Abstract
In the past two decades, with the discovery of RNA interference (RNAi) or post-transcriptional gene silencing (PTGS), the modern molecular biology field has been boosted with its immense applications. This rapid and powerful silencing method is useful in studying the gene function as well as in therapeutic applications for disease treatment. The RNAi or PTGS is a biological process of mRNA degradation induced by complementary double-stranded (ds) small interfering RNA (siRNA) sequences that mediate suppression of target protein-coding gene expression and provide resistance to both exogenous and endogenous microbial nucleic acids. This sequence-specific natural gene silencing mechanism has revolutionized experimental biology. RNAi technology has important practical applications in aquatic animal health, including functional genomics, therapeutic intervention, and other areas. Here in this chapter, we introduced the RNAi or PTGS mechanisms and the current understanding of gene silencing in aquatic animals in both fish and shellfish and will propose key areas of aquaculture fields where gene silencing could be applied.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Akhtar S, Patnaik SR, Kotapati Raghupathy R, Al-Mubrad TM, Craft JA, Shu X (2015) Histological characterization of the Dicer1 mutant zebrafish retina. J Ophthalmol 2015:1–8. https://doi.org/10.1155/2015/309510
Andrews OE, Cha DJ, Wei C, Patton JG (2014) RNAi-mediated gene silencing in zebrafish triggered by convergent transcription. Sci Rep 4:1–8. https://doi.org/10.1038/srep05222
Arenal A, Pimentel R, Guimarais M, Rodriguez A, Martinez R, Abad Z (2000) Gene transfer in shrimp (Litopenaeus schmitti) by electroporation of single-cell embryos and injection of naked DNA into adult muscle. Biotecnol Apl 17:247–250
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. Arch Virol 155:825–832. https://doi.org/10.1007/s00705-010-0649-5
Boonanuntanasarn S, Yoshizaki G, Takeuchi T (2003) Specific gene silencing using small interfering RNAs in fish embryos. Biochem Biophys Res Commun 310:1089–1095. https://doi.org/10.1016/j.bbrc.2003.09.127
Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655. https://doi.org/10.1016/j.cell.2009.01.035
Chen Y-H, Jia X-T, Zhao L, Li C-Z, Zhang S, Chen Y-G, Weng S-P, He J-G (2011) Identification and functional characterization of Dicer2 and five single VWC domain proteins of Litopenaeus vannamei. Dev Comp Immunol 35:661–671. https://doi.org/10.1016/j.dci.2011.01.010
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. J Invertebr Pathol 134:23–26. https://doi.org/10.1016/j.jip.2016.01.003
Da’dara AA, Skelly PJ (2015) Gene suppression in schistosomes using RNAi. In: Peacock C (ed) Parasite genomics protocols. Springer, New York, pp 143–164. https://doi.org/10.1007/978-1-4939-1438-8_8
De Santis C, Wade NM, Jerry DR, Preston NP, Glencross BD, Sellars MJ (2011) Growing backwards: an inverted role for the shrimp ortholog of vertebrate myostatin and GDF11. J Exp Biol 214:2671–2677. https://doi.org/10.1242/jeb.056374
Dechklar M, Udomkit A, Panyim S (2008) Characterization of Argonaute cDNA from Penaeus monodon and implication of its role in RNA interference. Biochem Biophys Res Commun 367:768–774. https://doi.org/10.1016/j.bbrc.2008.01.031
Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ, Joshua-Tor L (2012) The structure of human argonaute-2 in complex with miR-20a. Cell 150:100–110. https://doi.org/10.1016/j.cell.2012.05.017
Fabian MR, Sonenberg N, Filipowicz W (2010) Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 79:351–379. https://doi.org/10.1146/annurev-biochem-060308-103103
Fagutao FF, 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. FEBS J 276:5298–5306. https://doi.org/10.1111/j.1742-4658.2009.07225.x
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811
Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94–108. https://doi.org/10.1038/nrg2504.Small
Gong Y, Zhang X (2021) RNAi-based antiviral immunity of shrimp. Dev Comp Immunol 115:103907. https://doi.org/10.1016/j.dci.2020.103907
Gong Y, Ju C, Zhang X (2018) Shrimp miR-1000 functions in antiviral immunity by simultaneously triggering the degradation of two viral mRNAs. Front Immunol 9:2999. https://doi.org/10.3389/fimmu.2018.02999
Hammond SM, Caudy AA, Hannon GJ (2001) Post-transcriptional gene silencing by double- stranded RNA. Nat Rev Genet 2:110–119
Han B, Kaur VI, Baruah K, Nguyen VD, Bossier P (2019) High doses of sodium ascorbate act as a prooxidant and protect gnotobiotic brine shrimp larvae (Artemia franciscana) against Vibrio harveyi infection coinciding with heat shock protein 70 activation. Dev Comp Immunol 92:69–76. https://doi.org/10.1016/J.DCI.2018.11.007
He Y, Ju C, Zhang X (2015) Roles of small RNAs in the immune defense mechanisms of crustaceans. Mol Immunol 68:399–403. https://doi.org/10.1016/j.molimm.2015.07.008
Hipolito SG, Shitara A, Kondo H, Hirono I (2014) Role of Marsupenaeus japonicus crustin-like peptide against Vibrio penaeicida and white spot syndrome virus infection. Dev Comp Immunol 46:461–469. https://doi.org/10.1016/j.dci.2014.06.001
Ketting RF (2011) The many faces of RNAi. Dev Cell 20:148–161. https://doi.org/10.1016/j.devcel.2011.01.012
Kim DH, Rossi JJ (2008) RNAi mechanisms and applications. BioTechniques 44:613–616. https://doi.org/10.2144/000112792
Kretov DA, Walawalkar IA, Mora-Martin A, Shafik AM, Moxon S, Cifuentes D (2020) Ago2-dependent processing allows miR-451 to evade the global MicroRNA turnover elicited during erythropoiesis. Mol Cell 78:317–328.e6. https://doi.org/10.1016/j.molcel.2020.02.020
Kumar V (2020) Acute hepatopancreatic necrosis disease (AHPND) in shrimp: virulence. University of Ghent, pathogenesis and mitigation strategies
Kumar, Roy S, Meena DK, Sarkar UK (2016) Application of probiotics in shrimp aquaculture: importance, mechanisms of action, and methods of administration. Rev Fish Sci Aquac 24. https://doi.org/10.1080/23308249.2016.1193841
Kumar V, Baruah K, Nguyen DV, Smagghe G, Vossen E, Bossier P (2018) Phloroglucinol mediated Hsp70 production in crustaceans : protection against Vibrio parahaemolyticus in Artemia franciscana and Macrobrachium rosenbergii. Front Immunol 9:1091. https://doi.org/10.3389/fimmu.2018.01091
Kumar V, De Bels L, Couck L, Baruah K, Bossier P, Van den Broeck W (2019a) PirABVP toxin binds to epithelial cells of the digestive tract and produce pathognomonic AHPND lesions in germ-free Brine Shrimp. Toxins (Basel) 11:717. https://doi.org/10.3390/toxins11120717
Kumar V, Viet D, Baruah K, Bossier P (2019b) Probing the mechanism of VP AHPND extracellular proteins toxicity purified from Vibrio parahaemolyticus AHPND strain in germ-free Artemia test system. Aquaculture 504:414–419. https://doi.org/10.1016/j.aquaculture.2019.02.029
Kumar V, Roy S, Baruah K, Van Haver D, Impens F, Bossier P (2020a) Environmental conditions steer phenotypic switching in acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus, affecting PirAVP/PirBVP toxins production. Environ Microbiol 22:4212–4230. https://doi.org/10.1111/1462-2920.14903
Kumar V, Roy S, Behera BK, Bossier P, Das BK (2021) Acute hepatopancreatic necrosis disease (AHPND): virulence, pathogenesis and mitigation strategies in shrimp aquaculture. Toxins 13(8):524
Kumar V, Wille M, Lourenço TM, Bossier P (2020b) Biofloc-based enhanced survival of Litopenaeus vannamei upon AHPND-causing Vibrio parahaemolyticus challenge is partially mediated by reduced expression of its virulence genes. Front Microbiol 11. https://doi.org/10.3389/fmicb.2020.01270
Kumar V, Baruah K, Bossier P (2021) Bamboo powder protects gnotobiotically-grown brine shrimp against AHPND-causing Vibrio parahaemolyticus strains by cessation of PirAB VP toxin secretion. Aquaculture 736624. https://doi.org/10.1016/j.aquaculture.2021.736624
Labreuche Y, Veloso A, de la Vega E, Gross PS, Chapman RW, Browdy CL, Warr GW (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. Dev Comp Immunol 34:1209–1218. https://doi.org/10.1016/j.dci.2010.06.017
Li X, Yang L, Jiang S, Fu M, Huang J, Jiang S (2013) Identification and expression analysis of Dicer2 in black tiger shrimp (Penaeus monodon) responses to immune challenges. Fish Shellfish Immunol 35:1–8. https://doi.org/10.1016/j.fsi.2013.03.370
Lingel A, Izaurralde E (2004) RNAi: finding the elusive endonuclease. RNA 10:1675–1679. https://doi.org/10.1261/rna.7175704
Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343–349. https://doi.org/10.1038/nature02873
Nguyen DV, Christiaens O, Bossier P, Smagghe G (2016) RNA interference in shrimp and potential applications in aquaculture. Rev Aquac 1–12. https://doi.org/10.1111/raq.12187
Ohashi H, Umeda N, Hirazawa N, Ozaki Y, Miura C, Miura T (2007) Expression of vasa (vas)-related genes in germ cells and specific interference with gene functions by double-stranded RNA in the monogenean, Neobenedenia girellae. Int J Parasitol 37:515–523. https://doi.org/10.1016/j.ijpara.2006.11.003
Ongvarrasopone C, Saejia P, Chanasakulniyom M, Panyim S (2011) Inhibition of Taura syndrome virus replication in Litopenaeus vannamei through silencing the LvRab7 gene using double-stranded RNA. Arch Virol 156:1117–1123. https://doi.org/10.1007/s00705-011-0952-9
Phetrungnapha A, Ho T, Udomkit A, Panyim S, Ongvarrasopone C (2013) Molecular cloning and functional characterization of Argonaute-3 gene from Penaeus monodon. Fish Shellfish Immunol 35:874–882. https://doi.org/10.1016/j.fsi.2013.06.025
Qayoom U, Mushtaq Z (2020) RNAi technology in fish and shellfish-status and prospects: a review. Agric Rev:1–9. https://doi.org/10.18805/ag.r-2041
Reshi ML, Wu JL, Wang HV, Hong JR (2014) RNA interference technology used for the study of aquatic virus infections. Fish Shellfish Immunol 40:14–23. https://doi.org/10.1016/j.fsi.2014.06.008
Roy S (2020) Modulating innate immune memory in brine shrimp (Artemia franciscana) and in giant freshwater prawn (Macrobrachium rosenbergii). University of Ghent
Roy S, Kumar V, Bossier P, Norouzitallab P, Vanrompay D (2019) Phloroglucinol treatment induces transgenerational epigenetic inherited resistance against vibrio infections and thermal stress in a brine shrimp (Artemia franciscana) model. Front Immunol 10:2745. https://doi.org/10.3389/fimmu.2019.02745
Roy S, Bossier P, Norouzitallab P, Vanrompay D (2020) Trained immunity and perspectives for shrimp aquaculture. Rev Aquac. https://doi.org/10.1111/raq.12438
Saksmerprome V, Charoonnart P, Gangnonngiw W, Withyachumnarnkul B (2009) A novel and inexpensive application of RNAi technology to protect shrimp from viral disease. J Virol Methods 162:213–217. https://doi.org/10.1016/j.jviromet.2009.08.010
Saksmerprome V, Thammasorn T, Jitrakorn S, Wongtripop S, Borwornpinyo S, Withyachumnarnkul B (2013) Using double-stranded RNA for the control of Laem-Singh virus (LSNV) in Thai P. monodon. J Biotechnol 164:449–453. https://doi.org/10.1016/j.jbiotec.2013.01.028
Sarathi M, Simon MC, Venkatesan C, Hameed ASS (2008) Oral administration of bacterially expressed VP28dsRNA to protect Penaeus monodon from white spot syndrome virus. Mar Biotechnol 10:242–249. https://doi.org/10.1007/s10126-007-9057-6
Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ (2016) Structural analysis of human Argonaute-2 bound to a modified siRNA guide. J Am Chem Soc 138:8694–8697. https://doi.org/10.1021/jacs.6b04454
Schuster S, Miesen P, van Rij RP (2019) Antiviral RNAi in insects and mammals: parallels and differences. Viruses 11:1–32. https://doi.org/10.3390/v11050448
Su J, Oanh DTH, Lyons RE, Leeton L, van Hulten MCW, Tan S-H, Song L, Rajendran KV, Walker PJ (2008) A key gene of the RNA interference pathway in the black tiger shrimp, Penaeus monodon: identification and functional characterisation of Dicer-1. Fish Shellfish Immunol 24:223–233. https://doi.org/10.1016/j.fsi.2007.11.006
Su J, Zhu Z, Wang Y, Jang S (2009) Isolation and characterization of Argonaute 2: a key gene of the RNA interference pathway in the rare minnow, Gobiocypris rarus. Fish Shellfish Immunol 26:164–170. https://doi.org/10.1016/j.fsi.2008.10.002
Thammasorn T, Sangsuriya P, Meemetta W, Senapin S, Jitrakorn S, Rattanarojpong T, Saksmerprome V (2015) Large-scale production and antiviral efficacy of multi-target double-stranded RNA for the prevention of white spot syndrome virus (WSSV) in shrimp. BMC Biotechnol 15:5–8. https://doi.org/10.1186/s12896-015-0226-9
Timmons L, Fire A (1998) Specific interference by ingested dsRNA. Nature 395:854
Tirasophon W, Yodmuang S, Chinnirunvong W, Plongthongkum N, Panyim S (2007) Therapeutic inhibition of yellow head virus multiplication in infected shrimps by YHV-protease dsRNA. Antivir Res 74:150–155. https://doi.org/10.1016/j.antiviral.2006.11.002
Tran PTN, Kumar V, Bossier P (2020) Do acute hepatopancreatic necrosis disease-causing PirABVP toxins aggravate vibriosis? Emerg Microbes Infect 9:1919–1932. https://doi.org/10.1080/22221751.2020.1811778
Tseng FS, Tsai HJ, Liao IC, Song YL (2000) Introducing foreign DNA into tiger shrimp (Penaeus monodon) by electroporation. Theriogenology 54:1421–1432. https://doi.org/10.1016/S0093-691X(00)00464-7
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. Mol Syst Des Eng 3:38–48. https://doi.org/10.1039/C7ME00092H
Ventura T, Sagi A (2012) The insulin-like androgenic gland hormone in crustaceans: from a single gene silencing to a wide array of sexual manipulation-based biotechnologies. Biotechnol Adv 30:1543–1550. https://doi.org/10.1016/j.biotechadv.2012.04.008
Ventura T, Manor R, Aflalo ED, Weil S, Raviv S, Glazer L, Sagi A (2009) Temporal silencing of an androgenic gland-specific insulin-like gene affecting phenotypical gender differences and spermatogenesis. Endocrinology 150:1278–1286. https://doi.org/10.1210/en.2008-0906
Vikash Kumar, Suvra Roy, Bijay Kumar Behera, Peter Bossier, Basanta Kumar Das, (2021) Acute Hepatopancreatic Necrosis Disease (AHPND): Virulence, Pathogenesis and Mitigation Strategies in Shrimp Aquaculture. Toxins 13 (8):524
Wang S, Chen AJ, Shi LJ, Zhao XF, Wang JX (2012) TRBP and eIF6 homologue in Marsupenaeus japonicus play crucial roles in antiviral response. PLoS One 7:1–10. https://doi.org/10.1371/journal.pone.0030057
Wang PH, Wan DH, Chen YG, Weng SP, Yu XQ, He JG (2013) Characterization of four novel caspases from Litopenaeus vannamei (Lvcaspase2-5) and their role in WSSV infection through dsRNA-mediated gene silencing. PLoS One 8:1–14. https://doi.org/10.1371/journal.pone.0080418
Westenberg M, Heinhuis B, Zuidema D, Vlak JM (2005) siRNA injection induces sequence-independent protection in Penaeus monodon against white spot syndrome virus. Virus Res 114:133–139. https://doi.org/10.1016/j.virusres.2005.06.006
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 Shellfish Immunol 34:1421–1431. https://doi.org/10.1016/j.fsi.2013.02.030
Yang L, Li X, Huang J, Zhou F, Su T, Jiang S (2013) Isolation and characterization of homologous TRBP cDNA for RNA interference in Penaeus monodon. Fish Shellfish Immunol 34:704–711. https://doi.org/10.1016/j.fsi.2012.11.022
Yang L, Li X, Jiang S, Qiu L, Zhou F, Liu W, Jiang S (2014) Characterization of Argonaute2 gene from black tiger shrimp (Penaeus monodon) and its responses to immune challenges. Fish Shellfish Immunol 36:261–269. https://doi.org/10.1016/j.fsi.2013.11.010
Yao X, Wang L, Song L, Zhang H, Dong C, Zhang Y, Qiu L, Shi Y, Zhao J, Bi Y (2010) A Dicer-1 gene from white shrimp Litopenaeus vannamei: expression pattern in the processes of immune response and larval development. Fish Shellfish Immunol 29:565–570. https://doi.org/10.1016/j.fsi.2010.05.016
Yodmuang S, Tirasophon W, Roshorm Y, Chinnirunvong W, Panyim S (2006) YHV-protease dsRNA inhibits YHV replication in Penaeus monodon and prevents mortality. Biochem Biophys Res Commun 341:351–356. https://doi.org/10.1016/j.bbrc.2005.12.186
Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25–33. https://doi.org/10.1016/S0092-8674(00)80620-0
Acknowledgements
Authors are thankful to ICAR-Central Inland Fisheries Research Institute (ICAR-CIFRI) for ample help and support.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Kumar, V., Roy, S., Behera, B.K., Das, B.K. (2021). RNA Interference and Its Potential Applications in Aquatic Animal Health Management. In: Gupta, S.K., Giri, S.S. (eds) Biotechnological Advances in Aquaculture Health Management . Springer, Singapore. https://doi.org/10.1007/978-981-16-5195-3_2
Download citation
DOI: https://doi.org/10.1007/978-981-16-5195-3_2
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-16-5194-6
Online ISBN: 978-981-16-5195-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)