RNA suppression of termination

Suppression of termination (also referred to as stop codon readthrough) is an alternate mechanism of translation to produce a protein with an extended C-terminus. It is used as a regulatory strategy by a large number of plant, animal and prokaryot viruses (see table below).
UAG amber and UGA opal codons are normally recognized by a release factor (eRF) instead of a tRNA, thereby stopping translation. Readthrough of these stop codons occurs when a tRNA partially recognizes UGA or UAG and allows translation to proceed further. This readthrough is induced either by a pseudoknot (MMTV) or by few nucleotides sequence after the stop. The readthrough signals of prokaryote, plant and mammal viruses are different and have different mechanisms which are still poorly understood. The efficiency of suppression of termination is globally poor: 5 to 30%.

The picture below describes MMTV suppression of termination.

Family Genus/TD> Virus RefSeq STOP codon Insertion Efficiency Position Reference
Leviviridae Allolevivirus Enterobacteria phage Qbeta NC_001890 UGA (opal) Trp 5% 1742
Carmotetraviridae Alphacarmotetravirus Providence virus NC_014126 UAG (amber) 2104
Luteoviridae Enamovirus Pea enation mosaic virus 1 NC_003629 UGA (opal) 4566
Luteovirus Barley yellow dwarf virus NC_004750 UAG (amber) 3458
Polerovirus Potato leafroll virus NC_001747 UAG (amber) 4317
Reoviridae Coltivirus Colorado tick fever virus NC_004180 UGA (opal) 1052
Retroviridae Gammaretrovirus Moloney murine leukemia virus NC_001501 UAG (amber) Gln 4-10% 1974
Epsilonretrovirus Walleye dermal sarcoma virus NC_001867 UAG (amber) 2545
Togaviridae Alphavirus Sindbis virus NC_001547 UGA (opal) - 10% 7598
Tombusviridae Aureusvirus Pothos latent virus NC_000939 UAG (amber) 791
Avenavirus Oat chlorotic stunt virus NC_003633 UAG (amber) 684
Carmovirus Carnation mottle virus NC_001265 UAG (amber) 805
Machlomovirus Maize chlorotic mottle virus NC_003627 UAG (amber) 1451
UGA (opal) 3199
Alphanecrovirus Tobbaco necrosis virus A NC_001777 UAG (amber) 666
Panicovirus Panicium mosaic virus NC_002598 UAG (amber) 1304
Tombusvirus Tomato bushy stunt virus NC_001554 UAG (amber) 1054
Virgaviridae Furovirus Soil-borne wheat mosaic virus NC_001367 UGA (opal) 4032
NC_002042 UGA (opal) 862
Pecluvirus Peanut clump virus NC_003672 UGA (opal) 3567
Pomovirus Potato mop-top virus NC_003723 UGA (opal) 4024
NC_003724 UAG (amber) 842
Tobamovirus Tobacco mosaic virus NC_002041 UGA (opal) Tyr, Gln, Leu 31% 3417
Tobravirus Tobacco rattle virus NC_003805 UGA (opal) Trp 5-25% 3764

Matching UniProtKB/Swiss-Prot entries

78 entries grouped by protein (browse by keywords)

All proteins are shown (view only 76 complete proteome entries)

2 entries

Minor capsid protein A1

Select_allDeselect_all
A1_BPMX1
Enterobacteria phage MX1 (Bacteriophage MX1) reference strain
A1_BPSP
Enterobacteria phage SP (Bacteriophage SP) reference strain

4 entries

Minor capsid protein P3-RTD (P74) (Readthrough protein) (RT protein)

Select_allDeselect_all
MCAPS_BYDVP
Barley yellow dwarf virus (isolate PAV) (BYDV) reference strain

Minor capsid protein (P74) (Readthrough protein) (RT protein)

MCAPS_PLRV1
Potato leafroll virus (strain Potato/Scotland/strain 1/1984) (PLrV) reference strain
MCAPS_TYYVF
Turnip yellows virus (isolate FL-1) (TuYV) (BWYV-FL1) reference strain
MCAPS_PLRVW
Potato leafroll virus (strain Potato/Netherlands/Wageningen/1989) (PLrV)

1 entry

Uncharacterized protein p31

P31_MCMVK
Maize chlorotic mottle virus (isolate United States/Kansas/1987) (MCMV) reference strain

13 entries

Pol polyprotein

Select_allDeselect_all
POL_MLVMS
Moloney murine leukemia virus (isolate Shinnick) (MoMLV) reference strain

Gag-Pol polyprotein (Pr180gag-pol)

POL_WDSV
Walleye dermal sarcoma virus (WDSV) reference strain

Gag-Pol polyprotein

POL_XMRV6
Xenotropic MuLV-related virus (isolate VP62) (XMRV) reference strain

Gag-Pol polyprotein (Pr180gag-pol)

POL_BAEVM
Baboon endogenous virus (strain M7)
POL_GALV
Gibbon ape leukemia virus (GALV)
POL_KORV
Koala retrovirus (KoRV)

Pro-Pol polyprotein (Pr125Pol)

POL_MLVAV
AKV murine leukemia virus (AKR (endogenous) murine leukemia virus)
POL_MLVF5
Friend murine leukemia virus (isolate 57) (FrMLV)
POL_MLVFF
Friend murine leukemia virus (isolate FB29) (FrMLV)
POL_MLVFP
Friend murine leukemia virus (isolate PVC-211) (FrMLV)
POL_MLVRD
Radiation murine leukemia virus
POL_XMRV3
Xenotropic MuLV-related virus (isolate VP35) (XMRV)

Gag-Pol polyprotein (Pr180gag-pol)

POL_XMRV4
Xenotropic MuLV-related virus (isolate VP42) (XMRV)

Gag-Pol polyprotein (Pr180gag-pol)

25 entries

Non-structural polyprotein (Polyprotein nsP1234) (P1234)

Select_allDeselect_all
POLN_CHIKS
Chikungunya virus (strain S27-African prototype) (CHIKV) reference strain
POLN_SFV
Semliki forest virus (SFV) reference strain
POLN_SINDV
Sindbis virus (SINV) reference strain
POLN_AURAV
Aura virus (AURAV)
POLN_BFV
Barmah forest virus (BFV)
POLN_CHIK3
Chikungunya virus (strain 37997) (CHIKV)
POLN_EEEV1
Eastern equine encephalitis virus (strain PE-0.0155) (EEEV) (Eastern equine encephalomyelitis virus)
POLN_EEEV8
Eastern equine encephalitis virus (strain PE-3.0815) (EEEV) (Eastern equine encephalomyelitis virus)
POLN_EEEVF
Eastern equine encephalitis virus (strain Florida 91-469) (EEEV) (Eastern equine encephalomyelitis virus)
POLN_EEVV3
Venezuelan equine encephalitis virus (strain 3880) (VEEV)
POLN_EEVVC
Venezuelan equine encephalitis virus (strain CPA201) (VEEV)
POLN_EEVVM
Venezuelan equine encephalitis virus (strain Mena II) (VEEV)
POLN_EEVVP
Venezuelan equine encephalitis virus (strain P676) (VEEV)
POLN_EEVVT
Venezuelan equine encephalitis virus (strain Trinidad donkey) (VEEV)
POLN_GETV
Getah virus (GETV)
POLN_MAYAB
Mayaro virus (strain Brazil) (MAYV)
POLN_ONNVG
O'nyong-nyong virus (strain Gulu) (ONNV)
POLN_ONNVI
O'nyong-nyong virus (strain Igbo Ora) (ONNV) (Igbo Ora virus)
POLN_ONNVS
O'nyong-nyong virus (strain SG650) (ONNV)
POLN_RRVN
Ross river virus (strain NB5092) (RRV)
POLN_SAGV
Sagiyama virus (SAGV)
POLN_SINDO
Sindbis virus subtype Ockelbo (strain Edsbyn 82-5) (OCKV) (Ockelbo virus)
POLN_SLDV
Sleeping disease virus (SDV)
POLN_SPDV
Salmon pancreas disease virus (SPDV)
POLN_WEEV
Western equine encephalitis virus (WEEV)

32 entries

Replicase large subunit (EC 2.1.1.-) (EC 2.7.7.-) (EC 2.7.7.48) (EC 3.6.4.13) (183 kDa protein) (RNA-directed RNA polymerase)

Select_allDeselect_all
RDRP_CARMS
Carnation mottle virus (isolate China/Shanghai) (CarMV) reference strain

Probable RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p88)

RDRP_CGMVS
Cucumber green mottle mosaic virus (strain watermelon SH) (CGMMV) reference strain

Replicase large subunit (EC 2.7.7.48) (186 kDa protein)

RDRP_MCMVK
Maize chlorotic mottle virus (isolate United States/Kansas/1987) (MCMV) reference strain

RNA-directed RNA polymerase (EC 2.7.7.48) (111 kDa protein) (Protein p111)

RDRP_OCSVU
Oat chlorotic stunt virus (isolate United Kingdom) (OCSV) reference strain

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p84)

RDRP_PEMVW
Pea enation mosaic virus-1 (strain WSG) (PEMV-1) reference strain

Protein P1-P2

RDRP_PMVK
Panicum mosaic virus (strain United States/Kansas 109S) (PMV) reference strain

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p112)

RDRP_POLVP
Pothos latent virus (isolate Pigeonpea/India) (PoLV) reference strain

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p84)

RDRP_SHMV
Sunn-hemp mosaic virus (SHMV) (TMV strain cowpea) reference strain
RDRP_TBSVC
Tomato bushy stunt virus (strain Cherry) (TBSV) reference strain

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p92)

RDRP_TCV
Turnip crinkle virus (TCV) reference strain

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p88)

RDRP_TMGMV
Tobacco mild green mosaic virus (TMGMV) (TMV strain U2) reference strain
RDRP_TMV
Tobacco mosaic virus (strain vulgare) (TMV) (Tobacco mosaic virus (strain U1)) reference strain
RDRP_TMVOM
Tobacco mosaic virus (strain OM) (TMV) reference strain
RDRP_TNVA
Tobacco necrosis virus (strain A) (TNV-A) reference strain

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p82)

RDRP_TVCV
Turnip vein-clearing virus (TVCV) reference strain
RDRP_CARMV
Carnation mottle virus (CarMV)

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p88)

RDRP_CNV
Cucumber necrosis virus (CNV)

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p92)

RDRP_CRV
Cymbidium ringspot virus (CymRSV)

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p92)

RDRP_ORSVC
Odontoglossum ringspot virus (isolate Korean Cy) (ORSV-Cy)
RDRP_ORSVS
Odontoglossum ringspot virus (isolate Singapore 1) (ORSV)
RDRP_PMMVJ
Pepper mild mottle virus (strain Japan) (PMMV-J)
RDRP_PMMVS
Pepper mild mottle virus (strain Spain) (PMMV-S)
RDRP_TMOB
Tobamovirus Ob
RDRP_TMVB
Tobacco mosaic virus (strain B935A) (TMV)
RDRP_TMVKR
Tobacco mosaic virus (strain Korean NC 82) (TMV)
RDRP_TMVRA
Tobacco mosaic virus (strain Rakkyo) (TMV-R)
RDRP_TNVD
Tobacco necrosis virus (strain D) (TNV-D)

RNA-directed RNA polymerase (EC 2.7.7.48) (Protein p82)

RDRP_TOMK1
Tomato mosaic virus (strain Kazakh K1) (ToMV) (TMV strain K1)
RDRP_TOMK2
Tomato mosaic virus (strain Kazakh K2) (ToMV) (TMV strain K2)
RDRP_TOML
Tomato mosaic virus (strain L) (ToMV) (TMV strain tomato)
RDRP_TOMS1
Tomato mosaic virus (strain S-1) (ToMV)
RDRP_YOMV
Youcai mosaic virus (YoMV)

Replicase large subunit (EC 2.7.7.48) (182 kDa protein)

1 entry

Non structural protein VP9'

VP9P_CTFVL
Colorado tick fever virus (strain USA/Florio N-7180) (CTFV) reference strain