As a part of the introductory series of entries for my blog, I thought I would write a bit about what I do – some basic comments about my research area. Colloquially, what I do is study the ways that poly(A) tails are added to messenger RNAs in plants. Before getting into that subject, though, it helps to review just what I mean by the poly(A) tail, and what this feature of mRNAs does.
As illustrated in the following figure, a generic messenger RNA (mRNA) consists of a number of distinct features, each of which has different functions. The very 5’-end* of the mRNA has a so-called cap (the chemical structure of which is shown in the figure). The most recognizable part of the mRNA is the open-reading frame; this is the series of nucleotides that are “read” by ribosomes to yield the polypeptide that is coded by the mRNA. The open reading frame begins (almost always) with the nucleotide triplet AUG, and ends (after a number of nucleotides that is a multiple of three) with one of the three “stop codons” (UAA, UAG, UGA). At the 3’-end* lies a tract of adenosines – between 90 and 300 or so, at the outset of the life of an mRNA. Finally, the regions of the mRNA between the cap and open reading frame, and between the open reading frame and poly(A) tail, are designated as the 5’- and 3’- untranslated regions, or UTRs.
These different features all interact with other cellular factors; the complete story fills large review volumes, and I won’t bother to try and describe everything. However, it is important for this overview to note that the cap is bound by a so-called cap-binding complex, and the poly(A) tail by a poly(A)-specific RNA binding protein (the poly(A)-binding protein, or PAB). As a single PAB binds only 12 or so nucleotides, the poly(A) tail is “coated” with a number of PAB subunits.
The poly(A) tail functions in two ways. It promotes translation of the mRNA by ribosomes, via a process that is briefly sketched in the following figure. The poly(A) tail, via PAB, actually is “connected” with the cap of the mRNA, via interactions of PAB and the cap-binding complex with other translation initiation factors. This serves to circularize the mRNA-protein complex as shown, and to stabilize the interactions at the 5’-end of the mRNA. The cap-binding complex and other translation initiation factors eventually recruit the small (40S) ribosomal subunit to the vicinity of the cap; this subunit and some of the initiation factors then scan along the mRNA until it finds a suitable AUG triplet, whereupon the 60S ribosomal subunit, initiator tRNAs, and other factors come into play to begin the process of translation.
The poly(A) tail also protects the mRNA from nucleases, as illustrated in the following figures. In the course of the life of a mRNA, the poly(A) tail is systematically shortened by poly(A)-specific nucleases. Once the poly(A) tail is too short to allow binding of PAB, the circular structure shown above unravels, and both the cap and mRNA 3’ end become “exposed”.
As shown in the last figure, the mRNA ends become exposed to two sorts of enzymes. One is a class of enzymes that remove the cap structure from the mRNA; these decapping enzymes cannot access the mRNA as long as it is in the circular form shown above, but readily act on mRNAs that no longer have poly(A) tails. The second class is nucleases that act on the exposed 5’- and 3’- ends of the mRNA. Enzymes that act at the 5’-end are usually called Xrn (there are several forms of Xrns in eukaryotes; in yeast, it is Xrn1 that is the player that degrades mRNAs after decapping). 3’-acting nucleases are part of an RNA-degrading complex called the exosome. I will have more to say about exosomes in another essay, a repost of an essay on The Panda’s Thumb. (5’-specific nucleases cannot act on the cap structure, hence to involvement of the decapping enzymes.)
That’s the poly(A) tail in a nutshell. It’s both a positive-acting cis element for translation, AND the prime determinant of a messenger RNA’s lifetime in a cell. (This is because the rate with which the poly(A) tail is degraded varies from mRNA to mRNA, and it is this rate that determines the stability of the mRNA.)
* – RNA, like DNA, has a directionality to it, one that is typically represented as 5′ and 3′. This is explained here.
For a fairly recent Open Access review of the functioning of poly(A)-binding proteins (the proteins that mediate the functioning of the poly(A) tail), see: “Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression”, DA Mangus, MC Evans, A Jacobson, Genome Biology 2003, 4:223doi:10.1186/gb-2003-4-7-223. (link)