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Origins and diversification of animal innate immune responses against viral infections

Abstract

Immune systems are of pivotal importance to any living organism on Earth, as they protect the organism against deleterious effects of viral infections. Though the current knowledge about these systems is still biased towards the immune response in vertebrates, some studies have focused on the identification and characterization of components of invertebrate antiviral immune systems. Two classic model organisms, the insect Drosophila melanogaster and the nematode Caenorhabditis elegans, were instrumental in the discovery of several important components of the innate immune system, such as the Toll-like receptors and the RNA interference pathway. However, these two model organisms provide only a limited view of the evolutionary history of the immune system, as they both are ecdysozoan protostomes. Recent functional studies in non-classic models such as unicellular holozoans (for example, choanoflagellates), lophotrochozoans (for example, oysters) and cnidarians (for example, sea anemones) have added crucial information for understanding the evolution of antiviral systems, as they revealed unexpected ancestral complexity. This Review aims to summarize this information and present the ancestral nature of the antiviral immune response in animals. We also discuss lineage-specific adaptations and future perspectives for the comparative study of the innate immune system that are essential for understanding its evolution.

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Fig. 1: Detection of viral dsRNA and dsDNA by pattern recognition systems and their respective signalling cascades.
Fig. 2: The main events in the evolution of the innate immune system in Metazoa, as well as the presence and absence of the main PRRs and the components of their respective signalling cascades.
Fig. 3: Main components of RNAi in insects.

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References

  1. Harvey, E. & Holmes, E. C. Diversity and evolution of the animal virome. Nat. Rev. Microbiol. 20, 321–334 (2022).

    Article  CAS  Google Scholar 

  2. Flajnik, M. F. & du Pasquier, L. Evolution of innate and adaptive immunity: can we draw a line? Trends Immunol. 25, 640–644 (2004).

    Article  CAS  Google Scholar 

  3. Negishi, H., Taniguchi, T. & Yanai, H. The interferon (IFN) class of cytokines and the IFN regulatory factor (IRF) transcription factor family. Cold Spring Harb. Perspect. Biol 10, a028423 (2018).

    Article  CAS  Google Scholar 

  4. Ishikawa, H., Ma, Z. & Barber, G. N. STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity. Nature 461, 788–793 (2009).

    Article  CAS  Google Scholar 

  5. Zhou, A., Hassel, B. A. & Silverman, R. H. Expression cloning of 2-5A-dependent RNAase: a uniquely regulated mediator of interferon action. Cell 72, 753–765 (1993).

    Article  CAS  Google Scholar 

  6. Yoneyama, M. et al. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat. Immunol. 5, 730–737 (2004).

    Article  CAS  Google Scholar 

  7. Maillard, P. V., Veen, A. G., Poirier, E. Z. & Reis e Sousa, C. Slicing and dicing viruses: antiviral RNA interference in mammals. EMBO J. 38, e100941 (2019).

  8. Wang, W., Xu, L., Su, J., Peppelenbosch, M. P. & Pan, Q. Transcriptional regulation of antiviral interferon-stimulated genes. Trends Microbiol. 25, 573–584 (2017).

    Article  CAS  Google Scholar 

  9. Stirnweiss, A. et al. IFN Regulatory factor-1 bypasses IFN-mediated antiviral effects through Viperin gene induction. J. Immun. 184, 5179–5185 (2010).

    Article  CAS  Google Scholar 

  10. Tamura, T., Yanai, H., Negishi, H. & Taniguchi, T. The IRF family of transcription factors: inception, impact and implications in oncogenesis. OncoImmunology 1, 1376–1386 (2012).

  11. Taniguchi, K. & Karin, M. NF-kB, inflammation, immunity and cancer: coming of age. Nat. Rev. Immunol. 18, 309–324 (2018).

    Article  CAS  Google Scholar 

  12. Andreeva, L. et al. CGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein-DNA ladders. Nature 549, 394–398 (2017).

    Article  CAS  Google Scholar 

  13. Maekawa, H. et al. Mitochondrial damage causes inflammation via cGAS–STING signaling in acute kidney injury. Cell Rep. 29, 1261–1273.e6 (2019).

    Article  CAS  Google Scholar 

  14. Chen, H. et al. Activation of STAT6 by STING is critical for antiviral innate immunity. Cell 147, 436–446 (2011).

    Article  CAS  Google Scholar 

  15. Abe, T. & Barber, G. N. Cytosolic-DNA-mediated, STING-dependent proinflammatory gene induction necessitates canonical NF-κB activation through TBK1. J. Virol. 88, 5328–5341 (2014).

    Article  Google Scholar 

  16. McWhirter, S. M. et al. A host type I interferon response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP. J. Exp. Med. 206, 1899–1911 (2009).

    Article  CAS  Google Scholar 

  17. Liu, S. et al. Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Science 347, aaa2630 (2015).

    Article  Google Scholar 

  18. Rehwinkel, J. & Gack, M. U. RIG-I-like receptors: their regulation and roles in RNA sensing. Nat. Rev. Immunol. 20, 537–551 (2020).

    Article  CAS  Google Scholar 

  19. Kato, H. et al. Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses. Nature 441, 101–105 (2006).

    Article  CAS  Google Scholar 

  20. Cui, Y. et al. The Stat3/5 locus encodes novel endoplasmic reticulum and helicase-like proteins that are preferentially expressed in normal and neoplastic mammary tissue. Genomics 78, 129–134 (2001).

    Article  CAS  Google Scholar 

  21. Schimidt, A. et al. 5-triphosphate RNA requires base-paired structures to activate antiviral signaling via RIG-I. Proc. Natl Acad. Sci. USA 106, 12067–12072 (2009).

    Article  Google Scholar 

  22. Schlee, M. et al. Recognition of 5′-triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus. Immunity 31, 25–34 (2009).

    Article  CAS  Google Scholar 

  23. Hornung, V. et al. 5′-triphosphate RNA is the ligand for RIG-I. Science 314, 994–997 (2006).

    Article  Google Scholar 

  24. Pichlmair, A. et al. Activation of MDA5 requires higher-order RNA structures generated during virus infection. J. Virol. 83, 10761–10769 (2009).

    Article  CAS  Google Scholar 

  25. Wu, B. et al. Structural basis for dsRNA recognition, filament formation, and antiviral signal activation by MDA5. Cell 152, 276–289 (2013).

    Article  CAS  Google Scholar 

  26. Seth, R. B., Sun, L., Ea, C. K. & Chen, Z. J. Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-κB and IRF3. Cell 122, 669–682 (2005).

    Article  CAS  Google Scholar 

  27. Goubau, D., Deddouche, S. & Reis e Sousa, C. Cytosolic sensing of viruses. Immunity 38, 855–869 (2013).

    Article  CAS  Google Scholar 

  28. Bilak, H., Tauszig-Delamasure, S. & Imler, J. L. Toll and Toll-like receptors in Drosophila. Biochem. Soc. Trans. 31, 648–651 (2003).

    Article  CAS  Google Scholar 

  29. Anthoney, N., Foldi, I. & Hidalgo, A. Toll and Toll-like receptor signalling in development. Development 145, dev156018 (2018).

    Article  Google Scholar 

  30. Fitzgerald, K. A. & Kagan, J. C. Toll-like receptors and the control of immunity. Cell 180, 1044–1066 (2020).

    Article  CAS  Google Scholar 

  31. Orús-Alcalde, A., Lu, T. M., Børve, A. & Hejnol, A. The evolution of the metazoan Toll receptor family and its expression during protostome development. BMC Ecol. Evol. 21, 208 (2021).

  32. Leulier, F. & Lemaitre, B. Toll-like receptors—taking an evolutionary approach. Nat. Rev. Genet. 9, 165–178 (2008).

    Article  CAS  Google Scholar 

  33. Wilkins, C. et al. RNA interference is an antiviral defence mechanism in Caenorhabditis elegans. Nature 436, 1044–1047 (2005).

    Article  CAS  Google Scholar 

  34. Wang, X. H. et al. RNA interference directs innate immunity against viruses in adult Drosophila. Science 312, 452–454 (2006).

    Article  CAS  Google Scholar 

  35. Keene, K. M. et al. RNA interference acts as a natural antiviral response to O’nyong-nyong virus (Alphavirus; Togaviridae) infection of Anopheles gambiae. Proc. Natl Acad. Sci. USA 101, 17240–17245 (2004).

    Article  CAS  Google Scholar 

  36. Hamilton, A. J. & Baulcombe, D. C. A species of small antisense RNA in post-transcriptional gene silencing in plants. Science 286, 950–952 (1999).

    Article  CAS  Google Scholar 

  37. Papaefthimiou, I. et al. Replicating potato spindle tuber viroid RNA is accompanied by short RNA fragments that are characteristic of post-transcriptional gene silencing. Nucleic Acids Res. 29, 2395–2400 (2001).

    Article  CAS  Google Scholar 

  38. Hutvágner, G. et al. A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temperal RNA. Science 293, 834–838 (2001).

    Article  Google Scholar 

  39. Chendrimada, T. P. et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436, 740–744 (2005).

    Article  CAS  Google Scholar 

  40. Hammond, S. M., Bernstein, E., Beach, D. & Hannon, G. J. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404, 293–296 (2000).

    Article  CAS  Google Scholar 

  41. Bernstein, R., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001).

    Article  CAS  Google Scholar 

  42. Elbashir, S. M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188–200 (2001).

    Article  CAS  Google Scholar 

  43. Parker, J. S., Roe, S. M. & Barford, D. Structural insights into mRNA recognition from a PIWI domain–siRNA guide complex. Nature 434, 663–666 (2005).

    Article  CAS  Google Scholar 

  44. Cenik, E. S. & Zamore, P. D. Argonaute proteins. Curr. Biol. 21, 446–449 (2011).

    Article  Google Scholar 

  45. Berkhout, B. RNAi-mediated antiviral immunity in mammals. Curr. Opin. Virol. 32, 9–14 (2018).

    Article  CAS  Google Scholar 

  46. Pfeffer, S. et al. Identification of virus-encoded microRNAs. Crit. Rev. Biochem. Mol. Biol. 304, 734–736 (2001).

    Google Scholar 

  47. Kennedy, E. M. et al. Production of functional small interfering RNAs by an amino-terminal deletion mutant of human Dicer. Proc. Natl Acad. Sci. USA 112, E6945–E6954 (2015).

    Article  CAS  Google Scholar 

  48. Weng, K. F. et al. A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells. Nucleic Acids Res. 42, 12789–12805 (2014).

    Article  CAS  Google Scholar 

  49. Parameswaran, P. et al. Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems. PLoS Pathog. 6, e1000764 (2010).

    Article  Google Scholar 

  50. Chen, G. R., Sive, H. & Bartel, D. P. A Seed mismatch enhances Argonaute2-catalyzed cleavage and partially rescues severely impaired cleavage found in fish. Mol. Cell 68, 1095–1107.e5 (2017).

    Article  CAS  Google Scholar 

  51. Flemr, M. et al. XA retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell 155, 807–816 (2013).

    Article  CAS  Google Scholar 

  52. Cullen, B. R. Is RNA interference involved in intrinsic antiviral immunity in mammals? Nat. Immunol. 7, 563–567 (2006).

    Article  CAS  Google Scholar 

  53. Watson, S. F., Knol, L. I., Witteveldt, J. & Macias, S. Crosstalk between mammalian antiviral pathways. Non-coding RNA 5, 29 (2019).

  54. Poirier, E. Z. et al. An isoform of Dicer protects mammalian stem cells against multiple RNA viruses. Science 373, 231–236 (2021).

    Article  CAS  Google Scholar 

  55. Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. R. Soc. B 286, 20190831 (2019).

    Article  CAS  Google Scholar 

  56. Dostert, C. et al. The Jak–STAT signaling pathway is required but not sufficient for the antiviral response of Drosophila. Nat. Immunol. 6, 946–953 (2005).

    Article  CAS  Google Scholar 

  57. Paradkar, P. N., Trinidad, L., Voysey, R., Duchemin, J. B. & Walker, P. J. Secreted Vago restricts West Nile virus infection in Culex mosquito cells by activating the Jak–STAT pathway. Proc. Natl Acad. Sci. USA 109, 18915–18920 (2012).

    Article  CAS  Google Scholar 

  58. Li, C. et al. Activation of Vago by interferon regulatory factor (IRF) suggests an interferon system-like antiviral mechanism in shrimp. Sci. Rep. 5, 15078 (2015).

  59. Nehyba, J., Hrdličková, R. & Bose, H. R. in Encyclopedia of Life Sciences (eLS), https://doi.org/10.1002/9780470015902.a0022874 (2010).

  60. Nehyba, J., Hrdličková, R. & Bose, H. R. Dynamic evolution of immune system regulators: the history of the interferon regulatory factor family. Mol. Biol. Evol. 26, 2539–2550 (2009).

    Article  CAS  Google Scholar 

  61. Deddouche, S. et al. The DExD/H-box helicase Dicer-2 mediates the induction of antiviral activity in Drosophila. Nat. Immunol. 9, 1425–1432 (2008).

    Article  CAS  Google Scholar 

  62. Holleufer, A. et al. Two cGAS-like receptors induce antiviral immunity in Drosophila. Nature 597, 114–118 (2021).

    Article  CAS  Google Scholar 

  63. Slavik, K. M. et al. cGAS-like receptors sense RNA and control 3′2′-cGAMP signalling in Drosophila. Nature 597, 109–113 (2021).

    Article  CAS  Google Scholar 

  64. Cai, H. et al. 2′3′-cGAMP triggers a STING- and NF-κB-dependent broad antiviral response in Drosophila. Sci. Signal. 13, eabc4537 (2020).

    Article  CAS  Google Scholar 

  65. Goto, A. et al. The kinase IKKβ regulates a STING- and NF-κB-dependent antiviral response pathway in Drosophila. Immunity 49, 225–234.e4 (2018).

    Article  CAS  Google Scholar 

  66. Segrist, E., Dittmar, M., Gold, B. & Cherry, S. Orally acquired cyclic dinucleotides drive dSTING-dependent antiviral immunity in enterocytes. Cell Rep. 37, 110150 (2021).

    Article  CAS  Google Scholar 

  67. Martin, M., Hiroyasu, A., Guzman, R. M., Roberts, S. A. & Goodman, A. G. Analysis of Drosophila STING reveals an evolutionarily conserved antimicrobial function. Cell Rep. 23, 3537–3550 (2018).

    Article  CAS  Google Scholar 

  68. Liu, Y. et al. Inflammation-induced, STING-dependent autophagy restricts Zika virus infection in the Drosophila brain. Cell Host Microbe 24, 57–68 (2018).

    Article  CAS  Google Scholar 

  69. Levashina, E. A. et al. Constitutive activation of Toll-mediated antifungal defense in Serpin-deficient Drosophila. Science 285, 1917–1919 (1999).

    Article  CAS  Google Scholar 

  70. Ooi, J. Y., Yagi, Y., Hu, X. & Ip, Y. T. The Drosophila Toll-9 activates a constitutive antimicrobial defense. EMBO Rep. 3, 82–87 (2002).

    Article  CAS  Google Scholar 

  71. Tauszig, S., Jouanguy, E., Hoffmann, J. A. & Imler, J. L. Toll-related receptors and the control of antimicrobial peptide expression in Drosophila. Proc. Natl Acad. Sci. USA 97, 10520–10525 (2000).

    Article  CAS  Google Scholar 

  72. Orús-Alcalde, A., Børve, A. & Hejnol, A. The Toll and Imd pathway, the complement system and lectins during immune response of the nemertean Lineus ruber. Preprint at https://doi.org/10.1101/2022.04.26.489627 (2022).

  73. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998).

    Article  CAS  Google Scholar 

  74. Félix, M. A. et al. Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses. PLoS Biol. 9, e1000586 (2011).

    Article  Google Scholar 

  75. Ashe, A. et al. A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity. eLife 2, e00994 (2013).

    Article  Google Scholar 

  76. Tanguy, M. et al. An alternative STAT signaling pathway acts in viral immunity in Caenorhabditis elegans. mBio 8, e00927-17 (2017).

    Article  Google Scholar 

  77. Duchaine, T. F. et al. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell 124, 343–354 (2006).

    Article  CAS  Google Scholar 

  78. Coffman, S. R. et al. Caenorhabditis elegans RIG-I homolog mediates antiviral RNA interference downstream of Dicer-dependent biogenesis of viral small interfering RNAs. mBio 8, e00264-17 (2017).

    Article  Google Scholar 

  79. Guo, X., Zhang, R., Wang, J., Ding, S. W. & Lu, R. Homologous RIG-I-like helicase proteins direct RNA-mediated antiviral immunity in C. elegans by distinct mechanisms. Proc. Natl Acad. Sci. USA 110, 16085–16090 (2013).

    Article  CAS  Google Scholar 

  80. Li, K. et al. Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3). Nucleic Acids Res. 49, 9978–9991 (2021).

    Article  CAS  Google Scholar 

  81. Palmer, W. H., Hadfield, J. D. & Obbard, D. J. RNA-interference pathways display high rates of adaptive protein evolution in multiple invertebrates. Genetics 208, 1585–1599 (2018).

    Article  CAS  Google Scholar 

  82. Lewis, S. H. et al. Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Nat. Ecol. Evol. 2, 174–181 (2018).

    Article  Google Scholar 

  83. Wein, T. & Sorek, R. Bacterial origins of human cell-autonomous innate immune mechanisms. Nat. Rev. Immunol. 22, 629–638 (2022).

    Article  CAS  Google Scholar 

  84. Huang, B. et al. Characterization of the mollusc RIG-I/MAVS pathway reveals an archaic antiviral signalling framework in invertebrates. Sci. Rep. 7, 8217 (2017).

  85. de Jong, D. et al. Multiple Dicer genes in the early-diverging Metazoa. Mol. Biol. Evol. 26, 1333–1340 (2009).

    Article  Google Scholar 

  86. Dominguez-Huerta, G. et al. Diversity and ecological footprint of global ocean RNA viruses. Science 376, 1202–1208 (2022).

    Article  CAS  Google Scholar 

  87. Zayed, A. A. et al. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. Science 376, 156–162 (2022).

    Article  CAS  Google Scholar 

  88. Callanan, J. et al. Expansion of known ssRNA phage genomes: from tens to over a thousand. Sci. Adv. 6, eaay5981 (2020).

  89. Steward, G. F. et al. Are we missing half of the viruses in the ocean? ISME J. 7, 672–679 (2013).

    Article  CAS  Google Scholar 

  90. Woznica, A. et al. STING mediates immune responses in the closest living relatives of animals. eLife 10, e70436 (2021).

  91. Margolis, S. R. & Dietzen, P. A. The cyclic dinucleotide 2′3′-cGAMP induces a broad antibacterial and antiviral response in the sea anemone Nematostella vectensis. Proc. Natl Acad. Sci. USA 118, e2109022118 (2021).

  92. Whiteley, A. T. et al. Bacterial cGAS-like enzymes synthesize diverse nucleotide signals. Nature 567, 194–199 (2019).

    Article  CAS  Google Scholar 

  93. Cohen, D. et al. Cyclic GMP–AMP signalling protects bacteria against viral infection. Nature 574, 691–695 (2019).

    Article  CAS  Google Scholar 

  94. Morehouse, B. R. et al. STING cyclic dinucleotide sensing originated in bacteria. Nature 586, 429–433 (2020).

    Article  CAS  Google Scholar 

  95. Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).

  96. Bernheim, A. et al. Prokaryotic viperins produce diverse antiviral molecules. Nature 589, 120–124 (2021).

    Article  CAS  Google Scholar 

  97. Makarova, K. S., Wolf, Y. I., van der Oost, J. & Koonin, E. V. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol. Direct 4, 29 (2009).

  98. Brennan, J. J. et al. Sea anemone model has a single Toll-like receptor that can function in pathogen detection, NF-κB signal transduction, and development. Proc. Natl Acad. Sci. USA 114, E10122–E10131 (2017).

    Article  CAS  Google Scholar 

  99. Poole, A. Z. & Weis, V. M. TIR-domain-containing protein repertoire of nine anthozoan species reveals coral-specific expansions and uncharacterized proteins. Dev. Comp. Immunol. 46, 480–488 (2014).

    Article  CAS  Google Scholar 

  100. Williams, L. M. et al. A conserved Toll-like receptor-to-NF-κB signaling pathway in the endangered coral Orbicella faveolata. Dev. Comp. Immunol. 79, 128–136 (2018).

    Article  CAS  Google Scholar 

  101. Brennan, J. J. & Gilmore, T. D. Evolutionary origins of Toll-like receptor signalling. Mol. Biol. Evol. 35, 1576–1587 (2018).

    Article  CAS  Google Scholar 

  102. Roesel, C. L. & Vollmer, S. V. Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus. Ecol. Evol. 9, 8279–8293 (2019).

    Article  Google Scholar 

  103. Davidson, C. R., Best, N. M., Francis, J. W., Cooper, E. L. & Wood, T. C. Toll-like receptor genes (TLRs) from Capitella capitata and Helobdella robusta (Annelida). Dev. Comp. Immunol. 32, 608–612 (2008).

    Article  CAS  Google Scholar 

  104. Tassia, M. G., Whelan, N. V. & Halanych, K. M. Toll-like receptor pathway evolution in deuterostomes. Proc. Natl Acad. Sci. USA 114, 7055–7060 (2017).

    Article  CAS  Google Scholar 

  105. Ji, J. et al. Characterization of the TLR family in Branchiostoma lanceolatum and discovery of a novel TLR22-like involved in dsRNA recognition in amphioxus. Front Immunol. 9, 2525 (2018).

    Article  Google Scholar 

  106. Hibino, T. et al. The immune gene repertoire encoded in the purple sea urchin genome. Dev. Biol. 300, 349–365 (2006).

    Article  CAS  Google Scholar 

  107. Zhang, Y. et al. Characteristic and functional analysis of Toll-like receptors (TLRs) in the lophotrocozoan, Crassostrea gigas, reveals ancient origin of TLR-mediated innate immunity. PLoS ONE 8, e76464 (2013).

    Article  CAS  Google Scholar 

  108. Sarkar, D., Desalle, R. & Fisher, P. B. Evolution of MDA-5/RIG-I-dependent innate immunity: independent evolution by domain grafting. Proc. Natl Acad. Sci. USA 105, 17040–17045 (2008).

    Article  CAS  Google Scholar 

  109. Zou, J., Chang, M., Nie, P. & Secombes, C. J. Origin and evolution of the RIG-I like RNA helicase gene family. BMC Evol. Biol. 9, 85 (2009).

    Article  Google Scholar 

  110. Mukherjee, K., Korithoski, B. & Kolaczkowski, B. Ancient origins of vertebrate-specific innate antiviral immunity. Mol. Biol. Evol. 31, 140–153 (2014).

    Article  CAS  Google Scholar 

  111. Zhang, L. et al. Massive expansion and functional divergence of innate immune genes in a protostome. Sci. Rep. 5, 8693 (2015).

    Article  CAS  Google Scholar 

  112. Lewandowska, M., Sharoni, T., Admoni, Y., Aharoni, R. & Moran, Y. Functional characterization of the cnidarian antiviral immune response reveals ancestral complexity. Mol. Biol. Evol. 38, 4546–4561 (2021).

  113. Xu, L. et al. Loss of RIG-I leads to a functional replacement with MDA5 in the Chinese tree shrew. Proc. Natl Acad. Sci. USA 113, 10950–10955 (2016).

    Article  CAS  Google Scholar 

  114. Krchlíková, V. et al. Repeated MDA5 gene loss in birds: an evolutionary perspective. Viruses 13, 2131 (2021).

  115. Fischer, H., Tschachler, E. & Eckhart, L. Pangolins lack IFIH1/MDA5, a cytoplasmic RNA sensor that initiates innate immune defense upon coronavirus infection. Front. Immunol. 11, 939 (2020).

  116. Huang, B. et al. The first identified invertebrate LGP2-like homolog gene in the Pacific oyster Crassostrea gigas. Fish Shellfish Immunol. 128, 238–245 (2022).

    Article  CAS  Google Scholar 

  117. Lindbo, J. A., Silva-Rosales, L., Proebsting, W. M. & Dougherty, W. G. Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. Plant Cell 5, 1749–1759 (1993).

    Article  CAS  Google Scholar 

  118. Torres-Martínez, S. & Ruiz-Vázquez, R. M. The RNAi universe in fungi: a varied landscape of small RNAs and biological functions. Annu. Rev. Microbiol. 71, 371–391 (2017).

    Article  Google Scholar 

  119. Bonning, B. C. & Saleh, M. C. The interplay between viruses and RNAi pathways in insects. Annu. Rev. Entomol. 66, 61–79 (2021).

    Article  CAS  Google Scholar 

  120. Kuzmenko, A. et al. DNA targeting and interference by a bacterial Argonaute nuclease. Nature 587, 632–637 (2020).

    Article  CAS  Google Scholar 

  121. Olovnikov, I., Chan, K., Sachidanandam, R., Newman, D. K. & Aravin, A. A. Bacterial Argonaute samples the transcriptome to identify foreign DNA. Mol. Cell. 51, 594–605 (2013).

    Article  CAS  Google Scholar 

  122. Swarts, D. C. et al. DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507, 258–261 (2014).

    Article  CAS  Google Scholar 

  123. Mukherjee, K., Campos, H. & Kolaczkowski, B. Evolution of animal and plant dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants. Mol. Biol. Evol. 30, 627–641 (2013).

    Article  CAS  Google Scholar 

  124. Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69–81 (2004).

    Article  CAS  Google Scholar 

  125. Galiana-Arnoux, D., Dostert, C., Schneemann, A., Hoffmann, J. A. & Imler, J. L. Essential function in vivo for Dicer-2 in host defense against RNA viruses in Drosophila. Nat. Immunol. 7, 590–597 (2006).

    Article  CAS  Google Scholar 

  126. Moran, Y., Praher, D., Fredman, D. & Technau, U. The evolution of microRNA pathway protein components in Cnidaria. Mol. Biol. Evol. 30, 2541–2552 (2013).

    Article  CAS  Google Scholar 

  127. Veen, A. G. et al. The RIG‐I‐like receptor LGP2 inhibits Dicer‐dependent processing of long double‐stranded RNA and blocks RNA interference in mammalian cells. EMBO J. 37, e97479 (2018).

    Article  Google Scholar 

  128. Witteveldt, J., Ivens, A. & Macias, S. Inhibition of microprocessor function during the activation of the type I Interferon response. Cell Rep. 23, 3275–3285 (2018).

    Article  CAS  Google Scholar 

  129. Waldron, F. M., Stone, G. N. & Obbard, D. J. Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes. PLoS Genet. 14, e1007533 (2018).

    Article  Google Scholar 

  130. Tamura, T., Yanai, H., Savitsky, D. & Taniguchi, T. The IRF family transcription factors in immunity and oncogenesis. Annu. Rev. Immunol. 26, 535–584 (2008).

    Article  CAS  Google Scholar 

  131. Honda, K. & Taniguchi, T. IRFs: master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors. Nat. Rev. Immunol. 6, 644–658 (2006).

    Article  CAS  Google Scholar 

  132. Leger, M. M., Ros-Rocher, N., Najle, S. R. & Ruiz-Trillo, I. Rel/NF-κB transcription factors emerged at the onset of opisthokonts. Genome Biol. Evol. 14, evab289 (2022).

    Article  CAS  Google Scholar 

  133. Mercurio, F. & Manning, A. M. NF-kB as a primary regulator of the stress response. Oncogene 18, 6163–6171 (1999).

    Article  CAS  Google Scholar 

  134. Ozata, D. M., Gainetdinov, I., Zoch, A., O’Carroll, D. & Zamore, P. D. PIWI-interacting RNAs: small RNAs with big functions. Nat. Rev. Genet. 20, 89–108 (2019).

    Article  CAS  Google Scholar 

  135. Sarkar, A., Volff, J. N. & Vaury, C. piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation? FASEB J. 31, 436–446 (2017).

    Article  CAS  Google Scholar 

  136. Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11, 1017–1027 (2001).

    Article  CAS  Google Scholar 

  137. Miesen, P., Girardi, E. & van Rij, R. P. Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Res. 43, 6545–6556 (2015).

    Article  CAS  Google Scholar 

  138. Morazzani, E. M., Wiley, M. R., Murreddu, M. G., Adelman, Z. N. & Myles, K. M. Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma. PLoS Pathog. 8, e1002470 (2012).

    Article  CAS  Google Scholar 

  139. Miesen, P., Joosten, J. & van Rij, R. P. PIWIs go viral: arbovirus-derived piRNAs in vector mosquitoes. PLoS Pathog. 12, e1006017 (2016).

    Article  Google Scholar 

  140. Joosten, J., Overheul, G. J., van Rij, R. P. & Miesen, P. Endogenous piRNA-guided slicing triggers responder and trailer piRNA production from viral RNA in Aedes aegypti mosquitoes. Nucleic Acids Res. 49, 8886–8899 (2021).

    Article  CAS  Google Scholar 

  141. Petit, M. et al. piRNA pathway is not required for antiviral defense in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 113, E4218–E4227 (2016).

    Article  CAS  Google Scholar 

  142. Tassetto, M., Kunitomi, M. & Andino, R. Circulating immune cells mediate a systemic RNAi-based adaptive antiviral response in Drosophila. Cell 169, 314–325 (2017).

    Article  CAS  Google Scholar 

  143. Silverman, N. et al. Control of RNA viruses in mosquito cells through the acquisition of vDNA and endogenous viral elements. eLife 8, e41244 (2019).

  144. Chan, Y. K. & Gack, M. U. Viral evasion of intracellular DNA and RNA sensing. Nat. Rev. Microbiol. 14, 360–373 (2016).

    Article  CAS  Google Scholar 

  145. Christensen, M. H. & Paludan, S. R. Viral evasion of DNA-stimulated innate immune responses. Cell Mol. Immunol. 14, 4–13 (2017).

    Article  CAS  Google Scholar 

  146. Koonin, E. V. & Dolja, V. V. A virocentric perspective on the evolution of life. Curr. Opin. Virol. 3, 546–557 (2013).

    Article  Google Scholar 

  147. Drinnenberg, I. A. et al. Compatibility with killer explains the rise of RNAi-deficient fungi. Science 333, 1592 (2011).

    Article  CAS  Google Scholar 

  148. Nicolás, F. E. & Garre, V. RNA interference in Fungi: retention and loss. Microbiol. Spectr. 4, 657–671 (2016).

    Article  Google Scholar 

  149. Nicolás, F. E., Torres-Martínez, S. & Ruiz-Vázquez, R. M. Loss and retention of RNA interference in Fungi and parasites. PLoS Pathog. 9, e1003089 (2013).

  150. Mongelli, V. et al. Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster. Nat. Ecol. Evol. 6, 565–578 (2022).

    Article  Google Scholar 

  151. Phillips, J. E., Santos, M., Konchwala, M., Xing, C. & Pan, D. Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan role for the Hippo pathway in multicellular morphogenesis. eLife 11, e77598 (2022).

  152. Presnell, J. S., Bubel, M., Knowles, T., Patry, W. & Browne, W. E. Multigenerational laboratory culture of pelagic ctenophores and CRISPR–Cas9 genome editing in the lobate Mnemiopsis leidyi. Nat. Protoc. 17, 1868–1900 (2022).

    Article  CAS  Google Scholar 

  153. Chen, S. N., Zou, P. F. & Nie, P. Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) in fish: current knowledge and future perspectives. Immunology 151, 16–25 (2017).

    Article  Google Scholar 

  154. Sabbah, A. et al. Activation of innate immune antiviral responses by Nod2. Nat. Immunol. 10, 1073–1080 (2009).

    Article  CAS  Google Scholar 

  155. Bauernfried, S., Scherr, M. J., Pichlmair, A., Duderstadt, K. E. & Hornung, V. Human NLRP1 is a sensor for double-stranded RNA. Science 371, eabd0811 (2021).

    Article  CAS  Google Scholar 

  156. Richter, D. J., Fozouni, P., Eisen, M. B. & King, N. Gene family innovation, conservation and loss on the animal stem lineage. eLife 7, e34226 (2018).

    Article  Google Scholar 

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Acknowledgements

We thank S. Moineau and A. Culley (Université Laval) for advice on the diversity of DNA and RNA phages.

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Iwama, R.E., Moran, Y. Origins and diversification of animal innate immune responses against viral infections. Nat Ecol Evol 7, 182–193 (2023). https://doi.org/10.1038/s41559-022-01951-4

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