Programmed Translational Frameshifting
Recoding is the general term for non-canonical translational events caused by special sequences in mRNAs. Normally ribosomes read mRNAs in successive, adjacent three nucleotide (triplet) codons. At a recoding site the ribosome deviates from this method for example by skipping over one nucleotide. That is called +1 frameshifting since skipping a nucleotide changes the reading frame. Other recoding events include shifts in the opposite direction (e.g. -1 frameshifting), skipping many nucleotides (hopping) or reading through termination codons (readthrough).
Our laboratory studies programmed +1 frameshifting in the yeast Sac charomyces cerevisiae. Yeast carry a family of transposable elements, Ty elements, that are related to metazoan retroviruses. As in retroviruses, frameshifting is necessary to expres a critical Ty-encoded protein. Retroviruses express a protein called Gag, a structural protein that forms a structure within which the viruse replicates. Enzymes derived from a protein called Pol catalyze that replication. The Pol protein is expressed as a translational fusion to the Gag protein through a frameshift mechanism. The geometry of the fusion placeds the enzymatic activities inside the Gag particle. Thus in Ty elements as in retroviruses frameshifting accomplishes a morphogenetics purpose.
We have extensively characterized the mechanism of Ty frameshifting. There are two general types. In the Ty1, Ty2 and Ty4 elements frameshifting occurs on a sequence CUU-AGG-C. A leucyl-tRNA bound to CUU slips +1 onto UUA during slow recognition of the next codon, AGG (Belcourt and Farabaugh). This is a stochastic process: slowing recognition of the AGG increases frameshifting while accelerating recognition reduces it. The tRNA that reads CUU is unusual. It recognizes all four of the CUN family of codons. Its extended decoding properties depend on its unmodified wobble U which may allow the tRNA to decod by a two-our-of-three mechanism as first proposed by Lagerkvist. We had hypothesized that very weak recognition by the tRNA might predispose it to slip.
Frameshifting in the Ty3 element uses a different mechanism (Farabaugh et al.). Ribosomes shift +1 at the sequence GCG-AGU-U which is decoded as Ala (GCG)-Val (GUU). Again, slow decoding of the AGU codon stimulates frameshifting, but the tRNA reading GCG can not slip +1 while still base pairing to the mRNA. We proposed that frameshifting occurs by a different error, out-of-frame recognition by aminoacyl-tRNA in the ribosomal A site. Some special characteristic of the peptidyl-tRNA reading GCG, we assumed, causes this error. The Ty3 site also includes a downstream 14 nucleotide 'context' that stimulates frameshifting almost 10-fold.
Subsequently, we demonstrated that 11 codons can stimulate frameshifting when they precede a pause inducing codon (Vimaladithan and Farabaugh). Most of these codons could allow +1 peptidyl-tRNA slippage, but at least three (GCG, CGA and GUG) appear to use the alternative out-of-frame binding mechanism. We did not know why these tRNAs and no others could cause frameshifting. It was particularly odd that codons like UUU and AAA which a priori might be expected to be very 'slippery' induce little +1 frameshifting at the Ty site.