The catabolic nature of fermentative substrates influences proteomic rewiring in Escherichia coli under anoxic growth

Abstract

Background: 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. Results: 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− 1). 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. Conclusions: 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.