Comparative Proteomics Analysis Reveals New Features of the Oxidative Stress Response in the Polyextremophilic Bacterium Deinococcus radiodurans

Abstract

Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. radiodurans; however, the antioxidant mechanisms have not been fully characterized. In this study, comparative proteomics analysis of D. radiodurans grown under normal and oxidative stress conditions was conducted using label-free quantitative proteomics. The abundances of 852 of 1700 proteins were found to significantly differ between the two groups. These differential proteins are mainly associated with translation, DNA repair and recombination, response to stresses, transcription, and cell wall organization. Highly upregulated expression was observed for ribosomal proteins such as RplB, Rpsl, RpsR, DNA damage response proteins (DdrA, DdrB), DNA repair proteins (RecN, RecA), and transcriptional regulators (members of TetR, AsnC, and GntR families, DdrI). The functional analysis of proteins in response to oxidative stress is discussed in detail. This study reveals the global protein expression profile of D. radiodurans in response to oxidative stress and provides new insights into the regulatory mechanism of oxidative resistance in D. radiodurans.

Metaproteomics Reveals Alteration of the Gut Microbiome in Weaned Piglets Due to the Ingestion of the Mycotoxins Deoxynivalenol and Zearalenone

“…Ribosomal proteins and other translation and transcription elements were more abundant in the mycotoxin groups, such as 19 ribosomal proteins which increased in abundance in DONhigh and ZENhigh. Ribosomal proteins such as Rpsl, RpsR and RpsT were shown to be highly regulated by the extremophile Deinococcus radiodurans during oxidative stress [ 39 ]. It was hypothesized that damaged proteins need to be rapidly replaced when D. radiodurans is under oxidative stress.…”

Natural Pigments of Microbial Origin

“…Although works are mostly associated with plant pigments, more recently the microbial pigments production has been investigated by proteomics approach. These studies include the synthesis of pigments by Monascus purpureus under high ammonium chloride concentration (Zhou et al, 2020), the polyextremophilic bacterium Deinococcus radiodurans in response to oxidative stress (Gao et al, 2020), the pigmentation factors in Pseudomonas fluorescens ITEM 17298 (Quintieri et al, 2019), and the air-isolated Aspergillus sp. from International Space Station (Blachowicz et al, 2019).…”

Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum

“…PT9 T contains also various proteins implicated in defense mechanisms related to oxidative stress response, such as universal stress protein UspA, class III stress response-related ATPase ClpC, Fe-S center for redox-sensing, putative ATPdependent helicase DinG, putative ABC transporter YclH, ferric enterobactin transport ATP-binding protein FepC, daunorubicin/doxorubicin resistance ATP-binding protein DrrA. The proteins observed in response to oxidative stress of D. radiodurans were DNA repair proteins (PolA, RadA, RecA, RecF, RecO), DNA protein binding (ArgF, DnaE, HisS, RecN), ribosomal proteins (RplB, Rpsl, RpsR) and oxidation-reduction process proteins (GltA, NuoC) (Slade et al 2009;Ujaoney et al 2017;Gao et al 2020).…”