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Ribosomal frameshifting may be controlled by mechanisms found in the mRNA sequence (cis-acting). This generally refers to a slippery sequence, an RNA secondary structure, or both. A −1 frameshift signal consists of both elements separated by a spacer region typically 5–9 nucleotides long. [ 2 ]
A slippery sequence is a small section of codon nucleotide sequences (usually UUUAAAC) that controls the rate and chance of ribosomal frameshifting. A slippery sequence causes a faster ribosomal transfer which in turn can cause the reading ribosome to "slip."
The HIV-1 ribosomal frameshift signal requires two cis-acting elements: a heptameric "slippery site" and a downstream secondary RNA structure separated by an 8-nucleotide spacer. [3] [4] The "Slippery Site" in HIV-1 is the heptamer 5'-U UUU UUA-3' (gag ORF indicated by the spaces), where frameshifting occurs.
Translation can also be affected by ribosomal pausing, which can trigger endonucleolytic attack of the tRNA, a process termed mRNA no-go decay. Ribosomal pausing also aids co-translational folding of the nascent polypeptide on the ribosome, and delays protein translation while it is encoding tRNA. This can trigger ribosomal frameshifting. [7]
Frameshifting may also occur during prophase translation, producing different proteins from overlapping open reading frames, such as the gag-pol-env retroviral proteins. This is fairly common in viruses and also occurs in bacteria and yeast (Farabaugh, 1996).
The expression of ODC-AZ requires programmed, ribosomal frameshifting which is modulated according to the cellular concentration of polyamines. High levels of polyamines induce a +1 ribosomal frameshift in the translation of mRNA for the antizyme leading to the expression of a full-length protein.
The DnaX ribosomal frameshifting element is a RNA element found in the mRNA of the dnaX gene in E. coli. The dnaX gene has two encoded products, tau and gamma, which are produced in a 1:1 ratio. The gamma protein is synthesised due to programmed frameshifting and is shorter than tau.
The latter name refers to the fact that a slippery sequence in the mRNA that codes for the polypeptide causes ribosomal frameshifting, leading to two different lengths of peptidic chains (a and ab) at an approximately fixed ratio.