mRNA degradation involves multiple activities

KEY CONCEPTS:

• Degradation of yeast mRNA requires removal of the 5 cap and the 3 poly(A).
• One yeast pathway involves exonucleolytic degradation from 5–3.
• Another yeast pathway uses a complex of several exonucleases that work in the 3–5 direction.
• The deadenylase of animal cells may bind directly to the 5 cap.

 We know most about the degradation of mRNA in yeast. There are basically two pathways. Both start with removal of the poly(A) tail (for review see Beelman and Parker, 1995). This is catalyzed by a specific deadenylase which probably functions as part of a large protein complex (Tucker et al., 2001). (The catalytic subunit is the exonuclease Ccr4 in yeast, and is the exonuclease PARN in vertebrates, which is related to RNAase D.) The enzyme action is processive—once it has started to degrade a particular mRNA substrate, it continues to whittle away that mRNA, base by base.

 

The major degradation pathway is summarized in Figure 5.24. Deadenylation at the 3 end triggers decapping at the 5 end. The basis for this relationship is that the presence of the PABP (poly(A)-binding protein) on the poly(A) prevents the decapping enzyme from binding to the 5 end. PABP is released when the length of poly(A) falls below 10-15 residues. The decapping reaction occurs by cleavage 1-2 bases from the 5 end.

Each end of the mRNA influences events that occur at the other end. This is explained by the fact that the two ends of the mRNA are held together by the factors involved in protein synthesis (see 6.9 Eukaryotes use a complex of many initiation factors). The effect of PABP on decapping allows the 3 end to have an effect in stabilizing the 5 end. There is also a connection between the structure at the 5 end and degradation at the 3 end. The deadenylase directly binds to the 5 cap, and this interaction is in fact needed for its exonucleolytic attack on the poly(A) (Gao et al., 2000).

What is the rationale for the connection between events occurring at both ends of an mRNA? Perhaps it is necessary to ensure that the mRNA is not left in a state (having the structure of one end but not the other) that might compete with active mRNA for the proteins that bind to the ends.

Removal of the cap triggers the 5–3 degradation pathway in which the mRNA is degraded rapidly from the 5 end, by the 5–3 exonuclease XRN1 (Muhlrad, Decker, and Parker, 1994). The decapping enzyme is concentrated in discrete cytoplasmic foci, which may be “processing bodies” where the mRNA is deadenylated and then degraded after it has been decapped (Sheth and Parker, 2003).

In the second pathway, deadenylated yeast mRNAs can be degraded by the 3–5 exonuclease activity of the exosome , a complex of >9 exonucleases (Mitchell et al., 1997, Allmang et al., 1999). The exosome is also involved in processing precursors for rRNAs. The aggregation of the individual exonucleases into the exosome complex may enable 3–5 exonucleolytic activities to be coordinately controlled. The exosome may also degrade fragments of mRNA released by endonucleolytic cleavage. Figure 5.25 shows that the 3–5 degradation pathway may actually involve combinations of endonucleolytic and exonucleolytic action. The exosome is also found in the nucleus, where it degrades unspliced precursors to mRNA (Bousquet-Antonelli, Presutti, and Tollervey, 2000).

Yeast mutants lacking either exonucleolytic pathway degrade their mRNAs more slowly, but the loss of both pathways is lethal (Mitchell et al., 1997; for review see Jacobson and Peltz, 1996).