Abstract
Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro bacilliform virus (RTBV), member of the family Caulimoviridae, genus Tungrovirus, species Tungrovirus oryzae, infects rice in South- and Southeast Asia and causes severe symptoms of stunting, yellow-orange discoloration and twisting of leaf tips. To better understand the possible counter-defensive roles of RTBV against the host RNAi defense system, we explored the ability of the P4 protein of an Indian isolate of RTBV to act as a possible modulator of RNAi. Using a transient silencing and silencing suppression assay in Nicotiana benthamiana, we show that P4 not only displays an RNAi suppressor function, but also potentially enhances RNAi. The results also suggests that the N-terminal 168 amino acid residues of P4 are sufficient to maintain RNAi suppressor activity. Taken together with the earlier reports this work strengthens the view that the P4 protein carries out RNAi suppressor and a potential RNAi enhancer function.
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References
Borah BK, Sharma S, Kant R, Johnson AM, Saigopal DV, Dasgupta I (2013) Bacilliform DNA-containing plant viruses in the tropics: commonalities within a genetically diverse group. Mol Plant Pathol 14:759–771
Hull R (1996) Molecular biology of Rice tungro viruses. Annu Rev Phytopathol 34:275–297
Hibino H, Roechan M, Sudarisman S (1978) Association of two types of virus particles with penyakit habang (tungro Disease) of rice in Indonesia. Phytopathology 68:1412–1416
Sanfaçon H, Wellink J, Gall OL, Karasev A, Vlugt RV, Wetzel T (2009) Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Arch Virol 154:899–907
Bao Y, Hull R (1992) Characterization of the discontinuities in rice tungro bacilliform virus DNA. J Gen Virol 73:1297–1301
Hay JM, Jones MC, Blakebrough ML, Dasgupta I, Davies JW, Hull R (1991) An analysis of the sequence of an infectious clone of rice tungro bacilliform virus, a plant pararetrovirus. Nucleic Acid Res 19:2615–2621
Qu RD, Bhattacharyya M, Laco GS, De Kochko A, Rao BL, Kaniewska MB, Elmer JS, Rochester DE, Smith CE, Beachy RN (1991) Characterization of the genome of Rice tungro bacilliform virus: comparison with Commelina yellow mottle virus and caulimoviruses. Virology 185:354–364
Hay J, Grieco F, Druka A, Pinner M, Lee SC, Hull R (1994) Detection of rice tungro bacilliform virus gene products in vivo. Virology 205:430–437
Hagen LS, Jacquemond M, Lepingle A, Lot H, Tepfer M (1993) Nucleotide sequence and genomic organization of cacao swollen shoot virus. Virology 196:619–628
Rajeswaran R, Golyaev V, Seguin J, Zvereva A, Farinelli L, Pooggin M (2014) Interactions of rice tungro bacilliform pararetrovirus and its protein P4 with plant RNA silencing machinery. Mol Plant Microbe Interact 12:1370–1378
Brodersen P, Voinnet O (2006) The diversity of RNA silencing pathways in plants. Trends Genet 22:5
Pumplin N, Voinnet O (2013) RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 11:745–760
Himber C, Dunoyer P, Moissiard G, Ritzenthaler C, Voinnet O (2003) Transitivity-dependent and -independent cell-to-cell movement of RNA silencing. EMBO J 22:4523–4533
Voinnet O (2005) Non-cell autonomous RNA silencing. FEBS Lett 579:5858–5871
Dunoyer P, Himber C, Voinnet O (2006) Induction, suppression and requirement of RNA silencing pathways in virulent Agrobacterium tumefaciens Infections. Nat Genet 38:258–263
Dunoyer P, Schott G, Himber C, Meyer D, Takeda A, Carrington JC, Voinnet O (2010) Small RNA duplexes function as mobile silencing signals between plant cells. Science 328:912–916
Kalantidis K, Schumacher HT, Alexiadis T, Helm JM (2008) RNA silencing movement in plants. Biol Cell 100:13–26
Hamilton A, Voinnet O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J 21:4671–4679
Csorba T, Kontra L, Burgyán J (2015) Viral silencing suppressors: tools forged to fine-tune host-pathogen coexistence. Virology 479:85–103
Nath N, Mathur S, Dasgupta I (2002) Molecular analysis of two complete rice tungro bacilliform virus genomic sequences from India. Arch Virol 147:1173–1187
Roth BM, Pruss GJ, Vance VB (2004) Plant viral suppressors of RNA silencing. Virus Res 102:97–108
Baulcombe D (2004) RNA silencing in plants. Nature 431:356–363
Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: β-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J 6(13):3901–3907
Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
Naresh M, Purkayastha A, Dasgupta I (2023) Silencing suppressor protein PRT of rice tungro bacilliform virus interacts with the plant RNA silencing-related protein SGS3. Virology 581:71–80
Alizon S, Hurford A, Mideo N, Van Baalen M (2009) Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future. J Evol Biol 22(2):245–259
Doumayrou J, Avellan A, Froissart R, Michalakis Y (2013) An experimental test of the transmission virulence trade-off hypothesis in a plant virus. Evolution 67(2):477–486
Sharma S, Rabindran R, Robin S, Dasgupta I (2011) Analysis of the complete DNA sequence of Rice tungro bacilliform virus from southern India indicates it to be a product of recombination. Arch Virol 156:2257–2262
Mathur S, Dasgupta I (2013) Further support of genetic conservation in Indian isolates of Rice tungro bacilliform virus by sequence analysis of an isolate from North-Western India. Virus Genes 46:387–391
Chao JA, Lee JH, Chapados BR, Debler EW, Schneemann A, Williamson JR (2005) Dual modes of RNA-silencing suppression by Flock House virus protein B2. Nat Struct Mol Biol 12:952–957
Chen HY, Yang J, Lin C, Yuan A (2008) Structural basis for RNA-silencing suppression by tomato Aspermy virus protein 2b. EMBO Rep 9:754–760
Vinutha T, Kumar G, Garg V, Canto T, Palukaitis P, Ramesh SV, Praveen S (2018) Tomato geminivirus encoded RNAi suppressor protein, AC4 interacts with host AGO4 and precludes viral DNA methylation. Gene 678:184–195
Wang L, Ding Y, He L, Zhang G, Zhu JK, Lozano-Duran R (2020) A virus-encoded protein suppresses methylation of the viral genome through its interaction with AGO4 in the Cajal body. Elife 9:e55542
Ji LH, Ding SW (2001) The suppressor of transgene RNA silencing encoded by cucumber mosaic virus interferes with salicylic acid-mediated virus resistance. Mol Plant Microbe Interact 14(6):715–724
Love AJ, Geri C, Laird J, Carr C, Yun BW (2012) Cauliflower mosaic virus protein P6 inhibits signaling responses to salicylic acid and regulates innate immunity. PLoS ONE 7(10):e47535
Hunter LJR, Westwood JH, Heath G, Macaulay K, Smith AG (2013) Regulation of RNA-dependent RNA polymerase 1 and isochorismate synthase gene expression in Arabidopsis. PLoS ONE 8(6):e66530
Wang Y, Gong Q, Wu Y, Huang F, Ismayil A (2021) A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants. Cell Host Microbe 29(9):1393–1406
Malcuit I, Marano MR, Kavanagh TA, De Jong W, Forsyth A, Baulcombe DC (1999) The 25-kDa movement protein of PVX elicits Nb-mediated hypersensitive cell death in potato. Mol Plant Microbe Interact 12(6):536–543
Voinnet O, Pinto YM, Baulcombe DC (1999) Suppression of gene silencing: a general strategy used by diverse DNA and RNA of plants. Proc Natl Acad Sci 96(24):14147–14152
Ronde D, Pasquier A, Ying S, Butterbach P, Lohuis D, Kormelink R (2014) Analysis of Tomato spotted wilt virus NSs protein indicates the importance of the N-terminal domain for avirulence and RNA silencing suppression. Mol Plant Pathol 15(2):185–195
Ren T, Qu F, Morris TJ (2000) HRT gene function requires interaction between a NAC protein and viral capsid protein to confer resistance to turnip crinkle virus. Plant Cell 12(10):1917–1925
Baulcombe DC (2022) The role of viruses in identifying and analyzing RNA silencing. Annual Rev Virol 9:353–373
Devers EA, Brosnan C, Sarazin A, Albertini D, Amsler AC, Brioudes F, Jullien PE, Lim P, Schott G, Voinnet O (2020) Movement and differential consumption of short interfering RNA duplexes underlie mobile RNA interference. Nat Plants 6:789–799
Yan Y, Ham BK, Chong YH, Yeh SD, Lucas WJ (2020) A plant SMALL RNA-BINDING PROTEIN 1 family mediates cell-to-cell trafficking of RNAi signals. Mol Plant 13:321–335
Yan Y, Gan J, Tao Y, Okita TW, Tian L (2022) RNA-Binding proteins: the key modulator in stress granule formation and abiotic stress response. Front Plant Sci 13:882596
Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM, Carroll BJ (2007) Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc Natl Acad Sci 104:14741–14746
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MN acknowledges Rajiv Gandhi National Fellowship by University Grants Commission, New Delhi. ID acknowledges the financial support from University of Delhi (R&D and DU-DST PURSE) for this study.
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ID planned and conceived the experiments, AP cloned the viral genes, MN performed infiltrations, cloning, northern blot analysis, PCR-based assays, quantitative assays, ID acquired the funds and MN and ID wrote the paper.
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Naresh, M., Purkayastha, A. & Dasgupta, I. P4 protein of an Indian isolate of rice tungro bacilliform virus modulates gene silencing. Virus Genes 60, 55–64 (2024). https://doi.org/10.1007/s11262-023-02039-2
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DOI: https://doi.org/10.1007/s11262-023-02039-2