A quantitative model for the transcriptional landscape of the bacterial cell cycle. A quantitative model for the transcriptional landscape of the bacterial cell cycle

Regulation of gene activity during the cell cycle is fundamental to bacterial replication but is challenging to study in unperturbed, asynchronous bacterial populations. Using single cell RNA-sequencing of heterogeneous Staphylococcus aureus populations, we uncovered a global gene expression pattern dominated by chromosomal position. We show that this pattern results from the effect of DNA replication on gene expression, and in Escherichia coli, changes under different growth rates and modes of replication. By constructing a quantitative model in each species that links replication to cell cycle gene expression, we identified divergent genes that may be instead subject to distinct regulation, and applied this cell cycle framework to characterize heterogeneity in responses to antibiotic stress. Our approach reveals a highly dynamic cell cycle transcriptional landscape and may be broadly applicable across species. Overall design: scRNA-seq by the PETRI-seq method was performed on bacteria of species Escherichia coli and Staphylococcus aureus. scRNA-seq by the PETRI-seq method was performed on bacteria of species Escherichia coli and Bacillus subtilis.

细胞周期中的基因活性调控是细菌复制的核心基础，但在未受干扰的异步细菌群体中开展相关研究极具挑战。通过对异质性金黄色葡萄球菌（Staphylococcus aureus）群体开展单细胞RNA测序（single cell RNA-sequencing），我们发现了一类以染色体位置为主导的全局基因表达模式。研究证实，该模式源于DNA复制对基因表达的调控作用，且在大肠杆菌（Escherichia coli）中，该模式会随不同生长速率与复制模式发生改变。我们通过在两个物种中分别构建连接复制与细胞周期基因表达的定量模型，筛选出了可能受独特调控的差异基因，并运用该细胞周期分析框架解析了细菌对抗生素应激反应的异质性。本研究方法揭示了高度动态的细胞周期转录调控全景，且有望在跨物种研究中广泛应用。实验设计：采用PETRI-seq方法开展单细胞RNA测序的样本涵盖大肠杆菌（Escherichia coli）与金黄色葡萄球菌（Staphylococcus aureus）；此外还针对大肠杆菌（Escherichia coli）与枯草芽孢杆菌（Bacillus subtilis）完成了相同方法的单细胞RNA测序实验。