Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast

Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse subset of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were approximately 10% higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extant and signature of the post- transcriptional buffering. Ribosome profiling and RNA-seq of eight natural Saccharomyces cerevisiae isolates

已知基因表达在个体间存在差异，且该表达差异可影响自然种群中观测到的表型多样性。尽管转录组（transcriptome）与蛋白质组（proteome）已得到广泛研究，但学界对翻译过程本身的认知仍较为匮乏。为此，我们针对一组遗传与生态特征均具多样性的酿酒酵母（Saccharomyces cerevisiae）自然分离株子集，开展了核糖体谱（ribosome profiling）与转录组谱分析。有趣的是，我们发现：在每一对分离株的比较中，转录组层面的谱图与表达倍数变化之间的欧氏距离（Euclidean distances），较翻译层面高出约10%。这一观测结果明确表明，不同分离株间的转录变异可通过翻译层面的转录后缓冲（post-transcriptional buffering）现象得到缓解。此外，该现象呈现出特定的分子特征：它会优先作用于必需基因（essential genes）、参与复合物形成的蛋白编码基因，以及低转录水平基因。我们还对酿酒酵母泛基因组（pangenome）的翻译调控情况进行了探究，发现与渐渗事件（introgression events）相关的附属基因（accessory genes），其转录与翻译水平与核心基因组（core genome）基本一致。与之形成鲜明对比的是，通过水平基因转移（horizontal gene transfer）事件获得的基因，其翻译效率往往偏低。综上，本研究结果既证实了转录后缓冲现象的存在，也揭示了其独特的分子特征。本数据集包含8株酿酒酵母自然分离株的核糖体谱分析与RNA测序（RNA-seq）数据。