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." This allows a tRNA to shift by 1 base (−1) after it has paired with its anticodon, changing the reading frame. A −1 frameshift triggered by such a sequence is a programmed −1 ribosomal frameshift. It is followed by a spacer region, and an RNA secondary structure. Such sequences are common in virus polyproteins.
The frameshift occurs due to wobble pairing. The Gibbs free energy of secondary structures downstream give a hint at how often frameshift happens. Tension on the mRNA molecule also plays a role. A list of slippery sequences found in animal viruses is available from Huang et al.
Slippery sequences that cause a 2-base slip (−2 frameshift) have been constructed out of the HIV UUUUUUA sequence.
See also
- Nucleic acid tertiary structure
- Open reading frame
- Ribosomal frameshifting
- Translational frameshift
- Transposable element
External links
- Pseudobase
- Recode
- Frameshifting,+Ribosomal at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
- Wise2 - aligns a protein against a DNA sequence allowing frameshifts and introns
- FastY - compare a DNA sequence to a protein sequence database, allowing gaps and frameshifts
- Path Archived 2011-07-19 at the Wayback Machine - tool that compares two frameshift proteins (back-translation principle)
- Recode2 - Database of recoded genes, including those that require programmed Translational frameshift.
- Page for Coronavirus frameshifting stimulation element at Rfam
References
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Lin Z, Gilbert RJ, Brierley I (September 2012). "Spacer-length dependence of programmed -1 or -2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting". Nucleic Acids Research. 40 (17): 8674–89. doi:10.1093/nar/gks629. PMC 3458567. PMID 22743270. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458567 ↩
Huang X, Cheng Q, Du Z (2013). "A genome-wide analysis of RNA pseudoknots that stimulate efficient -1 ribosomal frameshifting or readthrough in animal viruses". BioMed Research International. 2013: 984028. doi:10.1155/2013/984028. PMC 3835772. PMID 24298557. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3835772 ↩
Lin Z, Gilbert RJ, Brierley I (September 2012). "Spacer-length dependence of programmed -1 or -2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting". Nucleic Acids Research. 40 (17): 8674–89. doi:10.1093/nar/gks629. PMC 3458567. PMID 22743270. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458567 ↩