Building upon these foundations, our study employs label-free quantitative (LFQ) pro ...[more]

PMID: 40559992

Similar Datasets

Project description:Abstract Background The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for one year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. In addition, a ground-based simulation experiment with conditions, mirroring those from Low Earth orbit, was performed. Methods We monitored Deinococcus radiodurans cells during early stage of recovery after Low Earth orbit exposure using electron microscopy tools. Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival of Deinococcus radiodurans in Low Earth orbit. Results D. radiodurans cells exposed to low Earth orbit conditions do not exhibit any morphological damage. However, an accumulation of numerous outer-membrane associated vesicles was observed. On levels of proteins and transcripts, a multifaceted response was detected to alleviate cell stress. The UvrABC endonuclease excision repair mechanism was triggered to cope with DNA damage. Defense against reactive oxygen species is mirrored by the increased abundance of catalases and is accompanied by the increased abundance of putrescine which works as scavenging molecule. In addition, several proteins and mRNAs, responsible for regulatory and transporting functions showed increased abundances. The decrease in primary metabolites indicate alternations in the energy status, which is needed to repair damaged molecules. Conclusion Low Earth orbit induced molecular rearrangements trigger multiple components of metabolic stress response and regulatory networks in exposed microbial cells. Presented results show that the non-sporulating bacterium Deinococcus radiodurans survived long-term Low Earth orbit exposure if wavelength below 200 nm are not present, which mirrors the UV spectrum of Mars, where CO2 effectively provides a shield below 190 nm. These results should be considered in the context of planetary protection concerns and the development of new sterilization techniques for future space missions.

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.

Dataset Information

Differential Proteomics of pprI-Knockout Deinococcus radiodurans: A Label-Free Quantitative Analysis

Dataset's files

Publications

Unraveling the Central Role of Global Regulator PprI in <i>Deinococcus radiodurans</i> Through Label-Free Quantitative Proteomics.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Dataset Information

Differential Proteomics of pprI-Knockout Deinococcus radiodurans: A Label-Free Quantitative Analysis

Dataset's files

Publications

Unraveling the Central Role of Global Regulator PprI in &lt;i&gt;Deinococcus radiodurans&lt;/i&gt; Through Label-Free Quantitative Proteomics.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Unraveling the Central Role of Global Regulator PprI in <i>Deinococcus radiodurans</i> Through Label-Free Quantitative Proteomics.