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)
[…] As explained here and here, eukaryotic mRNAs possess a distinctive chemical structure at their 5’-ends that is […]
This is becoming a very informative supplement to my education– you may need to start charging tuition. But seriously, are there known mutations to the poly(A)-specific nucleases that extend the life of mRNA’s?
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To answer your question, mutations in the various subunits of deadenylating complexes do indeed slow both rates of deadenylation and mRNA decay, apparently on a global basis.
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What are the effects to the cell of lowered mRNA decAy or deadenylation? Is there an abnormal increase in translation? Do the transcripts just build up in the cell? Or are there other garbage disposals that can help out?
Good questions. Yeast mutants that are impaired in the two deadenylases (CCR4 and PAN2/3) are viable, and they do not deadenylate very efficiently. However, they still degrade their mRNAs, via other pathways. Indeed, there is a multiplicity of RNA degrading systems, a redundancy that illustrates the importance of mRNA turnover. As one removes more and more of the degrading systems (nucleases, deadenylaes, decapping enzymes), the “health” of the yeast cell decreases. (Some of these proteins are essential, others are not. It’s a fairly lengthy and interesting story.)
Interestingly, many of these systems also interact with and function in other processes (such as ribosomal RNA processing and transcription). This complicates the interpretation of some mutant phenotypes (its hard at times to make an unequivocal link between mRNA degradation phenotypes and growth effects). It also shows an interesting interconnectedness of turnover with other processes.
I don’t recall the translation phenotypes of deadenylase mutants. That’s something to look into.
In eukaryotic cells, can there be a transcribed mRNA without a poly A tail, and in such a case could that mRNA be able to be transported from the nucleo to the cytoplasm and then be translated? I know that the poly A is part of the processing mechanism of the mRNA, and that its need it to be transported trough the nucleous membrane, as well as for translation, but I was searching for any exeptions. Well if you know of an exeption I´d really appreciate it if you could help me out.
Why is it a poly A tail ? why not poly C or U ???
Is it possible that non-coding RNA has a poly-a tail?
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The Poly(A) Tail | The RNA Underworld
Great write-up on the chemistry of the poly-a tail.
thank you dear,
nice post. but can you tell me? if we can do something to increase activity of such enzymes which can degrade harmful proteins like such in cancer. and can we slow down deadenylation by something to increase use of useful proteins ? have anyone idea about such research please mail me. i am interested.
[…] The Poly(A) Tail […]
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protein without poly-A tail m-RNA
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