Ribosomal frameshift

Proteins are translated by reading tri-nucleotides on the mRNA strand, also known as codons, from one end of the mRNA to the other (from the 5' to the 3' end) starting with the amino acid methionine as the start (initiation) codon AUG. Each codon is translated into a single amino acid. The code itself is considered degenerate, meaning that a particular amino acid can be specified by more than one codon. However, a shift of any number of nucleotides that is not divisible by 3 in the reading frame will cause subsequent codons to be read differently. This effectively changes the ribosomal reading frame. Sentence example In this example, the following sentence of three-letter words makes sense when read from the beginning: |Start|THE CAT AND THE MAN ARE FAT ... |Start|123 123 123 123 123 123 123 ... However, if the reading frame is shifted by one letter to between the T and H of the first word (effectively a +1 frameshift when considering the 0 position to be the initial position of T), T|Start|HEC ATA NDT HEM ANA REF AT... -|Start|123 123 123 123 123 123 12... then the sentence reads differently, making no sense. DNA example In this example, the following sequence is a region of the human mitochondrial genome with the two overlapping genes MT-ATP8 and MT-ATP6. When read from the beginning, these codons make sense to a ribosome and can be translated into amino acids (AA) under the vertebrate mitochondrial code: |Start|AAC GAA AAT CTG TTC GCT TCA ... |Start|123 123 123 123 123 123 123 ... | AA | N E N L F A S ... However, let's change the reading frame by starting one nucleotide downstream (effectively a "+1 frameshift" when considering the 0 position to be the initial position of A): A|Start|ACG AAA ATC TGT TCG CTT CA... -|Start|123 123 123 123 123 123 12... | AA | T K I C S L ... Because of this +1 frameshifting, the DNA sequence is read differently. The different codon reading frame therefore yields different amino acids. Effect In the case of a translating ribosome, a frameshift can either result in nonsense mutation, a premature stop codon after the frameshift, or the creation of a completely new protein after the frameshift. In the case where a frameshift results in nonsense, the nonsense-mediated mRNA decay (NMD) pathway may destroy the mRNA transcript, so frameshifting would serve as a method of regulating the expression level of the associated gene. If a novel or off-target protein is produced, it can trigger other unknown consequences. == Function in viruses and eukaryotes ==

In viruses this phenomenon may be programmed to occur at particular sites and allows the virus to encode multiple types of proteins from the same mRNA. Notable examples include HIV-1 (human immunodeficiency virus), RSV (Rous sarcoma virus) and the influenza virus (flu), which all rely on frameshifting to create a proper ratio of 0-frame (normal translation) and "trans-frame" (encoded by frameshifted sequence) proteins. Its use in viruses is primarily for compacting more genetic information into a shorter amount of genetic material. In eukaryotes it appears to play a role in regulating gene expression levels by generating premature stops and producing nonfunctional transcripts. == Types of frameshifting ==

The most common type of frameshifting is −1 frameshifting or programmed −1 ribosomal frameshifting (−1 PRF). Other, rarer types of frameshifting include +1 and −2 frameshifting. In this model, the motif structure is explained by the fact that the first and second positions of the anticodons must be able to pair perfectly in both the 0 and −1 frames. Therefore, nucleotides 2 and 1 must be identical, and nucleotides 3 and 2 must also be identical, leading to a required sequence of 3 identical nucleotides for each tRNA that slips. +1 ribosomal frameshifting The slippery sequence for a +1 frameshift signal does not have the same motif, and instead appears to function by pausing the ribosome at a sequence encoding a rare amino acid. Due to this lag, there exist in small sections of codons sequences that control the rate of ribosomal frameshifting. Specifically, the ribosome must pause to wait for the arrival of a rare tRNA, and this increases the kinetic favorability of the ribosome and its associated tRNA slipping into the new frame. In this model, the change in reading frame is caused by a single tRNA slip rather than two. == Controlling mechanisms ==

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. RNA secondary structure Efficient ribosomal frameshifting generally requires the presence of an RNA secondary structure to enhance the effects of the slippery sequence. Below are examples of predicted secondary structures for frameshift elements shown to stimulate frameshifting in a variety of organisms. The majority of the structures shown are stem-loops, with the exception of the ALIL (apical loop-internal loop) pseudoknot structure. In these images, the larger and incomplete circles of mRNA represent linear regions. The secondary "stem-loop" structures, where "stems" are formed by a region of mRNA base pairing with another region on the same strand, are shown protruding from the linear DNA. The linear region of the HIV ribosomal frameshift signal contains a highly conserved UUU UUU A slippery sequence; many of the other predicted structures contain candidates for slippery sequences as well. The mRNA sequences in the images can be read according to a set of guidelines. While A, T, C, and G represent a particular nucleotide at a position, there are also letters that represent ambiguity which are used when more than one kind of nucleotide could occur at that position. The rules of the International Union of Pure and Applied Chemistry (IUPAC) are as follows: These symbols are also valid for RNA, except with U (uracil) replacing T (thymine). Trans-acting elements Small molecules, proteins, and nucleic acids have been found to stimulate levels of frameshifting. For example, the mechanism of a negative feedback loop in the polyamine synthesis pathway is based on polyamine levels stimulating an increase in +1 frameshifts, which results in production of an inhibitory enzyme. Certain proteins which are needed for codon recognition or which bind directly to the mRNA sequence have also been shown to modulate frameshifting levels. MicroRNA (miRNA) molecules may hybridize to an RNA secondary structure and affect its strength. == See also ==