Ribosomal frameshifting (kw:KW-0688)

Programmed Ribosomal frameshifting is an alternate mechanism of translation to merge proteins encoded by two overlapping open reading frames. The frameshift occurs at low frequency and consists of ribosomes slipping by one base in either the 5'(-1) or 3'(+1) directions during translation. Some viruses contains both a +1 and a -1 ribosomal frameshifts

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-1 Ribosomal frameshift

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All cis-acting frameshift signals encoded in mRNAs are minimally composed of two functional elements: a heptanucleotide "slippery sequence" conforming to the general form X XXY YYZ, followed by a RNA structural element, usually a H-type RNA pseudoknot, positioned an optimal number of nucleotides (5 to 9) downstream. Mechanistically, the ribosome is stalled on the slippery sequence by the pseudoknot structure in 3'. In about 10% cases, the ribosome will backtrack one nucleotide, creating one or more mismatchs between tRNAs and mRNA. Translation resolves on the backtracked ribosome in the -1 frame.

Family Genus Virus Type RefSeq .......... XXXYYYZ .......... Frameshift position Freq Ref
-1/-2 FRAMESHIFTS
Totiviridae Giardiavirus Giardia lamblia virus -1 NC_003555 CGUGCGCCAU CCCUUUA UCCGAUCGUG 2871
Totivirus Saccharomyces cerevisiae virus L-A -1 NC_003745 GUACUCAGCA GGGUUUA GGAGUGGUAG 1964
Astroviridae Avastrovirus Turkey astrovirus 1 -1 NC_002470 CUACGUGUUC AAAAAAC UAGAUAGUCA 3307
Mamastrovirus Human astrovirus 1 -1 NC_001943 ACAAGGCCCC AAAAAAC UACAAAGGGC 2845
Luteoviridae Enamovirus Pea enation mosaic virus-1 -1 NC_003629 CCAGACGCUC GGGAAAC GGAUUAUUCC 2035
Luteovirus Barley yellow dwarf virus-PAV -1 NC_004750 TTGACTCTGT GGGUUUU AGAGGGGCTC 1159
Polerovirus Potato leafroll virus -1 NC_001747 CAAACAAGCC UUUAAAU GGGCAAGCGG 1774
Arteriviridae Arterivirus Equine arteritis virus -1 NC_002532 CAGUGAAUCA GUUAAAC UGAGAGCGCC 5405
Porcine reproductive and respiratory syndrome virus -2 NC_001961 UGAGCCGUCA GGUUUUU GACCUCGUCU 3887-3888
Coronaviridae Alphacoronavirus Human coronavirus 229E -1 NC_002645 AUAACAGUUA UUUAAAC GAGUCCGGGG 12520
Betacoronavirus Human SARS coronavirus -1 NC_004718 CAUCAACGUU UUUAAAC GGGUUUGCGG 13398
Gammacoronavirus Avian Infectious bronchitis virus -1 NC_002645 AUAAGAAUUA UUUAAAC GGGUACGGGG 12354
Bafinivirus White bream virus -1 NC_008516 AGCAGCCGCC UUUAAAC TGGAGGGCAG 14555 -
Torovirus Breda virus -1 NC_007447 CUGUUGGUGA UUUAAAC UGCUGAGAGA 14184 -
FLaviviridae Flavivirus West nile virus -1 NC_009942 UAUGAUUGAC CCUUUUC AGUUGGGCCU 3552 30-50%
Mesoniviridae Mesonivirus Alphamesonivirus 1 -1 NC_015668 GCACCCUUUG GAUUUUC CAAAGUGGGC 7841
Picornaviridae Cardiovirus Encephalomyocardidis virus -1 NC_001479 CAAGGAAACA GGUUUUC CAGACCCAAG 3998
Tombusviridae Dianthovirus Red clover necrotic mosaic virus -1 NC_003756 AAUCCCUUGA GGAUUUU UAGGCGGCGG 831
Retroviridae Alpharetrovirus Avian leukosis virus -1 NC_001408 UCCGCUUGAC AAAUUUA UAGGGAGGGC 2474
Betaretrovirus Mouse mammary tumor virus -1 NC_001503 CUGAAAAUUC AAAAAAC UUGUAAAGGG 2082
Deltaretrovirus Human T-lymphotropic virus 1 -1 NC_001436 UCCCACACCC AAAAAAC UCCAUAGGGG 1718
Lentivirus Human immunodeficiency virus 1 -1 NC_001802 GACAGGCUAA UUUUUUA GGGAAGAUCU 1637
Unclassified Sobemovirus Cocksfoot mottle sobemovirus -1 NC_002618 CAAUCCGGCC UUUAAAC UACCAGCGGG 1640
Umbravirus Groundnut rosette virus -1 NC_003603 CCGGGGCACA AAAUUUU UAGUUGGGGA 867
Myoviridae Mulikevirus Mu phage -2 NC_000929 CGCUGACACA AGAACGG GGGCGAGUGG 23960
Myoviridae P2likeviruses Enterobacteria phage P2 -1 NC_003603 CGGUAAGGUG GUCGGUU UUUUGUCGCC 19679
Siphoviridae Lambdalikevirus Phage lambda +1 NC_001416 AGAGCCUGUU UCUGCGG GAAAGTGTTC 10110
Togaviridae Alphavirus Sindbis virus +1 NC_001547 GCUGCCUGCC UUUUUUA GUGGUUCCGG 10028 10-18%


Source:Michael Bekaert, thesis (in french) etude du decalage de phase de lecture dans le genome de Saccharomyces cerevisiae

+1 ribosomal frameshift

This frameshift is mechanistically different from the -1. The ribosome stalls on a slippery sequence, making a long pause at a rare codon for which few tRNAs are available. This long pause can be resolved by a movement forward of one nucleotide, creating one or more mismatchs between tRNAs and mRNA. Translation resolves on the advanced ribosome in the +1 frame.

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Family Genus Virus Type RefSeq .......... XXXYYYZ .......... *{color:white}Frameshift position *{color:white}Freq *{color:white}Ref
+1 FRAMESHIFTS (rare codon in yellow)
Orthomyxoviridae Influenzavirus A Influenzavirus A +1 NC_002022 UCUGGGAUUC CUUUCGU CAGUCCGAG 599
Totiviridae Leishmaniavirus Leishmania RNA virus 1-4 +1 NC_003601 Not Identified NA
Siphoviridae Lambdalikevirus Bacillus phage SPP1 +1 NC_004166 ACTGTTCCCG CTCCCC TAATGCGCC 11,111 ~10%

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