Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Response to acid stress is critical for Escherichia coli to successfully complete its life-cycle by passing through the stomach to colonize the digestive tract. To develop a fundamental understanding of this response, we established a molecular mechanistic description of acid stress mitigation responses in E. coli and integrated them with a genome-scale model of its metabolism and macromolecular expression (ME-model). We considered three known mechanisms of acid stress mitigation: 1) change in membrane lipid fatty acid composition, 2) change in periplasmic protein stability over external pH and periplasmic chaperone protection mechanisms, and 3) change in the activities of membrane proteins. After integrating these mechanisms into an established ME-model, we could simulate their responses in the context of other cellular processes. We validated these simulations using RNA sequencing data obtained from five E. coli strains grown under external pH ranging from 5.5 to 7.0. We found: i) that for the differentially expressed genes accounted for in the ME-model, 80% of the upregulated genes were correctly predicted by the ME-model, and ii) that these genes are mainly involved in translation processes (45% of genes), membrane proteins and related processes (18% of genes), amino acid metabolism (12% of genes), and cofactor and prosthetic group biosynthesis (8% of genes). We also demonstrated several intervention strategies on acid tolerance that can be simulated by the ME-model. We thus established a quantitative framework that describes, on a genome-scale, the acid stress mitigation response of E. coli that has both scientific and practical uses.大肠杆菌（Escherichia coli）需通过胃部屏障并成功定植消化道以完成生命周期，酸应激应答对此过程至关重要。为深入解析该应激应答的分子机制，我们阐明了大肠杆菌酸应激缓解应答的具体分子机制，并将其与该菌的代谢与大分子表达基因组规模模型（macromolecular expression model, ME-model）进行整合。本研究涵盖三类已明确的酸应激缓解机制：1）细胞膜脂质脂肪酸组成的改变；2）周质蛋白稳定性随胞外pH的变化，以及周质分子伴侣的保护机制；3）膜蛋白活性的改变。将上述机制整合至已构建的ME-model后，我们得以在其他细胞生理过程的背景下模拟大肠杆菌的酸应激应答。我们采用在胞外pH 5.5至7.0环境中培养的5株大肠杆菌的RNA测序（RNA sequencing）数据，对上述模拟结果进行了验证。研究结果显示：其一，针对ME-model中纳入的差异表达基因（differentially expressed genes），该模型可正确预测80%的上调基因（upregulated genes）；其二，上述差异表达基因主要参与以下生理过程：翻译过程（占比45%）、膜蛋白及相关生理过程（占比18%）、氨基酸代谢（占比12%）以及辅因子与辅基生物合成（占比8%）。此外，我们还验证了若干可通过ME-model模拟的大肠杆菌酸耐受性干预策略。综上，本研究构建了一个基因组规模的定量分析框架，可用于描述大肠杆菌的酸应激缓解应答，该框架兼具科学研究与实际应用价值。