An adaptive biomolecular condensation response is conserved across environmentally divergent species

Cells must sense and respond to sudden maladaptive environmental changes—stresses—to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In e..., , Eight folders contain raw and processed data as well as R or Python scripts to produce the figures in the paper., This README file is for the data published in \"An adaptive biomolecular condensation response is conserved across environmentally divergent species\" by Keyport Kik et al. (2023) (preprint: ). These folders also contain custom R (version 4.2.2) scripts for data processing, analysis, and figure generation, organized into separate experimental folders. Some data have a separate R code for data processing and exporting data. The ordering of the figures may be different from what's shown in the paper. The code used to process raw RNA-seq data can be found on Github (. The rest of the data and scripts can be found on Dryad (). Below is a description of the contents of each folder. Raw RNA-seq data can be found under GEO accession code GSE234499.

Please note: The most recent version of this package has been updated to include changes recommended by the reviewers, including microscopy data and further analysis for the HDX-MS section.

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supp-files/

Within this folder are three supplemtanal...

细胞必须感知并响应突发的适应性不良环境变化（即胁迫），方能存活并繁衍壮大。在真核生物中，热激等胁迫会触发保守的响应程序：包括生长停滞、特异性转录响应，以及在严重胁迫下蛋白质与mRNA发生生物分子凝聚（biomolecular condensation），形成被称为应激颗粒（stress granules）的结构。这类凝聚结构的组成、形成机制、适应性意义，乃至进化保守性，目前仍有待阐明。本研究为胁迫诱导的生物分子凝聚、其进化保守性与调控适配机制，以及其与应激响应其他已被充分研究的环节的整合，提供了全新的认知视角。本研究选取3株形态学近乎一致的出芽酵母菌株，它们适配不同温度环境且分化时长可达1亿年。研究发现，蛋白质组规模的生物分子凝聚会根据物种特异性的温度生态位进行调控，其变化与对应菌株的生长及转录响应高度匹配。在e..., , 本数据集包含8个文件夹，分别存储原始与处理后的数据，以及用于复现论文图表的R或Python脚本。

本README文件对应Keyport Kik等人2023年发表的论文"An adaptive biomolecular condensation response is conserved across environmentally divergent species"的研究数据（预印本链接：）。各实验文件夹下均配备适配的R语言（版本4.2.2）脚本，用于数据处理、分析及图表生成；部分数据集还配有独立的R代码用于数据处理与导出。图表的排版顺序可能与论文中略有差异。用于处理原始RNA测序（RNA-seq）数据的代码可在GitHub（）获取；其余数据与脚本可在Dryad（）获取。下文将逐一介绍各文件夹的内容。原始RNA测序数据的GEO登录号为GSE234499。

请注意：本数据包的最新版本已根据审稿人建议进行更新，新增了显微成像数据以及氢氘交换质谱（HDX-MS）模块的补充分析内容。

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supp-files/
本文件夹内包含3个补充[原文疑似拼写错误，应为supplementary]……