Translation of Plant RNA Viruses
Abstract
:1. Introduction
2. Characteristics of 5′ and 3′ Ends of Viral RNAs in Plant RNA Viruses
3. Cap-Independent Translation in Plant RNA Viruses
3.1. IRESes in Plant RNA Viruses
3.1.1. IRESes in Members of Family Potyviridae
3.1.2. IRESes in Other Plant RNA Viruses
3.2. 3′CITE in Plant RNA Viruses
3.2.1. Translation Enhancer Domain (TED)
3.2.2. Barley Yellow Dwarf Virus (BYDV)-Like Element (BTE)
3.2.3. Panicum Mosaic Virus-Like Translation Element (PTE)
3.2.4. T-Shaped Structure (TSS)
3.2.5. I-Shaped Structure (ISS)
3.2.6. Y-Shaped Structure (YSS)
3.2.7. Cucurbit Aphid-Borne Yellows Virus (CABYV) Xinjiang-Like Translation Element (CXTE)
4. Translation Recoding
4.1. Leaky Scanning
4.2. Non-AUG Initiation
4.3. Ribosomal Frameshift
4.4. Ribosomal Read-Through
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Order | Family | Subfamily | Genus | Viral RNA or Subgenomic RNA | Translation Recoding Strategy | References | |
---|---|---|---|---|---|---|---|
5′ End | 3′ End | ||||||
Bunyavirales | Fimoviridae | Emaravirus | 5′ cap | no 3′ poly(A) | / | [8] | |
Phenuiviridae | Coguvirus | 5′ cap | no 3′ poly(A) | / | [9] | ||
Rubodvirus | 5′ cap | no 3′ poly(A) | / | [10] | |||
Tenuivirus | 5′ cap | no 3′ poly(A) | / | [11] | |||
Tospoviridae | Orthotospovirus | 5′ cap | no 3′ poly(A) | / | [12] | ||
Durnavirales | Amalgaviridae | Amalgavirus | no 5′ cap | no 3′ poly(A) | ribosomal frameshift | [13] | |
Partitiviridae | Alphapartitivirus | no 5′ cap | 3′ poly(A) | / | [14] | ||
Betapartitivirus | no 5′ cap | 3′ poly(A) | / | [15] | |||
Deltapartitivirus | no 5′ cap | 3′ poly(A) | / | [16] | |||
Hepelivirales | Benyviridae | Benyvirus | 5’ cap | 3′ poly(A) | ribosomal read-through, leaky scanning | [17] | |
Martellivirales | Bromoviridae | Alfamovirus | 5’ cap | no 3′ poly(A), has a 3’ tRNA-like structure | / | [18] | |
Anulavirus | 5’ cap | no 3′ poly(A), has a 3’ tRNA-like structure | / | [19] | |||
Bromovirus | 5’ cap | no 3′ poly(A), has a 3’ tRNA-like structure | / | [20] | |||
Cucumovirus | 5’ cap | no 3′ poly(A), has a 3’ tRNA-like structure | / | [21] | |||
Ilarvirus | 5’ cap | no 3′ poly(A), has a 3’ tRNA-like structure | / | [22] | |||
Oleavirus | 5’ cap | no 3′ poly(A), has a 3’ tRNA-like structure | / | [23] | |||
Closteroviridae | Ampelovirus | 5′ cap | no 3′ poly(A) | ribosomal frameshift | [24] | ||
Closterovirus | 5′ cap | no 3′ poly(A) | ribosomal frameshift | [25] | |||
Crinivirus | 5′ cap | no 3′ poly(A) | ribosomal frameshift | [26] | |||
Velarivirus | 5′ cap | no 3′ poly(A) | ribosomal frameshift | [27] | |||
Endornaviridae | Alphaendornavirus | no 5′ cap | no 3′ poly(A) | / | [28] | ||
Kitaviridae | Blunervirus | 5′ cap | no 3′ poly(A) | leaky scanning | [29] | ||
Cilevirus | 5′ cap | 3′ poly(A) | / | [30] | |||
Higrevirus | 5′ cap | 3′ poly(A) | / | [31] | |||
Mayoviridae | Idaeovirus | 5′ cap | no 3′ poly(A) | / | [32] | ||
Pteridovirus | 5′ cap | no 3′ poly(A) | / | [33] | |||
Virgaviridae | Furovirus | 5′ cap | no 3′ poly(A), has a 3′ tRNA-like structure | ribosomal read-through, leaky scanning | [34] | ||
Goravirus | 5′ cap | no 3′ poly(A), has a 3′ tRNA-like structure | ribosomal read-through, leaky scanning | [35] | |||
Hordeivirus | 5′ cap | no 3′ poly(A), has a 3′ tRNA-like structure | ribosomal read-through, leaky scanning | [36] | |||
Pecluvirus | 5′ cap | no 3′ poly(A), has a 3′ tRNA-like structure | ribosomal read-through, leaky scanning | [37] | |||
Pomovirus | 5′ cap | no 3′ poly(A), has a 3′ tRNA-like structure | ribosomal read-through, leaky scanning | [38] | |||
Tobamovirus | 5′ cap | no 3′ poly(A), has a 3′ tRNA-like structure | ribosomal read-through | [39] | |||
Tobravirus | 5′ cap | no 3′ poly(A), has a 3′ tRNA-like structure | ribosomal read-through, leaky scanning | [40] | |||
Mononegavirales | Rhabdoviridae | Alphanucleorhabdovirus | 5′ cap | 3′ poly(A) | / | [41] | |
Betanucleorhabdovirus | 5′ cap | 3′ poly(A) | / | [42] | |||
Gammanucleorhabdovirus | 5′ cap | 3′ poly(A) | / | [43] | |||
Cytorhabdovirus | 5′ cap | 3′ poly(A) | / | [44] | |||
Dichorhavirus | 5′ cap | 3′ poly(A) | / | [45] | |||
Varicosavirus | 5′ cap | 3′ poly(A) | / | [46] | |||
Ourlivirales | Botourmiaviridae | Ourmiavirus | no 5′ cap | no 3′ poly(A) | / | [47] | |
Patatavirales | Potyviridae | Arepavirus | 5’ VPg | 3′ poly(A) | / | [48] | |
Bevemovirus | 5’ VPg | 3′ poly(A) | / | [49] | |||
Brambyvirus | 5’ VPg | 3′ poly(A) | / | [50] | |||
Bymovirus | 5’ VPg | 3′ poly(A) | / | [51] | |||
Celavirus | 5’ VPg | 3′ poly(A) | / | [52] | |||
Ipomovirus | 5’ VPg | 3′ poly(A) | / | [53] | |||
Macluravirus | 5’ VPg | 3′ poly(A) | / | [54] | |||
Poacevirus | 5’ VPg | 3′ poly(A) | / | [55] | |||
Potyvirus | 5’ VPg | 3′ poly(A) | / | [56] | |||
Roymovirus | 5’ VPg | 3′ poly(A) | / | [57] | |||
Rymovirus | 5’ VPg | 3′ poly(A) | / | [58] | |||
Tritimovirus | 5’ VPg | 3′ poly(A) | / | [59] | |||
Picornavirales | Secoviridae | Cheravirus | 5’ VPg | 3′ poly(A) | leaky scanning | [60] | |
Sadwavirus | 5’ VPg | 3′ poly(A) | / | [61] | |||
Sequivirus | 5’ VPg | 3′ poly(A) | / | [62] | |||
Torradovirus | 5’ VPg | 3′ poly(A) | leaky scanning | [61] | |||
Waikavirus | 5’ VPg | 3′ poly(A) | / | [62] | |||
Comovirinae | Comovirus | 5’ VPg | 3′ poly(A) | / | [61] | ||
Fabavirus | 5’ VPg | 3′ poly(A) | / | [61] | |||
Nepovirus | 5’ VPg | 3′ poly(A) | leaky scanning | [62,63] | |||
Reovirales | Reoviridae | Sedoreovirinae | Phytoreovirus | 5′ cap | no 3′ poly(A) | leaky scanning | [64] |
Spinareovirinae | Fijivirus | 5′ cap | no 3′ poly(A) | / | [64] | ||
Oryzavirus | 5′ cap | no 3′ poly(A) | leaky scanning | [64] | |||
Serpentovirales | Aspiviridae | Ophiovirus | 5′cap | no 3′ poly(A) | ribosomal frameshift | [65] | |
Sobelivirales | Solemoviridae | Polemovirus | 5’ VPg | no 3′ poly(A) | ribosomal frameshift, leaky scanning | [66] | |
Sobemovirus | 5’ VPg | no 3′ poly(A) | ribosomal frameshift, leaky scanning | [67] | |||
Tymovirales | Alphaflexiviridae | Allexivirus | no 5′ cap | 3′ poly(A) | leaky scanning | [68] | |
Lolavirus | no 5′ cap | 3′ poly(A) | leaky scanning | [69] | |||
Mandarivirus | no 5′ cap | 3′ poly(A) | leaky scanning | [69] | |||
Platypuvirus | no 5′ cap | 3′ poly(A) | leaky scanning | [70] | |||
Potexvirus | 5′ cap | 3′ poly(A) | leaky scanning | [71] | |||
Quinvirinae | Carlavirus | 5′ cap | 3′ poly(A) | leaky scanning | [69,72] | ||
Foveavirus | 5′ cap | 3′ poly(A) | leaky scanning | [69,72,73] | |||
Robigovirus | 5′ cap | 3′ poly(A) | leaky scanning | [72] | |||
Betaflexivridae | Trivirinae | Capillovirus | no 5′ cap | 3′ poly(A) | / | [73] | |
Chordovirus | no 5′ cap | 3′ poly(A) | / | [74] | |||
Citrivirus | no 5′ cap | 3′ poly(A) | / | [75] | |||
Divavirus | no 5′ cap | 3′ poly(A) | / | [76] | |||
Prunevirus | 5′ cap | 3′ poly(A) | leaky scanning | [77] | |||
Ravavirus | 5′ cap | 3′ poly(A) | leaky scanning | [77] | |||
Tepovirus | no 5′ cap | 3′ poly(A) | / | [78] | |||
Trichovirus | no 5′ cap | 3′ poly(A) | / | [73] | |||
Vitivirus | 5′ cap | 3′ poly(A) | leaky scanning | [73] | |||
Wamavirus | no 5′ cap | 3′ poly(A) | leaky scanning | [79] | |||
Luteoviridae | Enamovirus | 5′ VPg | no 3′ poly(A) | leaky scanning, ribosomal frameshift, ribosomal read-through | [80] | ||
Luteovirus | 5′ VPg | no 3′ poly(A) | leaky scanning, ribosomal frameshift, ribosomal read-through | [81] | |||
Polerovirus | 5′ VPg | no 3′ poly(A) | leaky scanning, ribosomal frameshift, ribosomal read-through | [82] | |||
Tymoviridae | Maculavirus | 5′ cap | 3′ poly(A) | leaky scanning | [83] | ||
Marafivirus | 5′ cap | 3′ poly(A) | leaky scanning | [84] | |||
Tymovirus | 5′ cap | no 3′ poly(A), has a 3′ tRNA-like structure | leaky scanning | [85,86] | |||
Tolivirales | Tombusviridae | Calvusvirinae | Umbravirus | no 5′ cap | no 3′ poly(A) | ribosomal frameshifting | [87] |
Procedovirinae | Alphanecrovirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through | [88] | ||
Alphacarmovirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaky scanning | [89] | |||
Aureusvirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaking scanning | [90] | |||
Avenavirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through | [91] | |||
Betacarmovirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaking scanning | [92] | |||
Betanecrovirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through | [88] | |||
Gallantivirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through | [93] | |||
Gammacarmovirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaking scanning | [94] | |||
Macanavirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through | [95] | |||
Machlomovirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaking scanning | [96] | |||
Panicovirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaking scanning | [97] | |||
Pelarspovirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaking scanning | [98] | |||
Tombusvirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaking scanning | [99] | |||
Zeavirus | no 5′ cap | no 3′ poly(A) | ribosomal read-through, leaking scanning | [100] | |||
Regressovirinae | Dianthovirus | no 5′ cap | no 3′ poly(A) | ribosomal frameshift | [101] |
IRES Type | Group I with Unstructured cis-Elements | Group II with Structured cis-Elements | Group III with Unclear Structure Characteristic | |||||
---|---|---|---|---|---|---|---|---|
Single-Stem Loop Structure | Double-Stem Loop Structure | Equilibrium-State Structure | ||||||
Virus | TCV/HCRSV/PFBV/crTMV | BRV | TEV | PVY | TriMV | WYMV | TuMV/PVA | PLRV |
Structural characteristic | US-1 | US-2 | | | | | N/A | US-3 |
Binding translation factors | eIF4G | 18S rRNA | eIF4G/eIF4F/18S rRNA | N/A | eIF4G/eIFis-o4G/eIF4A | eIF4E | N/A | N/A |
References | [157,158,159,160] | [161] | [149,151] | [152] | [136,155] | [113] | [135,156] | [162] |
3′ CITE Type | TED | BTE | PTE | TSS | ISS | YSS | CXTE |
---|---|---|---|---|---|---|---|
Viruses | sTNV/PLPV/PCRPV | BYDV/TBTV | PMV/PEMV2 | TCV/CCFV/ PEMV2 | MNSV | TBSV/CIRV/ PLCV | CABYV |
Structure | | | | | | | |
Binding translation factor | eIF4F/eIFiso4F | eIF4G | eIF4G/eIF4E | 18S rRNA | eIF4G/eIF4F | eIF4F/eIFiso4F | N/A |
References | [98,104,180,181] | [182,183,184] | [185,186,187,188] | [189,190,191,192] | [193,194,195] | [2,196] | [197] |
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Geng, G.; Wang, D.; Liu, Z.; Wang, Y.; Zhu, M.; Cao, X.; Yu, C.; Yuan, X. Translation of Plant RNA Viruses. Viruses 2021, 13, 2499. https://doi.org/10.3390/v13122499
Geng G, Wang D, Liu Z, Wang Y, Zhu M, Cao X, Yu C, Yuan X. Translation of Plant RNA Viruses. Viruses. 2021; 13(12):2499. https://doi.org/10.3390/v13122499
Chicago/Turabian StyleGeng, Guowei, Deya Wang, Zhifei Liu, Yalan Wang, Mingjing Zhu, Xinran Cao, Chengming Yu, and Xuefeng Yuan. 2021. "Translation of Plant RNA Viruses" Viruses 13, no. 12: 2499. https://doi.org/10.3390/v13122499
APA StyleGeng, G., Wang, D., Liu, Z., Wang, Y., Zhu, M., Cao, X., Yu, C., & Yuan, X. (2021). Translation of Plant RNA Viruses. Viruses, 13(12), 2499. https://doi.org/10.3390/v13122499