E. coli 16S Ribosomal RNA Degradation Pathways during Starvation and by Quality Control

Abstract

Ribosomes are generally stable in growing E. coli cells. However, under conditions of starvation leading to slow cell growth, the need for functional ribosomes decreases and they may become substrates for degradation. In addition, assembling ribosomes that are somehow defective also are eliminated by a quality control process in exponentially growing cells. We examined the pathways of rRNA degradation during starvation and in quality control. During starvation, RNase PH initiates removal of nucleotides from the 3′ end of 16S rRNA until nt 1403. This process leads to an endonucleolytic cleavage by RNase E at position 919. The resulting fragments are further degraded to mononucleotides by RNase R and RNase II. Our findings further suggest that although RNase E makes the internal cut in the quality control process as well, the cutting site is different; moreover, RNase PH plays no role in 16S rRNA degradation in the quality control process demonstrating that the two degradation pathways differ. The pathways also differ in the exoribonucleases which complete the degradation as RNase R and PNPase are required to degrade the intermediate fragments produced in quality control. These differences can be explained as the starting substrates in the quality control pathway are defective ribosomes, whereas in starvation, they are fully assembled, functional particles. These studies provide a detailed description of the pathways of degradation of rRNA during starvation and during steady-state growth due to quality control.