How can 3' end polyadenylation protect cellular RNA from ribonuclease degridation?

Question

In this link, it states:

It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding within an RNA protein complex (ribonucleoprotein particle or RNP).

I do not understand how polyadenylation protects the intracellular RNA from ribonuclease. I always thought that polyadenylation was a way to mark RNA for degradation, not protect it from degradation. Perhaps it is speaking of protection from exoribonuclease only and not endoribonuclease?

Can someone explain this?

Answer 1

According to my book Molecular Biology Principles of Genome Function by Craig et al, eukaryotic RNA degradation does not have an initiation, as in bacteria where pyrophoasphate hydrolase hydrolyses the 5'-triphosphate to 5'-monophosphate, and is therefore the initiatior.

In eukaryotes the polyA-tail is shortened by a deadenylase enzyme complex which contains a 3'to 5' exonuclease called CCR4. But deadenylation of polyA-tail doesn't necessesarily need to lead to degradation since it is reversible by post-translational readenylation.

Poly A tail protects the mRNA by not letting the nucleases reach the mRNA itself. As long as poly A tail is degraded, its just fine, since it can readenylate back again. The figure below shows the degradation of mRNA in eukaryotes, which can be either in 5' to 3' direction or 3' to 5' direction.

What you are thinking of is ubiquitination of proteins, which is a post-translational process which can mark the proteins for degradation.

Answer 2

Actually, whether polyadenylation protects an mRNA or makes it susceptible to degradation depends on the organism. From Dreyfus and Régnier 2002:

In eukaryotes, poly(A) tails usually act as stabilizers of intact mRNAs, whereas in E. coli they serve to accelerate the destruction of fragments.

This is due to different protection mechanisms in prokaryotes and eukaryotes:

The Poly(A) Binding Protein (PABP) inhibits deadenylation in mammalian cell-free assays. Although poly(A) binding proteins exist in E. coli as well and although they can protect poly(A) tails against PNPase in vitro (Feng et al., 2001), they may be unable to exert a significant protection in vivo because poly(A) tails never grow long enough to enable them to bind.

Important to note is that bacterial mRNA degradation usually starts internally, in contrast to eukaryotic mRNA degradation which happens (exonucleotically?):

As noted above, another distinctive feature of bacteria is the fact that polyadenylation usually affects the degradation of fragments only, because the initial attack on most intact mRNAs is endonucleolytic.

All of these quotes come from the review I referenced at the top of my answer, I recommend reading it as it's very comprehensive (and interesting).