Ribosomal frameshift
Ribosomal frameshifting, also known as translational frameshifting or translational recoding, is a biological phenomenon that occurs during
Small molecules, proteins, and nucleic acids have also been found to stimulate levels of frameshifting. In December 2023, it was reported that in vitro-transcribed (IVT)
Process overview
Proteins are translated by reading tri-nucleotides on the mRNA strand, also known as
Sentence example
In this example, the following sentence with 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
. 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.[6]
If a novel or off-target protein is produced, it can trigger other unknown consequences.[4]
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
In eukaryotes it appears to play a role in regulating gene expression levels by generating premature stops and producing nonfunctional transcripts.[3][10]
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.[2] −1 and +1 frameshifting are believed to be controlled by different mechanisms, which are discussed below. Both mechanisms are kinetically driven.
Programmed −1 ribosomal frameshifting
In −1 frameshifting, the ribosome slips back one nucleotide and continues translation in the −1 frame. There are typically three elements that comprise a −1 frameshift signal: a slippery sequence, a spacer region, and an RNA secondary structure. The slippery sequence fits a X_XXY_YYH motif, where XXX is any three identical nucleotides (though some exceptions occur), YYY typically represents UUU or AAA, and H is A, C or U. Because the structure of this motif contains 2 adjacent 3-nucleotide repeats it is believed that −1 frameshifting is described by a tandem slippage model, in which the ribosomal P-site tRNA anticodon re-pairs from XXY to XXX and the A-site anticodon re-pairs from YYH to YYY simultaneously. These new pairings are identical to the 0-frame pairings except at their third positions. This difference does not significantly disfavor anticodon binding because the third nucleotide in a codon, known as the wobble position, has weaker tRNA anticodon binding specificity than the first and second nucleotides.[2][11] 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.[12]
+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.
Controlling mechanisms
Ribosomal frameshifting may be controlled by mechanisms found in the mRNA sequence (cis-acting). This generally refers to a slippery sequence, a RNA secondary structure, or both. A −1 frameshift signal consists of both elements separated by a spacer region typically 5–9 nucleotides long.[2] Frameshifting may also be induced by other molecules which interact with the ribosome or the mRNA (trans-acting).
Frameshift signal elements
Slippery sequence
RNA secondary structure
Efficient ribosomal frameshifting generally requires the presence of an RNA secondary structure to enhance the effects of the slippery sequence.[12] The RNA structure (which can be a stem-loop or pseudoknot) is thought to pause the ribosome on the slippery site during translation, forcing it to relocate and continue replication from the −1 position. It is believed that this occurs because the structure physically blocks movement of the ribosome by becoming stuck in the ribosome mRNA tunnel.[2] This model is supported by the fact that strength of the pseudoknot has been positively correlated with the level of frameshifting for associated mRNA.[3][17]
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 (
Symbol[18] | Description | Bases represented | Complement | ||||
---|---|---|---|---|---|---|---|
A | Adenine | A | 1 | T | |||
C | Cytosine | C | G | ||||
G | Guanine | G | C | ||||
T | Thymine | T | A | ||||
U | Uracil | U | A | ||||
W | Weak | A | T | 2 | W | ||
S | Strong | C | G | S | |||
M | aMino | A | C | K | |||
K | Keto | G | T | M | |||
R | puRine | A | G | R | |||
Y | pYrimidine | C | T | Y | |||
B | not A (B comes after A) | C | G | T | 3 | V | |
D | not C (D comes after C) | A | G | T | H | ||
H | not G (H comes after G) | A | C | T | D | ||
V | not T (V comes after T and U) | A | C | G | B | ||
N | any Nucleotide (not a gap) | A | C | G | T | 4 | N |
Z | Zero | 0 | Z |
These symbols are also valid for RNA, except with U (uracil) replacing T (thymine).[18]
Type | Distribution | Ref. |
---|---|---|
ALIL pseudoknot | Bacteria | [19] |
Antizyme RNA frameshifting stimulation element | Invertebrates | [20] |
Coronavirus frameshifting stimulation element | Coronavirus | [21] |
DnaX ribosomal frameshifting element | Eukaryota, bacteria
|
[22] |
HIV ribosomal frameshift signal | Viruses
|
|
Insertion sequence IS1222 ribosomal frameshifting element | Eukaryota, bacteria
|
|
Ribosomal frameshift | Viruses
|
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 a RNA secondary structure and affect its strength.[6]
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
- Ribosomal pause
- Slippery sequence
References
- PMID 27436286.
- ^ PMID 28593994.
- ^ PMID 23181069.
- ^ PMID 38057663.
- PMID 17332016.
- ^ PMID 29610120.
- ^ S2CID 4242582.
- ^ PMID 2846182.
- PMID 22745253.
- PMID 26661048.
- PMID 5969078.
- ^ PMID 7636469.
- ^ PMID 12217519.
- PMID 15937165.
- PMID 24949973.
- PMID 26322332.
- PMID 17389398.
- ^ a b c Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1984). "Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences". Retrieved 4 February 2008.
- PMID 18474594.
- PMID 15147837.
- PMID 15680415.
- PMID 9300054.
External links
- Frameshifting,+Ribosomal at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
- Wise2 — aligns a frameshifts and introns
- FastY — compare a frameshifts
- Path — tool that compares two translationprinciple)
- Recode2 — Database of recoded genes, including those that require programmed Translational frameshift.