Agricultural Reviews

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Agricultural Reviews, volume 42 issue 3 (september 2021) : 267-275

RNAi Technology in Fish and Shellfish- Status and Prospects: A Review

Ubaid Qayoom, Zahoor Mushtaq
1Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Mumbai-400 061, Maharashtra, India.
Cite article:- Qayoom Ubaid, Mushtaq Zahoor (2021). RNAi Technology in Fish and Shellfish- Status and Prospects: A Review. Agricultural Reviews. 42(3): 267-275. doi: 10.18805/ag.R-2041.
Ribonucleic acid interference (RNAi), a valuable tool for manipulating gene functionality in the laboratory, has also emerged as a powerful tool to suppress infection or replication of many pathogens that cause severe economic losses in fish farming. By taking advantage of the cell’s endogenous RNAi apparatus, small interfering RNA of ~21-22 bp can be introduced into cells to induce target specific mRNA degradation. With the growing appreciation for the potential of RNAi technology, the diversity in vivo relevance to aquaculture is seemingly vast. Studies in the future should address the hurdles like delivery strategy stability and degradation of RNAi therapeutic molecule by nucleases in aquatic animals. In this article, we review the literature in the field of RNAi technology in aquaculture, summarize the status and prospects, which may open doors to its applicability potential as a therapeutic strategy to modulate host-pathogen interactions and inspire further trials.
  1. Amilcar, A., Rafael, P., Mayrene, G., Armando, R. (2000). Gene transfer in shrimp (Litopenaeus schmitti) by electroporation of single-cell embryos and injection of naked DNA into adult muscle. Biotecnologia Aplicada. 17: 247-255.
  2. Attasart, P., Kaewkhaw, R., Chimwai, C., Kongphom, U., Namramoon, O., Panyim, S. (2010). Inhibition of Penaeus monodon densovirus replication in shrimp by double-stranded RNA. Archives of Virology. 155: 825-832.
  3. Attasart, P., Namramoon, O., Kongphom, U., Chimwai, C., Panyim, S. (2013). Ingestion of bacteria expressing dsRNA triggers specific RNA silencing in shrimp. Virus Research. 171: 252-256.
  4. Bagga, S., Bracht, J., Hunter, S., Massirer, K., Holtz, J., Eachus, R., Pasquinelli, A.E. (2005). Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell. 122: 553-563.
  5. Bernstein, E., Caudy, A.A., Hammond, S.M., Hannon, G.J. (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 409: 363-366.
  6. Bobbin, M.L., Rossi, J.J. (2016). RNA interference (RNAi)-based therapeutics: delivering on the promise? Annual Review of Pharmacology and Toxicology. 56: 103-122.
  7. Bohle, H., Lorenzen, N., Schyth, B.D. (2011). Species specific inhibition of viral replication using dicer substrate siRNAs (DsiRNAs) targeting the viral nucleoprotein of the fish pathogenic Rhabdovirus Viral Hemorrhagic Septicemia Virus (VHSV). Antiviral Research. 90: 187-194.
  8. Boonanuntanasarn, S., Yoshizaki, G., Takeuchi, T. (2003). Specific gene silencing using small interfering RNAs in fish embryos. Biochemical and Biophysical Research Communications. 310: 1089-1095.
  9. Caplen, N.J., Mousses, S. (2003). Short interfering RNA (siRNA)-mediated RNA interference (RNAi) in human cells. Annals of the New York Academy of Sciences. 1002: 56-62.
  10. Cha, G.H., Liu, Y., Peng, T., Huang, M.Z., Xie, C.Y., Xiao, Y.C., Wang, W.N. (2015). Molecular cloning, expression of a galectin gene in Pacific white shrimp Litopenaeus vannamei and the anti-bacterial activity of its recombinant protein. Molecular Immunology. 67: 325-340.
  11. Chang, S.H., Lee, B.C., Chen, Y.D., Lee, Y.C., Tsai, H.J. (2011). Development of transgenic zooplankton Artemia as a bioreactor to produce exogenous protein. Transgenic Research. 20:1099-1111.
  12. Charoensapsri, W., Amparyup, P., Hirono, I., Aoki, T., Tassanakajon, A. (2009). Gene silencing of a prophenoloxidase activating enzyme in the shrimp, Penaeus monodon, increases susceptibility to Vibrio harveyi infection. Developmental and Comparative Immunology. 33: 811-820.
  13. Chimwai, C., Tongboonsong, P., Namramoon, O., Panyim, S., Attasart, P. (2016). A formulated double-stranded RNA diet for reducing Penaeus monodon densovirus infection in black tiger shrimp. Journal of Invertebrate Pathology. 134: 23-26.
  14. Chu, B., Yao, F., Cheng, C., Wu, Y., Mei, Y., Li, X., Liu, Y., Wang, P., Hou, L., Zou, X. (2014). The potential role of As-sumo-1 in the embryonic diapause process and early embryo development of Artemia sinica. PLoS One. 9: 1. 
  15. Da’dara, A.A., Skelly, P.J. (2015). Gene suppression in schistosomes using RNAi. In: Parasite Genomics Protocols, Humana Press, New York. Pages 143-164
  16. Dang, L. T., Kondo, H., Hirono, I., Aoki, T. (2008). Inhibition of red seabream iridovirus (RSIV) replication by small interfering RNA (siRNA) in a cell culture system. Antiviral Research. 77: 142-149. 
  17. Dykxhoorn, D.M., Novina, C.D., Sharp, P.A. (2003). Killing the messenger: short RNAs that silence gene expression. Nature Reviews Molecular Cell Biology. 4: 457–67.
  18. Elbashir, S.M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., Tuschl, T. (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 411: 494–498.
  19. Fagutao, F.F., Koyama, T., Kaizu, A., Saito Taki, T., Kondo, H., Aoki, T., Hirono, I. (2009). Increased bacterial load in shrimp hemolymph in the absence of prophenoloxidase. The FEBS Journal. 276: 5298-5306. 
  20. Fenner, B.J., Goh, W., Kwang, J. (2006). Sequestration and protection of double-stranded RNA by the betanodavirus B2 protein. Journal of Virology. 80: 6822-6833. 
  21. Fenner, B.J., Goh, W., Kwang, J. (2007). Dissection of double-stranded RNA binding protein B2 from betanodavirus. Journal of Virology. 81: 5449-5459.
  22. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., Mello, C.C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 391: 806-811. 
  23. Hipolito, S.G., Shitara, A., Kondo, H., Hirono, I. (2014). Role of Marsupenaeus japonicus crustin-like peptide against Vibrio penaeicida and white spot syndrome virus infection. Developmental and Comparative Immunology. 46: 461-469.
  24. Ho, T., Yasri, P., Panyim, S., Udomkit, A. (2011). Double-stranded RNA confers both preventive and therapeutic effects against Penaeus stylirostris densovirus (PstDNV) in Litopenaeus vannamei. Virus Research. 155: 131-136.
  25. Hong-Geller, E., Micheva-Viteva, S. (2010). Functional gene discovery using RNA interference-based genomic screens to combat pathogen infection. Current Drug Discovery Technologies. 7: 86-94.
  26. Huang, Y., Zhang, R., Gao, T., Xu, H., Wu, T., Ren, Q. (2019). 2-Transmembrane C-type lectin from oriental river prawn Macrobrachium nipponense participates in anti-bacterial immune response. Fish and Shellfish Immunology. 91: 58-67.
  27. Hutvagner, G., Zamore, P.D. (2002). RNAi: nature abhors a double-strand. Current Opinion in Genetics and Development. 12: 225-232.
  28. Jinek, M., Doudna, J.A. (2009). A three-dimensional view of the molecular machinery of RNA interference. Nature. 457: 405-12.
  29. Kato, Y., Shiga, Y., Kobayashi, K., Tokishita, S., Yamagata, H., Iguchi, T., Watanabe, H. (2011). Development of an RNA interference method in the cladoceran crustacean Daphnia magna. Development Genes and Evolution. 220: 337-345.
  30. Kay, M.A., Glorioso, J.C., Naldini, L. (2001). Viral vectors for gene therapy: the art of turning infectious agents into vehicles of therapeutics. Nature Medicine. 7: 33-40.
  31. Labreuche, Y., O´Leary, N.A., de la Vega, E., Veloso, A., Gross, P.S. Browdy, C.L. Warr, G.W. (2009). Lack of evidence for Litopenaeus vannamei Toll receptor (lToll) involvement in activation of sequence-independent antiviral immunity in shrimp. Developmental and Comparative Immunology. 33: 806-810.
  32. Labreuche, Y., Veloso, A., de la Vega, E., Gross, P.S., Chapman, R.W., Browdy, C.L., Warr, G.W. (2010). Non-specific activation of antiviral immunity and induction of RNA interference may engage the same pathway in the Pacific white leg shrimp Litopenaeus vannamei. Developmental and Comparative Immunology. 34: 1209-1218.
  33. Leong, J.C., Fryer, J.L. (1993). Viral vaccines for aquaculture. Annual Review of Fish Diseases. 3: 225-240.
  34. Li, D.F., Zhang, M.C., Yang, H.J., Zhu, Y.B., Xu, X. (2007). Beta-integrin mediates WSSV infection. Virology. 368: 122-132. 
  35. Lima, P.C., Harris, J.O., Cook, M. (2013). Exploring RNAi as a therapeutic strategy for controlling disease in aquaculture. Fish and Shellfish Immunology. 34: 729-743.
  36. Liu, Y., Qian, Z., Qu, R., Wang, X., He, S., Hou, F., Liu, Q., Mi, X., Liu, X. (2014). Molecular characterization, immune responsive expression and functional analysis of QM, a putative tumor suppressor gene from the Pacific white shrimp, Litopenaeus vannamei. Fish and Shellfish Immunology. 37: 1-10.
  37. Lu, Y., Sun, P.S. (2005). Viral resistance in shrimp that express an antisense Taura syndrome virus coat protein gene. Antiviral Research. 67: 141-146.
  38. Mahy, B.W.J., Regenmortel, M.H.V. (2008). Encyclopedia of Virology. Oxford: Academic Press.
  39. Milhavet, O., Gary, D.S. Mattson, M.P. (2003). RNA interference in biology and medicine. Pharmacological Reviews. 55: 629-648.
  40. Napoli, C., Lemieux, C., Jorgensen, R. (1990). Introduction of a chimeric chalcone synthase gene into Petunia results in reversible co-suppression of homologous genes in trans. The Plant Cell. 2: 279-289. 
  41. Ohashi, H., Umeda, N., Hirazawa, N., Ozaki, Y., Miura, C., Miura, T. (2003). Expression of vasa (vas)-related genes in germ cells and specific interference with gene functions by double-stranded RNA in the monogenean, Neobenedenia girellae. International Journal for Parasitology. 37: 515-523.
  42. Provost, P., Dishart, D., Doucet, J., Frendewey, D., Samuelsson, B., Radmark, O. (2002). Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO Journal. 21: 5864-5874.
  43. Rijiravanich, A., Browdy, C.L., Withyachumnarnkul, B. (2008). Knocking down caspase-3 by RNAi reduces mortality in Pacific white shrimp Penaeus (Litopenaeus) vannamei challenged with a low dose of white-spot syndrome virus. Fish and Shellfish Immunology. 24: 308-313.
  44. Robalino, J., Bartlett, T., Shepard, E., Prior, S., Jaramillo, G., Scura, E., Chapman, R.W., Gross, P.S., Browdy, C.L., Warr, G.W. (2005). Double-stranded RNA induces sequence-specific antiviral silencing in addition to non-specific immunity in a marine shrimp: convergence of RNA interference and innate immunity in the invertebrate antiviral response? Journal of Virology. 79: 13561-13571.
  45. Robalino, J., Browdy, C.L., Prior, S., Metz, A., Parnell, P., Gross, P., Warr, G. (2004). Induction of antiviral immunity of double-stranded RNA in a marine invertebrate. Journal of Virology. 78: 10442-10448.
  46. Ruiz, S., Schyth, B.D., Encinas, P., Tafalla, C., Estepa, A., Lorenzen, N., Coll, J.M. (2009). New tools to study RNA interference to fish viruses: fish cell lines permanently expressing siRNAs targeting the viral polymerase of Viral Hemorrhagic Septicemia Virus. Antiviral Research. 82: 148-156.
  47. Saleh, M., Kumar, G., Abdel-Baki, A.A., Dkhil, M.A., El-Matbouli, M., Al-Quraishy, S. (2016). In Vitro gene silencing of the fish Microsporidian Heterosporis saurida by RNA interference. Nucleic Acid Therapeutics. 26: 250-256.
  48. Sarker, S., Menanteau-Ledouble, S., Kotob, M.H., El-Matbouli, M. (2017). A RNAi-based therapeutic proof of concept targets salmonid whirling disease in vivo. PLoS ONE. 12: 6.
  49. Schyth, B.D., Lorenzen, N. (2007). Pedersen FS. A high throughput in vivo model for testing delivery and antiviral effects of siRNAs in vertebrates. Molecular Therapy. 15: 1366-1372.
  50. Sharabi, O., Manor, R., Weil, S., Aflalo, E.D., Lezer, Y., Levy, T., Aizen, J., Ventura, T., Mather, P.B., Khalaila, I., Sagi, A. (2016). Identification and characterization of an insulin-like receptor involved in crustacean reproduction. Endocrinology. 57: 928-941.
  51. Shi, X.Z., Wang, L., Xu, S., Zhang, X.W., Zhao, X.F., Vasta, G.R., Wang, J.X. (2014). A galectin from the kuruma shrimp (Marsupenaeus japonicus) functions as an opsonin and promotes bacterial clearance from hemolymph. PLoS One. 9: 3.
  52. Shockey, J.E., O’Leary, N.A., de la Vega, E., Browdy, C.L., Baatz, J.E., Gross, P.S. (2009). The role of crustins in Litopenaeus vannamei in response to infection with shrimp pathogens: An in vivo approach. Developmental and Comparative Immunology. 33: 668-673.
  53. Sidahmed, A.E., Wilkie, B. (2010). Endogenous antiviral mechanisms of RNA interference: a comparative biology perspective. In: RNA interference. Humana Press, New York. Pages 3-19.
  54. Stevenson, F.K. (2004). DNA vaccines and adjuvants. Immunological Reviews. 199: 5-8.
  55. Stram, Y., Kuzntzova, L. (2006). Inhibition of viruses by RNA interference. Virus Genes. 32: 299-306.
  56. Su, J., Zhu, Z., Wang, Y., Zou, J., Wang, N., Jang, S. (2009b). Grass carp reovirus activates RNAi pathway in rare minnow, Gobiocypris rarus. Aquaculture. 289: 1-5.
  57. Su, Y.C., Wu, J.L., Hong J.R. (2009a). Betanodavirus non-structural protein B2: a novel necrotic death factor that induces mitochondria mediated cell death in fish cells. Virology. 385 :143-154.
  58. Sun, P.S., Venzon Jr, N.C., Calderon, F.R.O., Esaki, D.M. (2005). Evaluation of methods for DNA delivery into shrimp zygotes of Penaeus (Litopenaeus) vannamei. Aquaculture. 243: 19-26.
  59. Thammasorn, T., Somchai, P., Laosutthipong, C., Jitrakorn, S., Wongtripop, S., Thitamadee, S., Withyachumnarnkul, B., Saksmerprome, V. (2013). Therapeutic effect of Artemia enriched with Escherichia coli expressing double-stranded RNA in the black tiger shrimp Penaeus monodon. Antiviral Research. 100: 202-206.
  60. Thomas, C.E., Ehrhardt, A., Kay, M.A. (2003). Progress and problems with the use of viral vectors for gene therapy. Nature Reviews Genetics. 4: 346-358. 
  61. Tolentino, M. (2006). Interference RNA technology in the treatment of CNV. Ophthalmology Clinics of North America. 19: 393-399.
  62. Treerattrakool, S., Chartthai, C., Phromma-in, N., Panyim, S., Udomkit, A. (2013). Silencing of gonad-inhibiting hormone gene expression in Penaeus monodon by feeding with GIH dsRNA-enriched Artemia. Aquaculture. 404: 116-121.
  63. Tseng, F.S., Tsai, H.J., Liao, I.C., Song, Y.L. (2000). Introducing foreign DNA into tiger shrimp (Penaeus monodon) by electroporation. Theriogenology. 54: 1421-1432.
  64. Ufaz, S., Balter, A., Tzror, C., Einbender, S., Koshet, O., Shainsky-Roitman, J., Yaari, Z. Schroeder, A. (2018). Anti-viral RNAi nanoparticles protect shrimp against white spot disease. Molecular Systems Design and Engineering. 3: 38-48.
  65. Wang, P.H., Wan, D.H., Chen, Y.G., Weng, S.P., Yu, X.Q., He, J.G. (2013). Characterization of four novel caspases from Litopenaeus vannamei (Lvcaspase2-5) and their role in WSSV infection through dsRNA-mediated gene silencing. PLoS One. 8: 12.
  66. Wargelius, A., Ellingsen, S., Fjose, A. (1999). Double-stranded RNA induces specific developmental defects in zebrafish embryos. Biochemical and Biophysical Research Communications. 263: 156-161.
  67. Westenberg, M., Heinhuis, B., Zuidema, D., Vlak, J.M. (2005). siRNA injection induces sequence-independent protection in Penaeus monodon against white spot syndrome virus. Virus Research. 114: 133-139.
  68. Whyard, S., Singh, A.D., Wong, S. (2009). Ingested double-stranded RNAs can act as species-specific insecticides. Insect Biochemistry and Molecular Biology. 39: 824-832.
  69. Wise, T.G., Schafer, D.S., Lowenthal, J.W., Doran, T.J. (2008). The use of RNAi and transgenics to develop viral disease resistant livestock. Developmental Biology. 132: 377-382.
  70. Wu, H.W., Chiu, C.S., Wu, J.L., Chen, M.C., Li, M.W., Hong, J.R. (2008). Zebrafish anti-apoptotic protein zfBcl-xL can block betanodavirus protein á-induced mitochondria mediated apoptotic cell death. Fish Shellfish Immunology. 45: 1146-1152.
  71. Wu, W., Zhang, X. (2007). Characterization of a Rab GTPase up-regulated in the shrimp Peneaus japonicus by virus infection. Fish and Shellfish Immunology. 23: 438-445.
  72. Wu, Y., Lü, L., Yang, L.S., Weng, S.P., Chan, S.M., He, J.G. (2007). Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA. Aquaculture. 271: 21-30.
  73. Wuriyanghan, H., Rosa, C., Falk, B.W. (2011). Oral delivery of double-stranded RNAs and siRNAs induces RNAi effects in the potato/tomato psyllid, Bactericera cockerelli. PLoS One. 6: 11.
  74. Xie, B., Wang, P., Zhao, C., Qiu, L. (2017). Cloning, characterization, expression analysis and RNAi of Retinoblastoma like gene from black tiger shrimp (Penaeus monodon). Aquaculture Research. 48: 5765-5774.
  75. Xie, J., Lü, L., Deng, M., Weng, S., Zhu, J., Wu Y., Gan, L., Chan, S.M., He, J. (2005). Inhibition of reporter gene and Iridovirus- Tiger Frog Virus in fish cell by RNA interference. Virology. 338: 43-52.
  76. Xu, J., Han, F., Zhang, X. (2007). Silencing shrimp white spot syndrome virus (WSSV) genes by siRNA. Antiviral Research. 73: 126-131. 
  77. Yan, H., Zhang, S., Li, C.Z., Chen, Y.H., Chen, Y.G., Weng, S.P., He, J.G. (2013). Molecular characterization and function of a p38 MAPK gene from Litopenaeus vannamei. Fish and Shellfish Immunology. 34: 1421-1431.
  78. Yang, L.S., Yin, Z.X., Liao, J.X., Huang, X.D., Guo, C.J., Weng, S.P., Chan, S.M., Yu, X.Q., He, J.G. (2007). A Toll receptor in shrimp. Molecular Immunology. 44: 1999-2008.
  79. Zenke, K., Nam, Y., Kim, K. (2010). Development of siRNA expression vector utilizing Rock bream b-actin promoter: a potential therapeutic tool against viral infection in fish. Applied Microbiology and Biotechnology. 85: 679-690.
  80. Zhang, B., Luo, G., Zhao, L., Huang, L., Qin, Y., Su, Y., Yan, Q. (2018). Integration of RNAi and RNA-seq uncovers the immune responses of Epinephelus coioides to L321_RS 19110 gene of Pseudomonas plecoglossicida. Fish and Shellfish Immunology. 81: 121-129.
  81. Zhang, X., Goel, V., Robbie, G.J. (2020), Pharmacokinetics of Patisiran, the First Approved RNA Interference Therapy in Patients with Hereditary Transthyretin Mediated Amyloidosis. The Journal of Clinical Pharmacology. 60: 573-585.

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