Chapter 18 : mRNA Decay and Processing

Physical relationship of RNase E and RNase G. The numbers below the horizontal rectangles represent the approximate domain boundaries as determined by McDowall and Cohen ( 95 ) and Vanzo et al. ( 156 ). ARRBS (rectangle) indicates the arginine-rich RNA binding site. The locations of the RhlB RNA helicase, enolase, and PNPase are as described by Vanzo et al. ( 156 ). The rneΔ374 allele retains the catalytic domain and the ARRBS and has been described by Ow et al. ( 121 ). The RNase G protein is 34% identical to the first 488 amino acids of RNase E.

Secondary structures that affect mRNA decay. (A) Rho-independent transcription terminator at the 3′ terminus of the E. coli lpp mRNA. Of particular note is the very short region of single-stranded RNA that is present at the 3′ terminus. Poly(A) tails can be added at any of the three unpaired U's ( 22 , 101 ). (B) Schematic view of the 5′ UTR of the ompA transcript as determined by Emory and Belasco ( 45 ). (C) Stem-loop structure recognized by RNase III. This is the R5 structure from the bacteriophage T7 early RNA ( 34 ). Arrows indicate the location of the RNase III cleavages.

Model for mRNA decay involving degradosome attachment at both the 3′ and 5′ termini of a single mRNA. In this model, binding of PNPase to the 3′ terminus of the poly(A) tail would bring along RNase E. RNase E would then bind to the 5′ triphosphate terminus if this is a primary transcript. With such an arrangement, one could account for the rapid degradation of an individual mRNA.

Current working model for mRNA decay in E. coli. (A) Initiation of mRNA decay by RNase E. Based on its catalytic properties ( 89 , 90 ), RNase E, as part of the degradosome or independently, would first bind to an accessible 5′ end. The preference of RNase E for substrates that are 5′ monophosphorylated over those that contain 5′ triphosphates ( 89 ) suggests that this step will be the rate-limiting reaction in mRNA decay. Intermediates generated by the initial RNase E cleavage reaction can be further degraded endonucleolytically by either RNase E or RNase G or exonucleolytically by a combination of RNases. PNPase is probably the primary 3′ → 5′ exonuclease ( 106 ). Polyadenylation will be involved if an RNA fragment contains a stable stem-loop structure. Terminal degradation products (short oligonucleotides) will be degraded by oligoribonuclease ( 50 ). (B) Initiation of mRNA decay by either RNase III or RNase P. In a limited number of circumstances, such as observed with the eno or his mRNAs, either RNase III or RNase P, respectively, cleave within intercistronic regions of polycistronic mRNAs to generate a downstream fragment that would have a 5′ phosphomonoester, making it a better substrate for RNase G or RNase E. Unlike RNase E, which can cleave RNAs at internal sites without binding to a 5′ terminus ( 12 ), RNase G apparently cannot do this very efficiently. Once either RNase G or RNase E cleavages occur, the breakdown products would be susceptible to exonucleolytic degradation as in panel A. Some mRNAs may contain either potential RNase E or RNase G cleavage sites that are bypassed as shown in panels A and B, respectively. (C) mRNA decay in the absence of RNase E or for mRNAs that do not contain RNase E cleavage sites. In the absence of RNase E, decay of mRNAs dependent on this enzyme will proceed more slowly, either through RNase G cleavage or exonucleolytic degradation by PNPase and/or other exonucleases. For those mRNAs that do not contain any endonucleolytic cleavage sites, decay is probably initiated by polyadenylation of the 3′ terminus. Subsequently, the polyadenylated mRNA is degraded exonucleolytically as described for panel A. Ellipses, RNase E cleavage sites; squares, RNase G cleavage sites; circles, RNase III or RNase P cleavage sites. Heavy lines indicate gene 1 in a polycistronic mRNA. 5′ phosphomonoester termini are underlined; 5′ termini containing a triphosphate are not.