Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

To understand the contribution of mRNA synthesis and degradation rates towards setting protein concentrations, we performed RNA-sequencing based measurements of mRNA abundance and degradation to facilitate comparisons with recently collected proteomic datasets (Mori 2021) in the same E. coli strain. Overall design: For mRNA abundance determination, we grew E. coli exponentially in several different growth media and extracted total RNA. To determine mRNA degradation rates, Rifampicin was added to inhibit transcription initiation in exponentially growing E. coli and RNA was extracted from different samples over the next 11 minutes for sequencing.

为阐明mRNA合成与降解速率对蛋白质浓度设定的贡献，我们开展了基于RNA测序（RNA-sequencing）的mRNA丰度与降解检测，以便与同一大肠杆菌（E. coli）菌株中近期获取的蛋白质组学数据集（Mori 2021）进行对比。
实验总体设计：在mRNA丰度测定环节，我们将大肠杆菌在多种不同培养基中进行指数期培养，并提取总RNA。为测定mRNA降解速率，我们向处于指数生长期的大肠杆菌培养液中添加利福平（Rifampicin）以抑制转录起始，并在后续11分钟内从不同时间点的样本中提取RNA用于测序。