Synergistic and individual effects of RNase E, II, and R in the regulation of Escherichia coli growth and metabolism

Messenger RNA levels, crucial for cell survival and adaptation, are regulated through their degradation by ribonucleases (RNases). Although the molecular mechanisms of RNases in Escherichia coli are established, the broader effects of RNases on growth and metabolism remain unclear. Here, the roles of three RNases, E, II, and R, were examined individually and in combination in double and triple mutants. Growth behaviors and metabolic changes were analyzed on different carbon sources and under recombinant protein production conditions. C-terminal truncation of RNase E was unexpectedly found to have strong effects, promoting carbon-storage metabolism, thereby leading to glycogen accumulation, especially with glucose as a carbon source. Even more surprisingly, it accelerated growth on xylose. Synergistic interactions between the three RNases were also identified. Deleting RNase R amplified glycogen accumulation in the RNase E mutant, and further increased its growth rate. All three RNases were found to significantly contribute to acetate overflow regulation, with synergy between RNase E and R. Combined mutations had additional benefits under protein production conditions. Compared with the parental strain, the double mutant with both RNase E truncation and RNase II deletion produced up to twice as much recombinant protein, grew faster on xylose, and produced more glycogen on glucose. Overall, this work shows that RNase E, II, and R act both independently and synergistically in controlling E. coli growth and metabolism across carbon sources and bioproduction conditions. These findings highlight the strong relationship between RNA degradation and cell physiology and offer perspectives for engineering optimized microbial chassis in biotechnology.

IMPORTANCE

Messenger RNA degradation is a fundamental layer of gene regulation; however, its system-level impact on bacterial physiology remains poorly understood. Here, we show that RNase E, RNase II, and RNase R act both independently and synergistically to control Escherichia coli growth and metabolism across diverse carbon sources and bioproduction conditions. Unexpectedly, C-terminal truncation of RNase E, either alone or in combination with RNase II or RNase R, modulates glycogen and acetate metabolism and improves growth performance. Enhanced recombinant protein production was also observed, and the underlying mechanism was investigated. By directly linking the RNA degradation machinery to metabolic regulation and cellular performance, this work highlights RNases as powerful and underexploited targets for engineering improved microbial chassis for biotechnology.