MRC London Institute of Medical Sciences, London, UK.
Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
Nat Microbiol. 2019 Mar;4(3):480-491. doi: 10.1038/s41564-018-0330-4. Epub 2019 Feb 4.
Phenotypic cell-to-cell variability is a fundamental determinant of microbial fitness that contributes to stress adaptation and drug resistance. Gene expression heterogeneity underpins this variability but is challenging to study genome-wide. Here we examine the transcriptomes of >2,000 single fission yeast cells exposed to various environmental conditions by combining imaging, single-cell RNA sequencing and Bayesian true count recovery. We identify sets of highly variable genes during rapid proliferation in constant culture conditions. By integrating single-cell RNA sequencing and cell-size data, we provide insights into genes that are regulated during cell growth and division, including genes whose expression does not scale with cell size. We further analyse the heterogeneity of gene expression during adaptive and acute responses to changing environments. Entry into the stationary phase is preceded by a gradual, synchronized adaptation in gene regulation that is followed by highly variable gene expression when growth decreases. Conversely, sudden and acute heat shock leads to a stronger, coordinated response and adaptation across cells. This analysis reveals that the magnitude of global gene expression heterogeneity is regulated in response to different physiological conditions within populations of a unicellular eukaryote.
表型细胞间的可变性是微生物适应性和耐药性的基本决定因素，它是由基因表达异质性所支撑的，但全基因组研究具有挑战性。在这里，我们通过结合成像、单细胞 RNA 测序和贝叶斯真实计数恢复，研究了超过 2000 个在各种环境条件下分裂的单细胞酵母的转录组。我们在恒定培养条件下快速增殖过程中鉴定出了多组高度可变的基因。通过整合单细胞 RNA 测序和细胞大小数据，我们深入了解了在细胞生长和分裂过程中受到调控的基因，包括那些表达与细胞大小不成比例的基因。我们进一步分析了在适应和急性响应不断变化的环境时基因表达的异质性。进入静止期之前，基因调控会逐渐同步适应，当生长减缓时，基因表达会变得高度可变。相反，突然的急性热休克会导致细胞间更强、更协调的反应和适应。这项分析表明，在单细胞真核生物群体中，对不同生理条件的反应会调节全局基因表达异质性的幅度。
