The chemical ingenuity of the cell

If you know a bit of molecular biology, you know that messenger RNA (mRNA) has a tail of consecutive adenines added at its 5′ end (sorry ! ! !  3′ end — oh well). If you don’t know that much all the background you need can be found in https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/ — just follow the links.

The adenines are not coded in the genome. Why? I’ve always thought of it as something preventing the mRNA from being broken down before the ribosome translates it into protein. Gradually the adenines are nibbled off by cytoplasmic nucleases. The literature seems to agree — from my notes on various sources

Most mRNAs in mammalian cells are quite stable and have a half life measured in hours, but others turn over within 10 to 30 minutes. The 5′ cap structure in mRNA prevents attack by 5′ exonucleases and the polyadenine (polyA) tail prohibits the action of 3′ exonucleases. The absence of a polyA tail is associated with rapid degradation of mRNA. Histone mRNAs lack a polyA tail but have near their 3′ terminus a sequence which can form a stem loop structure this appears to confer resistance to exonucleolytic attack.

polyA — the polyAdenine tail found on most mRNAs must be removed before mRNA degradation can occur. Anything longer than 10 adenines in a row seems to protect mRNA. The polyA tail is homogenous in length in most species ( 70 – 90 in yeast, 220 – 250 nucleotides in mammalian cells). PolyA shortening can be separated into two phases, the first being the shortening of the tail down to 12 – 25 residues, and the second terminal deadenylation being the removal of some or all of them.

Molecular Biology of the Cell 4th Edition p. 449 — Once a critical threshold of tail shortening has been reached (about 30 As) the 5′ cap is removed (decapping) and the RNA is rapidly degraded. The proteins that carry out tail shortening compete directly with the machinery that catalyzes translation; therefore any factors increasing translation initiation efficiency increase mRNA stability. Many RNAs carry in the 3′ UTR sequences binding sites for specific proteins that increase or decrease the rate of polyA shortening.

But why polyAdenine? Why not polyCytosine or PolyGuanine or polyUridine? Here’s were the chemical ingenuity comes in. Of the 64 possible codons for amino acids only 3 tell the ribosome to stop. These are called various — termination codons, stop codons,and (idiotically) nonsense codons — they aren’t nonsense at all, and are  functionally vital for the following reason. Stop codons cause the ribosome to separate into two parts releasing the mRNA and the protein. Suppose a given mRNA doesn’t have a stop codon? Then the ribosome and the mRNA remain stuck together, and future protein synthesis by that particular ribosome becomes impossible. Not good.

This is probably why the codons for stop are so similar UAA, UAG and UGA — mutating a G to an A gives another one, and mutating either A in UAA to a G gives another stop codon. So the coding chosen for stop codons is somewhat resistant to mutation, because mRNAs with stop codons are disastrous for reasons shown above.

Well, randomness happens and suppose that the termination codon has been mutated to another amino acid. These are called nonStop RNAs which code for nonStop proteins. So the poor ribosome then translates the mRNA right to its 3′ end. Well what does AAA translate into — lysine. Lysine is quite basic and quickly becomes protonated on its epsilon lysine (even within the confines of the ribosome). The exit tunnel for the ribosome is strongly negatively charged, and so coulomb interaction grinds things to a halt. What other basic amino acids are there? There’s arginine, and perhaps histidine, but no codons for them is CCC or GGG or UUU.

Then the Ribosomal Quality Control system (RQC) then springs into action. I didn’t realize this until reading the following paper this year. Did you? Amazing cleverness on the part of the cell.

[ Nature vol. 531 pp. 191 – 195 ’16 ] Translation of an mRNA lacking a stop codon (nonStop mRNA) in eukaryotes results in a polyLysine protein (AAA codes for lysine). The positively charged lysine cause stalling in the negatively charged ribosomal exit tunnel. The Ribosomal Quality Control complex (RQC complex) recognizes nonStop proteins and mediates their ubiquitination and proteasomal degradation.

The eukaryotic RQC comprises Listerin (Ltn1) an E3 ubiquitin ligase, Rqc1, Rqc2 and the AAA+ protein CDC48. On dissociation of the stalled ribosome, Rqc binds to the peptidyl tRNA of the 60S sunit and recruits Ltn1 which curves around the 60S ribosome, positioning its ligase domain near the nascent chain exit. R2c2 is a nucleotide binding protein that recruits tRNA^Ala and tRNA^Thr to the 60S peptidyl tRNA complex. This results in the addition of a Carboxy terminal Ala/Thr sequence (a CAT tail) to the stalled nascent chain.

Mutation of Listerin causes neurodegeneration in mice.

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Comments

  • GCC  On March 17, 2016 at 9:33 pm

    Very interesting! I suspect that in an awful lot of cases if the normal stop codon were mutated or read through for some reason, there would be another in-frame stop codon (in what’s usually the 3’UTR) before the ribosome got to the polyA tail. But obviously there must be some exceptions!

  • luysii  On March 17, 2016 at 10:34 pm

    Yes you’d think that. The chances of not having a stop codon in any 3 bases is 61/64 == .95 — the chances of having 50 codons in a row none of which is stop is 8%. In 100 codons it’s .6%. At first I thought it might be 50 or 100 nucleotides, but that’s wrong, because the ribosome has already chosen one of the 3 reading frames.

    That is also the beauty of polyA; no matter what reading frame the ribosome was originally in, eventually it starts burping out lysines.

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