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For|the progressive rock/metal band|Frameshift (band) Translational frameshifting or ribosomal frameshifting refers to an alternate process of protein translation . A protein is translated from one end of the mRNA to the other, from the 5' to the 3' end. Normally a protein is translated from a template mRNA with consecutive blocks of 3 nucleotides being read as single amino acids. However, certain organisms may exhibit a change or shift in the ribosomes reading frame|frame by one or two nucleotides when translating the genetic code . This is deemed translational or ribosomal frameshiftingLéger M, Dulude D, Steinberg SV, Brakier-Gingras L. "The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift." Nucleic Acids Res. 2007;35(16):5581-92. Epub 2007 Aug 17.. The process can be programmed by the nucleotide sequence of the mRNA and is sometimes affected by the secondary or tertiary mRNA structure. It has been described mainly in viruses (especially retroviruses ), retrotransposons and bacterial insertion elements, and also in some cellular genes.
Process overview
Proteins are translated unidirectionally by reading tri-nucleotides on the mRNA strand also known as codons . Therefore, a shift of any number of nucleotides that is not divisible by 3 in the reading frame will result in subsequent codons to be read differentlyIvanov IP, Atkins JF. "Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation." Nucleic Acids Res. 2007;35(6):1842-58. Epub 2007 Mar 1. Review.. This effectively changes the ribosomal reading frame . For example, the following sentence when read from the beginning makes sense to a reader:
|Start|THE CAT AND THE MAN ARE FAT ... |Start|123 123 123 123 123 123 123 ...
However, changing the reading frame by say shifting the first reading up one letter between the T and H on the first word:
T|Start|HEC ATA NDT HEM ANA REF AT... -|Start|123 123 123 123 123 123 12...
Now the sentence makes absolutely no sense. In the case of a translating ribosome , a frameshift can result in nonsense being created after the frameshift or a completely different protein being created after the frameshift. When referring to translational frameshifting, the latter is always inferred, the former being a usual unfortunate result of a point mutation such as a deletion.
Controlling mechanisms
The main differences between a frameshift as a result of frameshift|mutation and a frameshift as a result of ribosome|ribosomal frameshifting is that there are a few mechanisms used to control the latter. All are based on the fact that ribosomes do not translate proteins at a steady rate regardless of the sequence. There are certain codons that take longer to translate because there are not equal amounts of tRNA of that particular codon in the cytosol de Crécy-Lagard V. "Identification of genes encoding tRNA modification enzymes by comparative genomics." Methods Enzymol. 2007;425:153-83. Review.. Hence there exists sequences known as choke points (small sections of harder to find codons, resulting in a slowed ribosome translation) and slippery sequences (small sections of very easily accessible codons, resulting in a quick ribosome translation) that control the rate of ribosomal frameshifting. Slippery sequences can potentially make the reading ribosome "slip" and skip a number of nucleotides (usually only 1) and read a completely different frame thereafter. Choke points reduce the probability of this happeningGreen L, Kim CH, Bustamante C, Tinoco I Jr. "Characterization of the Mechanical Unfolding of RNA Pseudoknots." J Mol Biol. 26 May 2007.
Examples
This type of frameshifting may be programmed to occur at particular recoding sites and is important in some viruses (e.g. SARS , HIV McNaughton BR, Gareiss PC, Miller BL. "Identification of a selective small-molecule ligand for HIV-1 frameshift-inducing stem-loop RNA from an 11,325 member resin bound dynamic combinatorial library." J Am Chem Soc. 2007 Sep 19;129(37):11306-7. Epub 2007 Aug 28.) and some cellular genes (e.g. prfB a release factor ). Its use is primarily for compacting more gene tic information into a shorter amount of genetic material.
Type !! Distribution !! Ref.
ALIL pseudoknot
Antizyme RNA frameshifting stimulation element
Coronavirus frameshifting stimulation element
DnaX ribosomal frameshifting element
HIV Ribosomal frameshift signal
Insertion sequence IS1222 ribosomal frameshifting element
Ribosomal frameshift
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See also
Antizyme RNA frameshifting stimulation element
Coronavirus frameshifting stimulation element
DnaX ribosomal frameshifting element
Frameshift mutation
HIV Ribosomal frameshift signal
Insertion sequence IS1222 ribosomal frameshifting element
Recode (database)|Recode database
Ribosomal frameshift
References
Reflist
External links
MeshName|Frameshifting,+Ribosomal
http://www.ebi.ac.uk/Tools/Wise2/index.htm Wise2 - aligns a protein against a DNA sequence allowing frameshift s and intron s
http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi? rm=select& pgm=fy FastY - compare a DNA sequence to a protein sequence database, allowing gaps and frameshift s
http://bioinfo.lifl.fr/path/ Path - tool that compares two frameshift proteins (back- Translation (genetics)|translation principle)
http://recode.ucc.ie Recode2 - Database of recoded genes, including those that require programmed Translational frameshift.
Use dmy dates|date=September 2010 DEFAULTSORT:Translational Frameshift Category:Genetics Category:Cis-regulatory RNA elements
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