Dallon Emma, Moran Haley M, Chidambaran Sadhana R, Kian Arman, Huang Betty Y H, Fried Stephen D, DiRuggiero Jocelyne
Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.
Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA.
bioRxiv. 2025 Jul 13:2025.04.08.647799. doi: 10.1101/2025.04.08.647799.
Oxidative stress induces a wide range of cellular damage, often causing disease and cell death. While many organisms are susceptible to the effects of oxidative stress, haloarchaea have adapted to be highly resistant. Several aspects of the haloarchaeal oxidative stress response have been characterized, however little is known about the impacts of oxidative stress at the translation level. Using the model archaeon , we performed RNA-seq and ribosome profiling (Ribo-seq) to characterize the global translation landscape during oxidative stress. We identified 281 genes with differential translation efficiency (TE). Downregulated genes were enriched in ribosomal and translation proteins, in addition to peroxidases and genes involved in the TCA cycle. We also identified 42 small noncoding RNAs (sRNAs) with ribosome occupancy. Size distributions of ribosome footprints revealed distinct patterns for coding and noncoding genes, with 12 sRNAs matching the pattern of coding genes, and mass spectrometry confirming the presence of seven small proteins encoded in these sRNAs. However, the majority of sRNAs with ribosome occupancy had no evidence of coding potential. Of these ribosome-associated sRNAs, 12 had differential ribosome occupancy or TE during oxidative stress, suggesting that they may play a regulatory role during the oxidative stress response. Our findings on ribosomal regulation during oxidative stress, coupled with potential roles for ribosome-associated noncoding sRNAs and sRNA-derived small proteins in , revealed additional regulatory layers and underscore the multifaceted architecture of stress-responsive regulatory networks.
氧化应激会引发广泛的细胞损伤，常常导致疾病和细胞死亡。虽然许多生物体易受氧化应激影响，但嗜盐古菌已经适应并具有高度抗性。嗜盐古菌氧化应激反应的几个方面已得到表征，然而，关于氧化应激在翻译水平上的影响却知之甚少。利用模式古菌，我们进行了RNA测序和核糖体谱分析（Ribo-seq），以表征氧化应激期间的全局翻译情况。我们鉴定出281个具有差异翻译效率（TE）的基因。除过氧化物酶和参与三羧酸循环的基因外（TCA循环），下调的基因在核糖体和翻译蛋白中富集。我们还鉴定出42个具有核糖体占据的小非编码RNA（sRNA）。核糖体足迹的大小分布揭示了编码基因和非编码基因的不同模式，其中12个sRNA与编码基因的模式匹配，质谱分析证实了这些sRNA中编码的7种小蛋白质的存在。然而，大多数具有核糖体占据的sRNA没有编码潜力的证据。在这些与核糖体相关的sRNA中，有12个在氧化应激期间具有差异核糖体占据或TE，这表明它们可能在氧化应激反应中发挥调节作用。我们关于氧化应激期间核糖体调控的研究结果，以及核糖体相关非编码sRNA和sRNA衍生的小蛋白质在[此处原文缺失相关内容]中的潜在作用，揭示了额外的调控层面，并强调了应激反应调控网络的多方面架构。
