State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China.
Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Mol Cell Proteomics. 2022 Nov;21(11):100423. doi: 10.1016/j.mcpro.2022.100423. Epub 2022 Oct 7.
Organisms have developed different mechanisms to respond to stresses. However, the roles of small ORF-encoded peptides (SEPs) in these regulatory systems remain elusive, which is partially because of the lack of comprehensive knowledge regarding these biomolecules. We chose the extremophile Deinococcus radiodurans R1 as a model species and conducted large-scale profiling of the SEPs related to the stress response. The integrated workflow consisting of multiple omics approaches for SEP identification was streamlined, and an SEPome of D. radiodurans containing 109 novel and high-confidence SEPs was drafted. Forty-four percent of these SEPs were predicted to function as antimicrobial peptides. Quantitative peptidomics analysis indicated that the expression of SEP068184 was upregulated upon oxidative treatment and gamma irradiation of the bacteria. SEP068184 was conserved in Deinococcus and exhibited negative regulation of oxidative stress resistance in a comparative phenotypic assay of its mutants. Further quantitative and interactive proteomics analyses suggested that SEP068184 might function through metabolic pathways and interact with cytoplasmic proteins. Collectively, our findings demonstrate that SEPs are involved in the regulation of oxidative resistance, and the SEPome dataset provides a rich resource for research on the molecular mechanisms of the response to extreme stress in organisms.
生物已经进化出不同的机制来应对压力。然而，小开放阅读框编码肽（SEP）在这些调节系统中的作用仍然难以捉摸，部分原因是缺乏对这些生物分子的全面了解。我们选择极端耐热菌 Deinococcus radiodurans R1 作为模式物种，并对与应激反应相关的 SEP 进行了大规模的分析。我们简化了包含多种组学方法的 SEP 鉴定的集成工作流程，并构建了含有 109 个新的和高可信度 SEP 的 D. radiodurans SEPome。这些 SEP 中有 44%被预测具有抗菌肽的功能。定量肽组学分析表明，SEP068184 的表达在细菌的氧化处理和伽马辐射后上调。SEP068184 在 Deinococcus 中保守，并在其突变体的比较表型测定中表现出对氧化应激抗性的负调控。进一步的定量和交互蛋白质组学分析表明，SEP068184 可能通过代谢途径发挥作用，并与细胞质蛋白相互作用。总的来说，我们的发现表明 SEPs 参与了氧化抗性的调节，而 SEPome 数据集为研究生物体对极端应激的分子机制提供了丰富的资源。
