The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
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siRNAs Derived from Cymbidium Mosaic Virus and Odontoglossum Ringspot Virus Down-modulated the Expression Levels of Endogenous Genes in Phalaenopsis equestris

  • Lan, Han-hong (School of Biological Sciences and Biotechnology, Minnan Normal University) ;
  • Wang, Cui-mei (School of Biological Sciences and Biotechnology, Minnan Normal University) ;
  • Chen, Shuang-shuang (School of Biological Sciences and Biotechnology, Minnan Normal University) ;
  • Zheng, Jian-ying (School of Biological Sciences and Biotechnology, Minnan Normal University)
  • Received : 2019.03.15
  • Accepted : 2019.07.09
  • Published : 2019.10.01
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Abstract

Interplay between Cymbidium mosaic virus (CymMV)/Odontoglossum ringspot virus (ORSV) and its host plant Phalaenopsis equestris remain largely unknown, which led to deficiency of effective measures to control disease of P. equestris caused by infecting viruses. In this study, for the first time, we characterized viral small interfering RNAs (vsiRNAs) profiles in P. equestris co-infected with CymMV and ORSV through small RNA sequencing technology. CymMV and ORSV small interfering RNAs (siRNAs) demonstrated several general and specific/new characteristics. vsiRNAs, with A/U bias at the first nucleotide, were predominantly 21-nt long and they were derived predominantly (90%) from viral positive-strand RNA. 21-nt siRNA duplexes with 0-nt overhangs were the most abundant 21-nt duplexes, followed by 2-nt overhangs and then 1-nt overhangs 21-nt duplexes in infected P. equestris. Continuous but heterogeneous distribution and secondary structures prediction implied that vsiRNAs originate predominantly by direct Dicer-like enzymes cleavage of imperfect duplexes in the most folded regions of the positive strand of both viruses RNA molecular. Furthermore, we totally predicted 54 target genes by vsiRNAs with psRNATarget server, including disease/stress response-related genes, RNA interference core components, cytoskeleton-related genes, photosynthesis or energy supply related genes. Gene Ontology classification showed that a majority of the predicted targets were related to cellular components and cellular processes and performed a certain function. All target genes were down-regulated with different degree by vsiRNAs as shown by real-time reverse transcription polymerase chain reaction. Taken together, CymMV and ORSV siRNAs played important roles in interplay with P. equestris by down modulating the expression levels of endogenous genes in host plant.

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References

  1. Baulcombe, D. 2006. RNA silencing in plants. Nature 431:356-363. https://doi.org/10.1038/nature02874
  2. Blevins, T., Rajeswaran, R., Shivaprasad, P. V., Beknazariants, D., Si-Ammour, A., Park, H.-S., Vazquez, F., Robertson, D., Meins, F. Jr., Hohn, T. and Pooggin, M. M. 2006. Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res. 34:6233-6246. https://doi.org/10.1093/nar/gkl886
  3. Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W.-C., Liu, K.-W., Chen, L.-J., He, Y., Xu, Q., Bian, C., Zheng, Z., Sun, F., Liu, W., Hsiao, Y.-Y., Pan, Z.-J., Hsu, C.-C., Yang, Y.-P., Hsu, Y.-C., Chuang, Y.-C., Dievart, A., Dufayard, J.-F., Xu, X., Wang, J.-Y., Wang, J., Xiao, X.-J., Zhao, X.-M., Du, R., Zhang, G.-Q., Wang, M., Su, Y.-Y., Xie, G.-C., Liu, G.-H., Li, L.-Q., Huang, L.-Q., Luo, Y.-B., Chen, H.-H., Van de Peer, Y. and Liu, Z.-J. 2015. The genome sequence of the orchid Phalaenopsis equestris. Nat. Genet. 47:65-72. https://doi.org/10.1038/ng.3149
  4. Dai, X. and Zhao, P. X. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 39:W155-W159. https://doi.org/10.1093/nar/gkr319
  5. Deleris, A., Gallego-Bartolome, J., Bao, J., Kasschau, K. D., Carrington, J. C. and Voinnet, O. 2006. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313:68-71. https://doi.org/10.1126/science.1128214
  6. Derrien, B., Baumberger, N., Schepetilnikov, M., Viotti, C., De Cillia, J., Ziegler-Graff, V., Isono, E., Schumacher, K. and Genschik, P. 2012. Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway. Proc. Natl. Acad. Sci. U. S. A. 109:15942-15946. https://doi.org/10.1073/pnas.1209487109
  7. DeYoung, B. J. and Innes, R. W. 2006. Plant NBS-LRR proteins in pathogen sensing and host defense. Nat. Immunol. 7:1243-1249. https://doi.org/10.1038/ni1410
  8. Ding, S.-W. 2010. RNA-based antiviral immunity. Nat. Rev. Immunol. 10:632-644. https://doi.org/10.1038/nri2824
  9. Donaire, L., Barajas, D., Martinez-García, B., Martinez-Priego, L., Pagan, I. and Llave, C. 2008. Structural and genetic requirements for the biogenesis of Tobacco rattle virus-derived small interfering RNAs. J. Virol. 82:5167-5177. https://doi.org/10.1128/JVI.00272-08
  10. Earley, K., Smith, M. R., Weber, R., Gregory, B. D. and Poethig, R. S. 2010. An endogenous F-box protein regulates ARGONAUTE1 in Arabidopsis thaliana. Silence 1:15. https://doi.org/10.1186/1758-907X-1-15
  11. Gibbs, A. 2000. Viruses of orchids in Australia: their identification, biology and control. Aust. Orchid Rev. 65:10-21.
  12. Gouin, E., Welch, M. D. and Cossart, P. 2005. Actin-based motility of intracellular pathogens. Curr. Opin. Microbiol. 8:35-45. https://doi.org/10.1016/j.mib.2004.12.013
  13. Greber, U. F. and Way, M. 2006. A superhighway to virus infection. Cell 124:741-754. https://doi.org/10.1016/j.cell.2006.02.018
  14. Gruenheid, S. and Finlay, B. B. 2003. Microbial pathogenesis and cytoskeletal function. Nature 422:775-781. https://doi.org/10.1038/nature01603
  15. Ho, T., Wang, H., Pallett, D. and Dalmay, T. 2007. Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins. FEBS Lett. 581:3267-3272. https://doi.org/10.1016/j.febslet.2007.06.022
  16. Hong, W., Qian, D., Sun, R., Jiang, L., Wang, Y., Wei, C., Zhang, Z. and Li, Y. 2015. OsRDR6 plays role in host defense against double-stranded RNA virus, Rice Dwarf Phytoreovirus. Sci Rep. 5:11324. https://doi.org/10.1038/srep11324
  17. Jiang, L., Qian, D., Zheng, H., Meng, L.-Y, Chen, J., Le, W.-J., Zhou, T., Zhou, Y.-J., Wei, C.-H. and Li, Y. 2012. RNAdependent RNA polymerase 6 of rice (Oryza sativa) plays role in host defense against negative-strand RNA virus, Rice stripe virus. Virus Res. 163:512-519. https://doi.org/10.1016/j.virusres.2011.11.016
  18. Jones-Rhoades, M. W., Bartel, D. P. and Bartel, B. 2006. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57:19-53. https://doi.org/10.1146/annurev.arplant.57.032905.105218
  19. Kapoor, M., Arora, R., Lama, T., Nijhawan, A., Khurana, J. P., Tyagi, A. K. and Kapoor, S. 2008. Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics 9:451. https://doi.org/10.1186/1471-2164-9-451
  20. Kim, H. S. and Delaney, T. P. 2002. Arabidopsis SON1 is an FBox protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance. Plant Cell 14:1469-1482. https://doi.org/10.1105/tpc.001867
  21. Koh, K. W., Lu, H.-C. and Chan, M.-T. 2014. Virus resistance in orchids. Plant Sci. 228:26-38. https://doi.org/10.1016/j.plantsci.2014.04.015
  22. Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I. and Simon, R. 2009. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology 388:1-7. https://doi.org/10.1016/j.virol.2009.03.024
  23. Lacombe, S., Bangratz, M., Vignols, F. and Brugidou, C. 2010. The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing. Plant J. 61:371-382. https://doi.org/10.1111/j.1365-313X.2009.04062.x
  24. Lan, H., Chen, H., Liu, Y., Jiang, C., Mao, Q., Jia, D., Chen, Q. and Wei, T. 2015. Small interfering RNA pathway modulates initial viral infection in midgut epithelium of insect after ingestion of virus. J. Virol. 90:917-929. https://doi.org/10.1128/JVI.01835-15
  25. Lan, H., Hong, X., Huang, R., Lin, X., Li, Q., Li, K. and Zhou, T. 2018a. RNA interference-mediated knockdown and virusinduced suppression of Troponin C gene adversely affect the behavior or fitness of the green rice leafhopper, Nephotettix cincticeps. Arch. Insect Biochem. Physiol. 97:e21438. https://doi.org/10.1002/arch.21438
  26. Lan, H., Wang, H., Chen, Q., Chen, H., Jia, D., Mao, Q. and Wei, T. 2016. Small interfering RNA pathway modulates persistent infection of a plant virus in its insect vector. Sci. Rep. 6:20699. https://doi.org/10.1038/srep20699
  27. Lan, Y., Li, Y., E. Z., Sun, F., Du, L., Xu, Q., Zhou, T., Zhou, Y. and Fan, Y. 2018b. Identification of virus-derived siRNAs and their targets in RBSDV-infected rice by deep sequencing. J. Basic Microbiol. 58:227-237. https://doi.org/10.1002/jobm.201700325
  28. Li, R., Gao, S., Berendsen, S., Fei, Z. and Ling, K.-S. 2015. Complete genome sequence of a novel genotype of squash mosaic virus infecting squash in Spain. Genome Announc. 3:e01583-14.
  29. Li, R., Gao, S., Fei, Z. and Ling, K.-S. 2013. Complete genome sequence of a new tobamovirus naturally infecting tomatoes in Mexico. Genome Announc. 1:e00794-13.
  30. Li, R., Gao, S., Hernandez, A. G., Wechter, W. P., Fei, Z. and Ling, K.-S. 2012. Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation. PLoS ONE 7:e37127. https://doi.org/10.1371/journal.pone.0037127
  31. Li, Y., Deng, C., Shang, Q., Zhao, X., Liu, X. and Zhou, Q. 2016. Characterization of siRNAs derived from cucumber green mottle mosaic virus in infected cucumber plants. Arch. Virol. 161:455-458. https://doi.org/10.1007/s00705-015-2687-5
  32. Liu, B., Chen, Z., Song, X., Liu, C., Cui, X., Zhao, X., Fang, J., Xu, W., Zhang, H., Wang, X., Chu, C., Deng, X., Xue, Y. and Cao, X. 2007. Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell 19:2705-2718. https://doi.org/10.1105/tpc.107.052209
  33. Liu, C., Chen, Z., Hu, Y., Ji, H., Yu, D., Shen, W., Li, S., Ruan, J., Bu, W. and Gao, S. 2018. Complemented palindrome small RNAs first discovered from SARS coronavirus. Genes 9:442. https://doi.org/10.3390/genes9090442
  34. Mandadi, K. K. and Scholthof, K.-B. G. 2015. Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. Plant Cell 27:71-85. https://doi.org/10.1105/tpc.114.133991
  35. McHale, L., Tan, X., Koehl, P. and Michelmore, R. W. 2006. Plant NBS-LRR proteins: adaptable guards. Genome Biol. 7:212.
  36. Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C., Chen, S., Hannon, G. J. and Qi, Y. 2008. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5'-terminal nucleotide. Cell 133:116-127. https://doi.org/10.1016/j.cell.2008.02.034
  37. Mitter, N., Koundal, V., Williams, S. and Pappu, H. 2013. Differential expression of Tomato spotted wilt virus-derived viral small RNAs in infected commercial and experimental host plants. PLoS ONE 8:e76276. https://doi.org/10.1371/journal.pone.0076276
  38. Molnar, A., Csorba, T., Lakatos, L., Varallyay, E., Lacomme, C. and Burgyan, J. 2005. Plant virus-derived small interfering RNAs originate predominantly from highly structured singlestranded viral RNAs. J. Virol. 79:7812-7818. https://doi.org/10.1128/JVI.79.12.7812-7818.2005
  39. Morris, E. R. and Walker, J. C. 2003. Receptor-like protein kinases: the keys to response. Curr. Opin. Plant Biol. 6:339-342. https://doi.org/10.1016/S1369-5266(03)00055-4
  40. Niu, S.-C., Xu, Q., Zhang, G.-Q., Zhang, Y.-Q., Tsai, W.-C., Hsu, J.-L., Liang, C.-K., Luo, Y.-B. and Liu, Z.-J. 2016. De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris. Sci. Data 3:160083. https://doi.org/10.1038/sdata.2016.83
  41. Niu, X., Sun, Y., Chen, Z., Li, R., Padmanabhan, C., Ruan, J., Kreuze, J. F., Ling, K., Fei, Z. and Gao, S. 2017. Using small RNA-seq data to detect siRNA duplexes induced by plant viruses. Genes 8:163. https://doi.org/10.3390/genes8060163
  42. Prabha, K., Baranwal, V. K. and Jain, R. K. 2013. Applications of next generation high throughput sequencing technologies in characterization, discovery and molecular interaction of plant viruses. Indian J. Virol. 24:157-165. https://doi.org/10.1007/s13337-013-0133-4
  43. Rubio, M., Rodriguez-Moreno, L., Ballester, A. R., de Moura, M. C., Bonghi, C., Candresse, T. and Martinez-Gomez, P. 2015. Analysis of gene expression changes in peach leaves in response to Plum pox virus infection using RNA-Seq. Mol. Plant Pathol. 16:164-176. https://doi.org/10.1111/mpp.12169
  44. Sharma, N., Sahu, P. P., Puranik, S. and Prasad, M. 2013. Recent advances in plant-virus interaction with emphasis on small interfering RNAs (siRNAs). Mol. Biotechnol. 55:63-77. https://doi.org/10.1007/s12033-012-9615-7
  45. Sinha, P., Pazhamala, L. T., Singh, V. K., Saxena, R. K., Krishnamurthy, L., Azam, S., Khan, A. W. and Varshney, R. K. 2016. Identification and validation of selected universal stress protein domain containing drought-responsive genes in Pigeonpea (Cajanus cajan L.). Front. Plant Sci. 6:1065. https://doi.org/10.3389/fpls.2015.01065
  46. Vaucheret, H. 2006. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev. 20:759-771. https://doi.org/10.1101/gad.1410506
  47. Wang, A. 2015. Dissecting the molecular network of virus-plant interactions: the complex roles of host factors. Annu. Rev. Phytopathol. 53:45-66. https://doi.org/10.1146/annurev-phyto-080614-120001
  48. Wang, F., Sun, Y., Ruan, J., Chen, R., Chen, X., Chen, C., Kreuze, J. F., Fei, Z., Zhu, X. and Gao, S. 2016. Using small RNA deep sequencing data to detect human viruses. BioMed Res. Int. 2016:2596782.
  49. Wong, S. M., Chng, C. G., Lee, Y. H., Tan, K. and Zettler, F. W. 1994. Incidence of cymbidium mosaic and odontoglossum ringspot viruses and their significance in orchid cultivation in Singapore. Crop Prot. 13:235-239. https://doi.org/10.1016/0261-2194(94)90084-1
  50. Wu, Q., Luo, Y., Lu, R., Lau, N., Lai, E. C., Li, W.-X. and Ding, S.-W. 2010. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc. Natl. Acad. Sci. U. S. A. 107:1606-1611. https://doi.org/10.1073/pnas.0911353107
  51. Xia, Z., Peng, J., Li, Y., Chen, L., Li, S., Zhou, T. and Fan, Z. 2014. Characterization of small interfering RNAs derived from Sugarcane mosaic virus in infected maize plants by deep sequencing. PLoS ONE 9:e97013. https://doi.org/10.1371/journal.pone.0097013
  52. Xu, D. and Zhou, G. 2017. Characteristics of siRNAs derived from Southern rice black-streaked dwarf virus in infected rice and their potential role in host gene regulation. Virol. J. 14:27. https://doi.org/10.1186/s12985-017-0699-3
  53. Yan, F., Zhang, H., Adams, M. J., Yang, J., Peng, J., Antoniw, J. F., Zhou, Y. and Chen, J. 2010. Characterization of siRNAs derived from rice stripe virus in infected rice plants by deep sequencing. Arch. Virol. 155:935-940. https://doi.org/10.1007/s00705-010-0670-8
  54. Yang, J., Zheng, S.-L., Zhang, H.-M., Liu, X.-Y., Li, J., Li, J.-M. and Chen, J.-P. 2014. Analysis of small RNAs derived from Chinese wheat mosaic virus. Arch. Virol. 159:3077-3082. https://doi.org/10.1007/s00705-014-2155-7
  55. Zettler, F. W., Ko, N. J., Wisler, G. C., Elliott, M. S. and Wong, S. M. 1990. Viruses of orchids and their control. Plant Dis. 74:621-626. https://doi.org/10.1094/PD-74-0621
  56. Zheng, Y., Gao, S., Padmanabhan, C., Li, R., Galvez, M., Gutierrez, D., Fuentes, S., Ling, K.-S., Kreuze, J. and Fei, Z. 2017. VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology 500:130-138. https://doi.org/10.1016/j.virol.2016.10.017