Supplementary data: Overriding bioprocess perturbations with a cell-machine interface for reliable microbial stress-response control

Supplementary data for the paper: Overriding bioprocess perturbations with a cell-machine interface for reliable microbial stress-response control Abstract Controlling cell population dynamics and phenotypic diversification is a key objective in systems and synthetic biology, particularly for ensuring uniform responses from engineered gene circuits. While cell-machine interfaces have been employed to modulate host-gene circuit interactions, environmental perturbations typical of industrial bioreactor conditions remain underexplored. In this study, we investigate the impact of such perturbations on the general stress response in Escherichia coli and Saccharomyces cerevisiae. Using scale-down bioreactor experiments, we evaluate the performance of the Segregostat, a real-time control system that leverages automated flow cytometry to induce dynamic nutrient shifts. The Segregostat achieves robust stress response control, even under severe perturbations such as extended residence times in a two-compartment reactor. We hypothesize that this robustness arises from the system’s ability to amplify host-compatible fluctuations beyond bioreactor-induced perturbations. Our findings highlight the importance of integrating environmental factors into control strategies for reliable gene circuit behavior in industrial bioprocessing environments.论文补充数据： 基于细胞-机器接口抵消生物过程扰动，实现可靠的微生物应激响应控制 摘要 调控细胞群体动力学与表型分化是系统生物学与合成生物学的核心目标之一，尤其对于保障工程化基因回路的响应一致性至关重要。尽管已有研究借助细胞-机器接口（cell-machine interface）调控宿主-基因回路的相互作用，但工业生物反应器典型环境中的扰动仍未得到充分探索。本研究针对此类扰动对大肠杆菌（Escherichia coli）与酿酒酵母（Saccharomyces cerevisiae）全局应激响应的影响展开探究。本研究通过缩尺生物反应器实验，评估了Segregostat的调控性能——这是一套借助自动化流式细胞术诱导动态营养偏移的实时控制系统。即便在双室反应器内延长停留时间这类强扰动条件下，Segregostat仍可实现稳定可靠的应激响应调控。我们推测，该系统的鲁棒性源于其可放大宿主兼容波动、抵消生物反应器诱发扰动的能力。本研究结果凸显了在工业生物加工环境中，将环境因素纳入调控策略以保障基因回路稳定运行的重要性。