Regulation of RNase PH during nutrient deprivation: the role of proteases, GroEL, and RNase II

RNase PH is a critical exoribonuclease in Escherichia coli that participates in tRNA maturation and RNA degradation. In earlier work, it was observed that levels of RNase PH decreased as much as 90% under conditions of nutrient deprivation, such as induced starvation and prolonged stationary phase, and that its removal was likely due to the degradation of the protein. Here, we examine the mechanisms involved in this regulatory process. We find that the protease Lon is primarily responsible for the removal of RNase PH that occurs in stationary phase and starvation. Conversely, RNase PH remains stable during the exponential phase of growth due to a protective interaction with the chaperonin protein, GroEL. Overproduction of GroEL protects RNase PH even under conditions of nutrient deprivation. Additionally, we find that RNase II activity also is required for the degradation of RNase PH, implying the involvement of an RNA molecule in the overall regulatory process. In mutant strains devoid of RNase II activity, even though retaining RNase II protein, RNase PH levels remain unchanged during nutrient deprivation which leads to excessive rRNA removal and ultimately to loss of viability. These findings provide another example of the complex regulatory mechanisms that underscore the importance of maintaining appropriate RNase levels under varying physiological conditions.IMPORTANCEThis work provides important new information on the regulation of a bacterial ribonuclease as it responds to nutrient deprivation. We find that RNase PH levels decrease up to 90% in late stationary phase and upon carbon starvation. We show that the enzyme is degraded by a protease under the stress conditions but that it is protected during growth by interaction with another protein, the chaperonin GroEL. This interaction does not occur under the stress conditions rendering RNase PH susceptible to degradation by protease Lon. We also find that the activity of another ribonuclease, RNase II, plays a role in the process, and that in the absence of RNase II activity, RNase PH does not decrease in stationary phase leading to cell death due to ribosome degradation. These studies identify a new mechanism of ribonuclease regulation and emphasize the importance of this regulation for cellular homeostasis.