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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

Messenger RNA Decay

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • Author: Sidney R. Kushner1
  • Editors: Susan T. Lovett2, Susan T. Lovett3
    Affiliations: 1: Department of Genetics, University of Georgia, Athens, GA 30602-7223; 2: Brandeis University, Waltham, MA; 3: Brandeis University, Waltham, MA
  • Received 05 January 2007 Accepted 12 March 2007 Published 01 June 2007
  • Address correspondence to Sidney R. Kushner [email protected].
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  • Abstract:

    This chapter discusses several topics relating to the mechanisms of mRNA decay. These topics include the following: important physical properties of mRNA molecules that can alter their stability; methods for determining mRNA half-lives; the genetics and biochemistry of proteins and enzymes involved in mRNA decay; posttranscriptional modification of mRNAs; the cellular location of the mRNA decay apparatus; regulation of mRNA decay; the relationships among mRNA decay, tRNA maturation, and ribosomal RNA processing; and biochemical models for mRNA decay. has multiple pathways for ensuring the effective decay of mRNAs and mRNA decay is closely linked to the cell's overall RNA metabolism. Finally, the chapter highlights important unanswered questions regarding both the mechanism and importance of mRNA decay.

  • Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4


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This chapter discusses several topics relating to the mechanisms of mRNA decay. These topics include the following: important physical properties of mRNA molecules that can alter their stability; methods for determining mRNA half-lives; the genetics and biochemistry of proteins and enzymes involved in mRNA decay; posttranscriptional modification of mRNAs; the cellular location of the mRNA decay apparatus; regulation of mRNA decay; the relationships among mRNA decay, tRNA maturation, and ribosomal RNA processing; and biochemical models for mRNA decay. has multiple pathways for ensuring the effective decay of mRNAs and mRNA decay is closely linked to the cell's overall RNA metabolism. Finally, the chapter highlights important unanswered questions regarding both the mechanism and importance of mRNA decay.

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Image of Figure 1
Figure 1

(A) The Rho-independent transcription terminator found at the 3′ terminus of the mRNA. The presence of a very short single-stranded region prevents the efficient binding of RNase R, RNase II, and PNPase. Both RNase II and PNPase are inhibited by the presence of the stem structure. Addition of a poly(A) tail will permit the binding of any of the three 3′ → 5′ exonucleases. (B) Stem-loop structure recognized by RNase III. This is the R5 structure from the bacteriophage T7 early RNA ( 36 ). Note that the stem structures recognized by RNase III are considerably longer than those associated with Rho-independent transcription terminators.

Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4
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Image of Figure 2
Figure 2

For a mRNA that does not contain endonucleolytic cleavage sites and/or is terminated with a Rho-independent transcription terminator, the first step in the decay process is probably the addition of a poly(A) tail since neither PNPase, RNase II, or RNase R can bind efficiently to the very short 3′ single-stranded region. Binding of PAP I to the 3′ terminus is facilitated by its interaction with Hfq and PNPase in a multiprotein complex ( 75 ). It is not clear whether the PNPase associated with the polyadenylation complex subsequently initiates decay or if it dissociates providing access to any of the three exonucleases. If the polyadenylation complex does dissociate, initiation of decay could involve a competition for the substrate by PNPase, RNase II, and RNase R. The three possible outcomes are shown. With PNPase, the stem-loop structure would be degraded into nucleoside diphosphates either through a series of repeated polyadenylation steps ( 53 ) or possibly through the combined action of PNPase and RhlB ( 161 ). Since RNase R is not inhibited by secondary structures, the entire molecule would be rapidly degraded to mononucleotides ( 51 ). RNase II binding would be least productive because the enzyme would stall near the base of the stem after the poly(A) had been degraded. Retention of RNase II would restrict access of other ribonucleases or PAP I from the terminus, effectively protecting it from further degradation ( 78 ). The terminal oligonucleotides (2 to 5 nt in length) would be substrates for RNase R ( 149 ).

Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4
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Image of Figure 3
Figure 3

A schematic representation of RNase E is presented showing the catalytic region, ARRBS (arginine-rich RNA binding site) and the degradosome scaffold region including the RhlB, enolase, and PNPase binding regions ( 202 , 297 , 298 , 299 ). The subdomains in the catalytic region as identified by the crystallographic analysis of Callaghan et al. ( 183 ) are color coded: S1 RNA binding domain (blue); RNase H (green); 5′ sensor region (purple); DNase I domain (yellow); Zn-link (black); and a small downstream domain (orange). There is a 34.1% identity between RNase G and RNase E over the first 489 aa. The most highly conserved regions fall within the S1 and DNase I domains.

Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4
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Image of Figure 4-01
Figure 4-01

Initiation of decay for a monocistronic mRNA. In the example shown here there are single cleavage sites for both RNase E and RNase G that are in close proximity. The binding of RNase E, the more abundant of the two ribonucleases that bind at 5′ termini, sterically prevents the binding of RNase G. Once the RNase E cleavage has taken place, the enzyme dissociates and RNase G may bind to the new 5′-phosphomonoester end. In this scenario the three decay intermediates will subsequently be degraded exonucleolytically as described in Fig. 5 . Alternatively, after RNase E cleavage, RNase G will not act, leaving two fragments to be degraded by the 3′ → 5′ exonucleases.

Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4
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Image of Figure 4-02
Figure 4-02

Initiation of decay for a polycistronic mRNA containing three open reading frames. Intercistronic regions are marked by small black vertical bars. As noted in panel A, the most abundant ribonuclease, RNase E, will bind to the 5′-triphosphate terminus to initiate decay. Its binding sterically prevents the binding of RNase LS at a contiguous site. However, the ability of RNase III to cleave the stem-loop structure in the intercistronic region is independent of RNase E action. Similarly, RNase P cleavage within the downstream intercistronic region is also independent of the initial RNase E cleavage. Once the RNase III and/or RNase P cleavages have taken place, the downstream RNase G and RNase Z cleavage sites may be recognized, independent of RNase E binding at the 5′ terminus. Thus the first round of endonucleolytic cleavage events will yield from between 5 and 7 decay intermediates. Subsequent cleavages by RNase E, RNase LS, RNase G, and RNase Z could lead to a total of 11 decay intermediates if all of the sites are cleaved. However, it is likely that some cleavages will not take place, if exonucleolytic degradation of the initial decay intermediates proceeds rapidly enough such that some endonucleolytic cleavage sites are degraded before they are recognized by their respective enzymes. In addition, it should also be noted that Baker and Mackie ( 188 ) have shown that under certain circumstances RNase E can cleave at internal sites without binding to a 5′ terminus. Sizes of the various endonucleases reflect an estimate of their relative participation in mRNA decay. For the sake of simplicity, RNase E is shown without the other components of the degradosome. In addition, it should also be noted that there may in fact be an enzyme that converts the 5′ terminus triphosphate to a 5′-monophosphate prior to the binding of RNase E or RNase G.

Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4
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Image of Figure 5
Figure 5

It has recently been reported that the degradosome forms a filament as part of the bacterial cytoskeleton ( 405 ). Furthermore, it has been demonstrated that at least the 5′ catalytic region of RNase E forms tetramers that are more active than monomers ( 89 , 300 , 301 ). Based on these findings, the model shown here involves that binding of the 5′ terminus of an mRNA through the 5′ sensor region and S1 binding domains of one RNase E molecule within the filament (white circles). Catalysis is carried out within the DNase I domain (yellow circles) while the 3′ terminus is bound to PNPase (red circles). The energy derived from phosphodiester bond cleavage is used to move the new 5′ terminus to an adjacent 5′ binding region in the filament. Cleavage would then take place within the cleavage site associated with the adjacent 5′ binding region. The 3′ terminus could remain attached to the original PNPase molecule or as shown here moved to the adjacent PNPase protein. This process would continue around the filament until all of the RNase E sites within a particular mRNA molecule have been cleaved and the remaining 3′-terminal fragments had been degraded by PNPase. Similar sets of reactions could be occurring all along the filament, providing an efficient mechanism for rapidly degrading large numbers of mRNA molecules. The rate-limiting steps would be the initial binding of the 5′ terminus to the degradosome filament.

Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4
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Image of Figure 6
Figure 6

Most 3′ → 5′ exonucleolytic degradation takes place on cleavage products arising from the endonucleolytic events depicted in Fig. 2 . For any RNA molecule that has a 3′ terminus that contains at least a 10-nt single-stranded region, either PNPase, RNase II, or RNase R can efficiently degrade it. For RNA fragments lacking a 3′ single-stranded region, polyadenylation by PAP I, as part of a multiprotein complex that also contains Hfq and PNPase ( 75 ), convert the molecule into an effective substrate for any of the three exonucleases. Oligoribonuclease is required to degrade the short oligoribonucleotides that are no longer substrates for PNPase, RNase II, and RNase R ( 149 ). At this point it is not known how frequently PNPase works biosynthetically to generate polynucleotide additions or what conditions trigger the biosynthetic reaction ( 75 , 77 ).

Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4
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Table 1

Enzymes, proteins, and RNAs involved in mRNA decay

Citation: Kushner S. 2007. Messenger RNA Decay, EcoSal Plus 2007; doi:10.1128/ecosalplus.4.6.4

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