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Although vigorous research efforts, aimed to understand the mechanism of mRNA degradation that is important in regulation of gene expression, have been directed entirely to RNases to identify putative mRNases since the discovery of the mRNA instability, the elucidation of the mRNA degradation mechanism has been the slowest process among principal gene regulatory processes in Escherichia coli. In respect of shorter half-lives of prokaryotic mRNAs than those of eucaryotic mRNAs, a 5'-to-3' directionality of mRNA decay in accordance with the 5'-to-3' directionality of coupled transcription-translation in prokaryotes has been paid special attention. Formerly, in this line of research works, a putative ribosome-associated 5'-to-3' exoribonuclease (RNase V) had been proposed as an mRNase, but it is known that such a 5'-to-3' exoribonuclease does not exist in E. coli. Therefore, current models suggest that mRNA degradation is initiated by a certain endoribonuclease(s) (functional inactivation of message) and the subsequent degradation of resulting fragments is carried out by 3'-to-5' exoribonucleases (mass decay). According to the case of polycistronic lac mRNA degradation, it is initiated near the 5' end and progressed in the net 5'-to-3' direction, and predominant cleavage sites are the phosphodiester bonds between pyrimidine and adenine residues (e.g., U ↓ A). Furthermore, most of the mRNA degradation products in growing E. coli have 5'-OH ends. These specificities are also known to correspond to those of non-enzymatic hydrolysis of RNA, nonetheless, the possibility of non-enzymatic degradation was neglected. For example, an enzyme, RNase M was proposed as a new mRNase candidate for the characteristic activity. However, it was failed to identify the structural gene for RNase M. Again, in line of “only RNases degrade (inactivate) mRNA” concept, RNase E which is an essential enzyme carrying out 5S rRNA maturation and a 5'-end-dependent endoribonuclease showing the sequence specificity of A+U rich single-stranded regions, and RNase E-based degradosome assembly have attracted so much attention as alternative mRNase candidates. However, RNase E not only shows marked preference for cleaving RNA that carries a monophosphate group at the 5' end rather than a triphosphate or a hydroxyl, but also generates 5'-phosphate ends instead of 5'OH ends (Fig. 1). In addition, the observation of rapid degradation of rpsO mRNA (ribosomal protein S15 mRNA) in a triple mutant (RNase E−, PNPase−, and RNase E−)16 and of normal half-lives for several mRNAs in cells containing truncated forms of RNase E which preclude degradosome assembly, may indicate that RNase E and the degradosome assembly are irrelevant to the functional decay of mRNA. Consequently, there is no obvious evidence to support the concept of “only RNases degrade mRNA”. Three decades ago, in advance of the discovery of RNase-free self-cleavage activity of RNA, a possibility of non-enzymatic E. coli mRNA degradation mediated by protein biosynthetic machinery was proposed by Ko. Recently, it has been discovered that translational pausing can promote endonucleolytic mRNA cleavage near the paused sites of ribosomes even in the absence of known endoribonucleases of E. coli. This finding led in this field to suppose the possibility that ribosomes may be involved in the endonucleolytic cleavage event.

Possibility of Non-enzymatic mRNA Degradation in E. coli : I. Bell-shaped Kinetic Feature