Table S18 from Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation

The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.

生物钟（circadian clock）调控着维系生长与存活的核心生理过程。迄今为止，绝大多数植物生物钟相关研究均以昼夜转录组变化为核心研究手段，旨在阐明野生型植物中生物钟与可观测表型之间的分子关联。本研究整合了RNA测序（RNA-sequencing）与蛋白质质谱（protein mass spectrometry）数据，对处于昼末与夜末阶段的lhycca1、prr7prr9、gi以及toc1四种生物钟突变体莲座叶丛进行了比较分析。各突变体均可特异性影响特定的基因与蛋白集合，提示生物钟的调控机制具有模块化特征。此外，每一种生物钟突变体均拥有其专属的、与亚细胞区室特异性匹配的动态波动转录组与蛋白质组特征谱。绝大多数检测到的蛋白水平与其对应转录本的丰度变化并无显著相关性。丰度呈现协同变化的转录本与蛋白，其富集的基因类别多为碳水化合物响应基因与低温响应基因。四种生物钟突变体的转录组变化还会影响编码淀粉降解酶、转录因子以及蛋白激酶的基因表达。本研究获取的全面转录组与蛋白质组数据集证实，未来开展系统驱动型的生物钟研究必须采用多维度实验手段。本研究同时表明，仍需开展进一步研究以阐明翻译后修饰与蛋白降解在生物钟相关调控过程中的具体作用。