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Molecular characterization and analysis of conserved potyviral motifs in bean common mosaic virus (BCMV) for RNAi-mediated protection

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Abstract

Australian bean common mosaic virus (BCMV) isolates were sequenced, and the sequences were compared to global BCMV and bean common mosaic necrosis virus (BCMNV) sequences and analysed for conserved potyviral motifs to generate in planta RNA-interference (RNAi) resistance. Thirty-nine out of 40 previously reported potyvirus motifs were conserved among all 77 BCMV/BCMNV sequences. Two RNAi target regions were selected for dsRNA construct design, covering 920 bp of the nuclease inclusion b (NIb) protein and 461 bp of the coat protein (CP). In silico prediction of the effectiveness of these constructs for broad-spectrum defence against the 77 BCMV and BCMNV sequences was done via analysis of putative 21-nucleotide (nt) and 22-nt small-interfering RNAs (siRNAs) generated from the target regions. The effectiveness of both constructs for siRNA generation and BCMV RNAi-mediated resistance was validated in Nicotiana benthamiana transient assays.

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References

  1. International Service for the Acquisition of Agri-Biotech Applications (ISAAA) (2018) Bean (Phaseolus vulgaris) GM Events

  2. Aleman-Verdaguer M-E, Goudou-Urbino C, Dubern J, Beachy RN, Fauquet C (1997) Analysis of the sequence diversity of the P1, HC, P3, NIb and CP genomic regions of several yam mosaic potyvirus isolates: implications for the intraspecies molecular diversity of potyviruses. J Gen Virol 78:1253–1264

    Article  PubMed  Google Scholar 

  3. Anuradha C, Balasubramanian V, Selvarajan R (2015) Sequence motif comparison and homology modeling of helper component proteinase (HC–Pro) of banana bract mosaic virus.

  4. Bartel D (2004) MicroRNAs: genomics, biogensis, mechanism and function. Cell 116:281–297

    Article  PubMed  CAS  Google Scholar 

  5. Baulcombe D (2004) RNA silencing in plants. Nature 431:356–363

    Article  PubMed  CAS  Google Scholar 

  6. Bhadramurthy V, Bhat A (2009) Biological and molecular characterization of Bean common mosaic virus associated with vanilla in India. Indian J Virol 20:70–77

    Google Scholar 

  7. Bonfim K, Faria JC, Nogueira EO, Mendes ÉA, Aragão FJ (2007) RNAi-mediated resistance to Bean golden mosaic virus in genetically engineered common bean (Phaseolus vulgaris). Mol Plant-microbe Interact 20:717–726

    Article  PubMed  CAS  Google Scholar 

  8. Borges F, Martienssen RA (2015) The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol 16:727

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Bravo E, Calvert LA, Morales FJ (2008) The complete nucleotide sequence of the genomic RNA of bean common mosaic virus strain nl4. Rev Acad Colomb Cienc Exactas 32:37–46

    Google Scholar 

  10. Brosnan C, Mitter N, Christie M, Smith N, Waterhouse P, Carroll B (2007) Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc Natl Acad Sci 104:14741–14746

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  11. Burand JP, Hunter WB (2013) RNAi: Future in insect management. J Invertebr Pathol 112:S68–S74

    Article  PubMed  CAS  Google Scholar 

  12. Cheng G, Dong M, Xu Q, Peng L, Yang Z, Wei T, Xu J (2017) Dissecting the molecular mechanism of the subcellular localization and cell-to-cell movement of the sugarcane mosaic virus P3N-PIPO. Sci Rep 7:9868

    Article  PubMed  PubMed Central  Google Scholar 

  13. Damayanti T, Susilo D, Nurlaelah S, Sartiami D, Okuno T, Mise K (2008) First report of Bean common mosaic virus in yam bean [Pachyrhizus erosus (L.) Urban] in Indonesia. J Gen Plant Pathol 74:438–442

    Article  CAS  Google Scholar 

  14. Duan C-G, Wang C-H, Guo H-S (2012) Application of RNA silencing to plant disease resistance. Silence 3:5

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. El-Sawy MA, Mohamed HAE, Elsharkawy MM (2013) Serological and molecular characterisations of the Egyptian isolate of Bean common mosaic virus. Arch Phytopathol Plant Protect 47:1–13

    Google Scholar 

  16. Flores-Estévez N, Acosta-Gallegos J, Silva-Rosales L (2003) Bean common mosaic virus and Bean common mosaic necrosis virus in Mexico. Plant disease 87:21–25

    Article  PubMed  Google Scholar 

  17. Gleave AP (1992) A versatile binary vector system with a T-DNA organisational structure conducive to efficient integration of cloned DNA into the plant genome. Plant Mol Biol 20:1203–1207

    Article  PubMed  CAS  Google Scholar 

  18. Gong D, Wang J-H, Lin Z-S, Zhang S-Y, Zhang Y-L, Yu N-T, Xiong Z, Liu Z-X (2011) Genomic sequencing and analysis of Chilli ringspot virus, a novel potyvirus. Virus Genes 43:439–444

    Article  PubMed  CAS  Google Scholar 

  19. Gordon KH, Waterhouse PM (2007) RNAi for insect-proof plants. Nat Biotechnol 25:1231–1232

    Article  PubMed  CAS  Google Scholar 

  20. Guyatt K, Proll D, Menssen A, Davidson A (1996) The complete nucleotide sequence of bean yellow mosaic potyvirus RNA. Arch Virol 141:1231–1246

    Article  PubMed  CAS  Google Scholar 

  21. Hamid A, Ahmad M, Padder B, Shah M, Saleem S, Sofi T, Mir A (2013) Pathogenic and coat protein characterization confirming the occurrence of Bean common mosaic virus on common bean (Phaseolus vulgaris) in Kashmir, India. Phytoparasitica 42:1–6

    Google Scholar 

  22. Ivanov K, Eskelin K, Lõhmus A, Mäkinen K (2014) Molecular and cellular mechanisms underlying potyvirus infection. J Gen Virol 95:1415–1429

    Article  PubMed  CAS  Google Scholar 

  23. Ivanov KI, Mäkinen K (2012) Coat proteins, host factors and plant viral replication. Curr Opin Virol 2:712–718

    Article  PubMed  CAS  Google Scholar 

  24. Kamenova I, Lohuis H, Peters D (2002) Loss of aphid transmissibility of plum pox virus isolates. Biotechnol Biotechnol Equip 16:48–54

    Article  CAS  Google Scholar 

  25. Kelly J, Afanador L, Haley S (1995) Pyramiding genes for resistance to Bean common mosaic virus. Euphytica 82:207–212

    Article  Google Scholar 

  26. Knierim D, Menzel W, Winter S (2017) Analysis of the complete genome sequence of euphorbia ringspot virus, an atypical member of the genus Potyvirus. Arch Virol 162:291–293

    Article  PubMed  CAS  Google Scholar 

  27. Koch A, Biedenkopf D, Furch A, Weber L, Rossbach O, Abdellatef E, Linicus L, Johannsmeier J, Jelonek L, Goesmann A (2016) An RNAi-based control of Fusarium graminearum infections through spraying of long dsRNAs involves a plant passage and is controlled by the fungal silencing machinery. PLoS Pathog 12:e1005901

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Kwapata K, Nguyen T, Sticklen M (2012) Genetic transformation of common bean (Phaseolus vulgaris L.) with the gus color marker, the bar herbicide resistance, and the barley (Hordeum vulgare) HVA1 drought tolerance genes. Int J Agron 2012:1–8

    Article  Google Scholar 

  29. Li F, Xu D, Abad J, Li R (2012) Phylogenetic relationships of closely related potyviruses infecting sweet potato determined by genomic characterization of Sweet potato virus G and Sweet potato virus 2. Virus Genes 45:118–125

    Article  PubMed  CAS  Google Scholar 

  30. Li Y, Jia A, Qiao Y, Xiang J, Zhang Y, Wang W (2017) Virome analysis of lily plants reveals a new potyvirus. Arch Virol 163:1–4

    Google Scholar 

  31. Li YQ, Liu ZP, Yang YS, Zhao B, Fan ZF, Wan P (2014) First report of Bean common mosaic virus infecting Azuki bean (Vigna angularis Ohwi & Ohashi) in China. Plant Disease 98:1017

    Article  PubMed  CAS  Google Scholar 

  32. Liang WX, Song LM, Tian GZ, Li HF, Fan ZF (2006) The genomic sequence of Wisteria vein mosaic virus and its similarities with other potyviruses. Arch Virol 151:2311–2319

    Article  PubMed  CAS  Google Scholar 

  33. Lilley C, Davies L, Urwin P (2012) RNA interference in plant parasitic nematodes: a summary of the current status. Parasitology 139:630–640

    Article  PubMed  CAS  Google Scholar 

  34. Lin J-J (1995) Electrotransformation of Agrobacterium. 171–178

  35. Lopez-Moya J, Wang R, Pirone T (1999) Context of the coat protein DAG motif affects potyvirus transmissibility by aphids. J Gen Virol 80:3281–3288

    Article  PubMed  CAS  Google Scholar 

  36. Maillard P, Ciaudo C, Marchais A, Li Y, Jay F, Ding S, Voinnet O (2013) Antiviral RNA interference in mammalian cells. Science 342:235–238

    Article  PubMed  CAS  Google Scholar 

  37. Mangrauthia SK, Jain R, Praveen S (2008) Sequence motifs comparisons establish a functional portrait of a multifunctional protein HC-Pro from papaya ringspot potyvirus. J Plant Biochem Biotechnol 17:201–204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Mann KS, Johnson KN, Dietzgen RG (2015) Cytorhabdovirus phosphoprotein shows RNA silencing suppressor activity in plants, but not in insect cells. Virology 476:413–418

    Article  PubMed  CAS  Google Scholar 

  39. Maoka T, Hataya T (2005) The complete nucleotide sequence and biotype variability of Papaya leaf distortion mosaic virus. Phytopathology 95:128–135

    Article  PubMed  CAS  Google Scholar 

  40. Mishra R, Verma RK, Gaur RK (2015) Analysis of genome comparison of two Indian isolates of Cowpea aphid-borne mosaic virus from India. Virus Genes 51:306–309

    Article  PubMed  CAS  Google Scholar 

  41. Mitter N, Worrall EA, Robinson KE, Li P, Jain RG, Taochy C, Fletcher SJ, Carroll BJ, Lu G, Xu ZP (2017) Clay nanosheets for topical delivery of RNAi for sustained protection against plant viruses. Nat Plants 3:16207

    Article  PubMed  CAS  Google Scholar 

  42. Moghal S, Francki R (1976) Towards a system for the identification and classification of potyviruses: I. Serology and amino acid composition of six distinct viruses. Virology 73:350–362

    Article  PubMed  CAS  Google Scholar 

  43. Moradi Z, Mehrvar M, Nazifi E, Zakiaghl M (2017) Iranian johnsongrass mosaic virus: the complete genome sequence, molecular and biological characterization, and comparison of coat protein gene sequences. Virus Genes 53:77–88

    Article  PubMed  CAS  Google Scholar 

  44. Moura MF, Marubayashi JM, Mituti T, Gioria R, Kobori RF, Pavan MA, Krause-Sakate R (2012) Comparative analysis of coding region for the coat protein of PepYMV and PVY isolates collected in sweetpepper. Summa Phytopathol 38:93–96

    Article  Google Scholar 

  45. Mukeshimana G, Paneda A, Rodríguez-Suárez C, Ferreira JJ, Giraldez R, Kelly JD (2005) Markers linked to the bc-3 gene conditioning resistance to bean common mosaic potyviruses in common bean. Euphytica 144:291–299

    Article  Google Scholar 

  46. Pasev G, Kostova D, Sofkova S (2014) Identification of genes for resistance to Bean common mosaic virus and Bean common mosaic necrosis virus in snap bean (Phaseolus vulgaris L.) breeding lines ssing conventional and molecular methods. J Phytopathol 162:19–25

    Article  CAS  Google Scholar 

  47. Perotto MC, Pozzi EA, Celli MG, Luciani CE, Mitidieri MS, Conci VC (2018) Identification and characterization of a new potyvirus infecting cucurbits. Arch Virol 163:719–724

    Article  PubMed  CAS  Google Scholar 

  48. Puli’uvea C, Khan S, Chang W-L, Valmonte G, Pearson MN, Higgins CM (2017) First complete genome sequence of vanilla mosaic strain of Dasheen mosaic virus isolated from the Cook Islands. Arch Virol 162:591–595

    Article  PubMed  CAS  Google Scholar 

  49. Rajamäki M, Merits A, Rabenstein F, Andrejeva J, Paulin L, Kekarainen T, Kreuze J, Forster R, Valkonen J (1998) Biological, serological, and molecular differences among isolates of potato A potyvirus. Phytopathology 88:311–321

    Article  PubMed  Google Scholar 

  50. Revers F, Garcia J (2015) Molecular biology of potyviruses. Adv Virus Res 92:101–199

    Article  PubMed  CAS  Google Scholar 

  51. Rojas MR, Zerbini FM, Allison RF, Gilbertson RL, Lucas WJ (1997) Capsid protein and helper component-proteinase function as potyvirus cell-to-cell movement proteins. Virology 237:283–295

    Article  PubMed  CAS  Google Scholar 

  52. Saqib M, Jones RAC, Cayford B, Jones MGK (2005) First report of Bean common mosaic virus in Western Australia. Plant Pathol 54:563

    Article  Google Scholar 

  53. Saqib M, Nouri S, Cayford B, Jones RAC, Jones MGK (2010) Genome sequences and phylogenetic placement of two isolates of Bean common mosaic virus from Macroptilium atropurpureum in north-west Australia. Aust Plant Pathol Soc 39:184–191

    Article  CAS  Google Scholar 

  54. Sastry KS (2013) Mechanism of seed transmission. Seed-borne plant virus diseases. Springer, Heidelberg, pp 85–100

    Book  Google Scholar 

  55. Sengooba TN, Spence NJ, Walkey DGA, Allen DJ, Femi Lana A (1997) The occurrence of Bean common mosaic necrosis virus in wild and forage legumes in Uganda. Plant Pathol 46:95–103

    Article  Google Scholar 

  56. Shapter FM, Waters DL Genome walking T cereal genomics, pp 133–146

  57. Shukla DD, Frcnkel M, Ward CW (1991) Structure and function of the potyvirus genome with special reference to the coat protein coding region. Can J Plant Pathol 13:178–191

    Article  CAS  Google Scholar 

  58. Silbernagel MJ, Mink GI, Zhao RL, Zheng GY (2001) Phenotypic recombination between bean common mosaic and bean common mosaic necrosis potyviruses in vivo. Arch Virol 146:1007–1020

    Article  PubMed  CAS  Google Scholar 

  59. Singh SP, Schwartz HF (2010) Breeding common bean for resistance to diseases: a review. Crop Sci 50:2199–2223

    Article  Google Scholar 

  60. Spence N, Walkey D (1995) Variation for pathogenicity among isolates of Bean common mosaic virus in Africa and a reinterpretation of the genetic relationship between cultivars of Phaseolus vulgaris and pathotypes of BCMV. Plant Pathol 44:527–546

    Article  Google Scholar 

  61. Urchqui-Inchima S, Haenni A-L, Bernardi F (2001) Potyvirus proteins: a wealth of functions. Virus Res 74:157–175

    Article  Google Scholar 

  62. Valli A, López-Moya JJ, García JA (2007) Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J Gen Virol 88:1016–1028

    Article  PubMed  CAS  Google Scholar 

  63. Velasco L, Salem N, Willemsen A, Lapidot M, Mansour AN, Rubio L, Galipienso L (2016) Genetic variation and evolutionary forces shaping Cucumber vein yellowing virus populations: risk of emergence of virulent isolates in Europe. Plant Pathol 65:847–856

    Article  CAS  Google Scholar 

  64. Verma P, Gupta U (2010) Immunological detection of Bean common mosaic virus in French bean (Phaseolus vulgaris L.) leaves. Indian j Microbiol 50:263–265

    Article  PubMed  PubMed Central  Google Scholar 

  65. Worrall EA, Wamonje FO, Mukeshimana G, Harvey JJ, Carr JP, Mitter N (2015) Bean common mosaic virus and Bean common mosaic necrosis virus: relationships, biology, and prospects for control. Adv Virus Res 93:1–46

    Article  PubMed  CAS  Google Scholar 

  66. Zheng L, Wayper PJ, Gibbs AJ, Fourment M, Rodoni BC, Gibbs MJ (2008) Accumulating variation at conserved sites in potyvirus genomes is driven by species discovery and affects degenerate primer design. PLoS One 3:e1586

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgments

The authors would like to thank Queensland Alliance of Agriculture and Food Innovation (QAAFI), Australia and the University of Queensland, Australia, for their support.

Funding

This study was funded by the Accelerated Partnership Grant, Queensland Government (2014000652), awarded to N.M. with Nufarm Australia Limited as the industry partner. E.A.W. PhD programme with N.M. is supported by a scholarship from the University of Queensland.

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Authors and Affiliations

  1. Centre of Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia

    Elizabeth A. Worrall, Alice C. Hayward, Stephen J. Fletcher & Neena Mitter

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  1. Elizabeth A. Worrall
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  2. Alice C. Hayward
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  3. Stephen J. Fletcher
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  4. Neena Mitter
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Correspondence to Neena Mitter.

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The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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The datasets generated and/or analysed during the current study are available in the NCBI GenBank repository, https://www.ncbi.nlm.nih.gov. Only complete genomes of BCMV and BCMNV were used.

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Handling Editor: F. Murilo Zerbini.

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Worrall, E.A., Hayward, A.C., Fletcher, S.J. et al. Molecular characterization and analysis of conserved potyviral motifs in bean common mosaic virus (BCMV) for RNAi-mediated protection. Arch Virol 164, 181–194 (2019). https://doi.org/10.1007/s00705-018-4065-6

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  • DOI: https://doi.org/10.1007/s00705-018-4065-6

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