Momin Huda, Appukuttan Deepti, Venkatesh K V
Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
Microb Cell Fact. 2025 Mar 25;24(1):71. doi: 10.1186/s12934-025-02658-4.
During anaerobic batch fermentation of substrates by Escherichia coli, there is a decline in cell proliferation rates and a huge demand is placed on cellular proteome to cater to its catabolic and anabolic needs under anoxic growth. Considering cell growth rates as a physiological parameter, previous studies have established a direct relationship between E. coli growth rate and cellular ribosomal content for fast-proliferating cells. In this study, we integrated experimental findings with a systemic coarse-grained proteome allocation model, to characterize the physiological outcomes at slow growth rate during anaerobic fermentative catabolism of different glycolytic and non-glycolytic substrates.
The anaerobic catabolism of substrates favored high ribosomal abundances at lower growth rates. Interestingly, a modification of the previously discussed "growth law", the ratio of active to inactive ribosomal proteome was found to be linearly related to the growth rate for cells proliferating at slow to moderate regime (growth rate < 0.8 h). Also, under nutrient- and oxygen-limiting growth conditions, the proteome proportion allocated for ribosomal activity was reduced, and the resources were channelized towards metabolic activities to overcome the limitations imposed during uptake and metabolizing substrate. The energy-intensive uptake mechanism or lower substrate affinity, expended more catabolic proteome, which reduced its availability to other cellular functions.
Thus, the nature of catabolic substrates imposed either uptake limitation or metabolic limitation coupled with ribosomal limitation (arising due to anoxic and nutritional stress), which resulted in higher proteome expenditure leading to sub-optimal growth phenotype. This study can form the basis for analyzing E. coli's ability to optimize metabolic efficiency under different environmental conditions- including stress responses. It can be further extended to optimizing the industrial anaerobic conversions for improving productivity and yield.
在大肠杆菌对底物进行厌氧分批发酵的过程中，细胞增殖速率会下降，并且在缺氧生长条件下，细胞蛋白质组需要满足其分解代谢和合成代谢的需求，面临巨大压力。将细胞生长速率视为一个生理参数，先前的研究已经确定了快速增殖细胞中大肠杆菌生长速率与细胞核糖体含量之间的直接关系。在本研究中，我们将实验结果与一个系统的粗粒度蛋白质组分配模型相结合，以表征在不同糖酵解和非糖酵解底物的厌氧发酵分解代谢过程中，低生长速率下的生理结果。
底物的厌氧分解代谢有利于在较低生长速率下具有较高的核糖体丰度。有趣的是，对先前讨论的“生长规律”进行修正后发现，对于在缓慢至中等生长状态（生长速率<0.8 h⁻¹）下增殖的细胞，活性核糖体蛋白质组与非活性核糖体蛋白质组的比例与生长速率呈线性相关。此外，在营养和氧气限制的生长条件下，分配给核糖体活性的蛋白质组比例降低，资源被引导至代谢活动，以克服在摄取和代谢底物过程中所面临的限制。能量密集型的摄取机制或较低的底物亲和力消耗了更多的分解代谢蛋白质组，从而减少了其可用于其他细胞功能的量。
因此，分解代谢底物的性质施加了摄取限制或代谢限制，再加上核糖体限制（由于缺氧和营养应激引起），这导致了更高的蛋白质组消耗，从而产生次优的生长表型。本研究可为分析大肠杆菌在不同环境条件下优化代谢效率的能力（包括应激反应）奠定基础。它可以进一步扩展到优化工业厌氧转化过程，以提高生产率和产量。
