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  • Review Article
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At the centre: influenza A virus ribonucleoproteins

Key Points

  • This paper describes the trafficking and functions of influenza A virus (IAV) viral ribonucleoproteins (vRNPs), which contain the genetic material of IAV, within the host cell. We emphasize how vRNPs interact with, and depend on, host factors and pathways, how vRNP structure contributes to its function and the key open questions that still need to be answered.

  • The structure of vRNPs in their native form is described.

  • The mechanism of vRNP nuclear import is explained, including a discussion of how vRNP components interact with the cellular importin-α–importin-β1 nuclear import pathway.

  • Primary genome transcription and genome replication is described, focusing on how host factors contribute to these processes.

  • Nuclear export of vRNP, which is mediated by the cellular CRM1 (also known as exportin-1) nuclear export pathway, is illustrated.

  • Recent work implicating the cellular RAB11 vesicle transport system and microtubules in vRNP cytoplasmic transport in late-stage infection is described.

  • We highlight important open questions and suggest methods that could be used to address these gaps in our knowledge.

Abstract

Influenza A viral ribonucleoprotein (vRNP) complexes comprise the eight genomic negative-sense RNAs, each of which is bound to multiple copies of the vRNP and a trimeric viral polymerase complex. The influenza virus life cycle centres on the vRNPs, which in turn rely on host cellular processes to carry out functions that are necessary for the successful completion of the virus life cycle. In this Review, we discuss our current knowledge about vRNP trafficking within host cells and the function of these complexes in the context of the virus life cycle, highlighting how structure contributes to function and the crucial interactions with host cell pathways, as well as on the information gaps that remain. An improved understanding of how vRNPs use host cell pathways is essential to identify mechanisms of virus pathogenicity, host adaptation and, ultimately, new targets for antiviral intervention.

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Figure 1: Influenza vRNP complex.
Figure 2: Model for vRNP nuclear import.
Figure 3: Model for genome transcription and replication.
Figure 4: Model for vRNP nuclear export.

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References

  1. World Health Organization. Influenza (Seasonal) Fact sheet N°211. WHO [online], (2009).

  2. Molinari, N. A. et al. The annual impact of seasonal influenza in the US: measuring disease burden and costs. Vaccine 25, 5086–5096 (2007).

    Article  PubMed  Google Scholar 

  3. Simonsen, L. The global impact of influenza on morbidity and mortality. Vaccine 17 (Suppl. 1), 3–10 (1999).

    Article  Google Scholar 

  4. van der Vries, E., Schutten, M., Fraaij, P., Boucher, C. & Osterhaus, A. Influenza virus resistance to antiviral therapy. Adv. Pharmacol. 67, 217–246 (2013).

    Article  CAS  PubMed  Google Scholar 

  5. Matsuoka, Y. et al. A comprehensive map of the influenza A virus replication cycle. BMC syst. biol. 7, 97 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Shaw, M. L. & Palese, P. in Fields Virology. Section II: Specific Virus Families (eds Knipe, D. M. & Howley, P.) (Lippincott Williams and Wilkins, 2013).

    Google Scholar 

  7. Wright, P. F., Neumann, G. & Kawaoka, Y. in Fields Virology. Section II: Specific Virus Families (eds Knipe, D. M. & Howley, P.) (Lippincott Williams and Wilkins, 2013).

    Google Scholar 

  8. Gabriel, G. & Fodor, E. Molecular determinants of pathogenicity in the polymerase complex. Curr. Top. Microbiol. Immunol. 385, 35–60 (2014).

    PubMed  Google Scholar 

  9. Scholtissek, C. & Becht, H. Binding of ribonucleic acids to the RNP-antigen protein of influenza viruses. J. General Virol. 10, 11–16 (1971).

    Article  CAS  Google Scholar 

  10. Baudin, F., Bach, C., Cusack, S. & Ruigrok, R. W. Structure of influenza virus RNP. I. Influenza virus nucleoprotein melts secondary structure in panhandle RNA and exposes the bases to the solvent. EMBO J. 13, 3158–3165 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Compans, R. W., Content, J. & Duesberg, P. H. Structure of the ribonucleoprotein of influenza virus. J. Virol. 10, 795–800 (1972).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Yamanaka, K., Ishihama, A. & Nagata, K. Reconstitution of influenza virus RNA-nucleoprotein complexes structurally resembling native viral ribonucleoprotein cores. J. Biol. Chem. 265, 11151–11155 (1990).

    CAS  PubMed  Google Scholar 

  13. Hsu, M. T., Parvin, J. D., Gupta, S., Krystal, M. & Palese, P. Genomic RNAs of influenza viruses are held in a circular conformation in virions and in infected cells by a terminal panhandle. Proc. Natl Acad. Sci. USA 84, 8140–8144 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Fodor, E., Seong, B. L. & Brownlee, G. G. Photochemical cross-linking of influenza A polymerase to its virion RNA promoter defines a polymerase binding site at residues 9 to 12 of the promoter. J. General Virol. 74, 1327–1333 (1993).

    Article  CAS  Google Scholar 

  15. Arranz, R. et al. The structure of native influenza virion ribonucleoproteins. Science 338, 1634–1637 (2012). This paper describes the three-dimensional structure of native RNPs derived from influenza virions.

    Article  CAS  PubMed  Google Scholar 

  16. Moeller, A., Kirchdoerfer, R. N., Potter, C. S., Carragher, B. & Wilson, I. A. Organization of the influenza virus replication machinery. Science 338, 1631–1634 (2012). This paper describes the three-dimensional structure of native RNPs derived from cells expressing influenza RNP complex components.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Martin, K. & Helenius, A. Nuclear transport of influenza virus ribonucleoproteins: the viral matrix protein (M1) promotes export and inhibits import. Cell 67, 117–130 (1991). This paper was the first to establish that the influenza M1 protein regulates both nuclear import and nuclear export of influenza vRNPs.

    Article  CAS  PubMed  Google Scholar 

  18. Bui, M., Whittaker, G. & Helenius, A. Effect of M1 protein and low pH on nuclear transport of influenza virus ribonucleoproteins. J. Virol. 70, 8391–8401 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Stewart, M. Molecular mechanism of the nuclear protein import cycle. Nature Rev. Mol. Cell Biol. 8, 195–208 (2007).

    Article  CAS  Google Scholar 

  20. Kutay, U., Bischoff, F. R., Kostka, S., Kraft, R. & Gorlich, D. Export of importin α from the nucleus is mediated by a specific nuclear transport factor. Cell 90, 1061–1071 (1997).

    Article  CAS  PubMed  Google Scholar 

  21. Martin, K. & Helenius, A. Transport of incoming influenza virus nucleocapsids into the nucleus. J. Virol. 65, 232–244 (1991). This paper was the first to show that influenza vRNPs enter the nucleus through the nuclear pore complex by an active mechanism.

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Kemler, I., Whittaker, G. & Helenius, A. Nuclear import of microinjected influenza virus ribonucleoproteins. Virology 202, 1028–1033 (1994).

    Article  CAS  PubMed  Google Scholar 

  23. O'Neill, R. E., Jaskunas, R., Blobel, G., Palese, P. & Moroianu, J. Nuclear import of influenza virus RNA can be mediated by viral nucleoprotein and transport factors required for protein import. J. Biol. Chem. 270, 22701–22704 (1995).

    Article  CAS  PubMed  Google Scholar 

  24. Chou, Y. Y. et al. Colocalization of different influenza viral RNA segments in the cytoplasm before viral budding as shown by single-molecule sensitivity FISH analysis. PLoS Pathog. 9, e1003358 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Tarendeau, F. et al. Structure and nuclear import function of the C-terminal domain of influenza virus polymerase PB2 subunit. Nature Struct. Mol. Biol. 14, 229–233 (2007).

    Article  CAS  Google Scholar 

  26. Nath, S. T. & Nayak, D. P. Function of two discrete regions is required for nuclear localization of polymerase basic protein 1 of A/WSN/33 influenza virus (H1 N1). Mol. Cell. Biol. 10, 4139–4145 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Fodor, E. & Smith, M. The PA subunit is required for efficient nuclear accumulation of the PB1 subunit of the influenza A virus RNA polymerase complex. J. Virol. 78, 9144–9153 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Neumann, G., Castrucci, M. R. & Kawaoka, Y. Nuclear import and export of influenza virus nucleoprotein. J. Virol. 71, 9690–9700 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Wang, P., Palese, P. & O'Neill, R. E. The NPI-1/NPI-3 (karyopherin α) binding site on the influenza a virus nucleoprotein NP is a nonconventional nuclear localization signal. J. Virol. 71, 1850–1856 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Weber, F., Kochs, G., Gruber, S. & Haller, O. A classical bipartite nuclear localization signal on Thogoto and influenza A virus nucleoproteins. Virology 250, 9–18 (1998).

    Article  CAS  PubMed  Google Scholar 

  31. Nieto, A., de la Luna, S., Barcena, J., Portela, A. & Ortin, J. Complex structure of the nuclear translocation signal of influenza virus polymerase PA subunit. J. General Virol. 75, 29–36 (1994).

    Article  CAS  Google Scholar 

  32. Cros, J. F., Garcia-Sastre, A. & Palese, P. An unconventional NLS is critical for the nuclear import of the influenza A virus nucleoprotein and ribonucleoprotein. Traffic 6, 205–213 (2005).

    Article  CAS  PubMed  Google Scholar 

  33. Gabriel, G. et al. Differential use of importin-α isoforms governs cell tropism and host adaptation of influenza virus. Nature Commun. 2, 156 (2011).

    Article  CAS  Google Scholar 

  34. Wu, W. W., Weaver, L. L. & Pante, N. Ultrastructural analysis of the nuclear localization sequences on influenza A ribonucleoprotein complexes. J. Mol. Biol. 374, 910–916 (2007).

    Article  CAS  PubMed  Google Scholar 

  35. Gabriel, G., Herwig, A. & Klenk, H. D. Interaction of polymerase subunit PB2 and NP with importin α1 is a determinant of host range of influenza A virus. PLoS Pathog. 4, e11 (2008).

  36. Mark, G. E., Taylor, J. M., Broni, B. & Krug, R. M. Nuclear accumulation of influenza viral RNA transcripts and the effects of cycloheximide, actinomycin D, and α-amanitin. J. Virol. 29, 744–752 (1979).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Bouloy, M., Plotch, S. J. & Krug, R. M. Globin mRNAs are primers for the transcription of influenza viral RNA in vitro. Proc. Natl Acad. Sci. USA 75, 4886–4890 (1978).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Plotch, S. J., Bouloy, M. & Krug, R. M. Transfer of 5′-terminal cap of globin mRNA to influenza viral complementary RNA during transcription in vitro. Proc. Natl Acad. Sci. USA 76, 1618–1622 (1979).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Plotch, S. J., Bouloy, M., Ulmanen, I. & Krug, R. M. A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell 23, 847–858 (1981).

    Article  CAS  PubMed  Google Scholar 

  40. Jorba, N., Coloma, R. & Ortin, J. Genetic trans-complementation establishes a new model for influenza virus RNA transcription and replication. PLoS Pathog. 5, e1000462 (2009). This paper describes a new model for influenza virus RNA transcription and replication. Specifically, the data suggest that primary transcription is carried out by the resident polymerase complex bound to the double-stranded end of the vRNP, whereas genome replication is carried out by soluble polymerase complexes and another polymerase complex directs the encapsidation of progeny vRNPs.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Robertson, J. S., Schubert, M. & Lazzarini, R. A. Polyadenylation sites for influenza virus mRNA. J. Virol. 38, 157–163 (1981).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Poon, L. L., Pritlove, D. C., Fodor, E. & Brownlee, G. G. Direct evidence that the poly(A) tail of influenza A virus mRNA is synthesized by reiterative copying of a U track in the virion RNA template. J. Virol. 73, 3473–3476 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Fodor, E. The RNA polymerase of influenza a virus: mechanisms of viral transcription and replication. Acta Virol. 57, 113–122 (2013).

    Article  CAS  PubMed  Google Scholar 

  44. Yanguez, E. & Nieto, A. So similar, yet so different: selective translation of capped and polyadenylated viral mRNAs in the influenza virus infected cell. Virus Res. 156, 1–12 (2011).

    Article  CAS  PubMed  Google Scholar 

  45. Schneider, J. & Wolff, T. Nuclear functions of the influenza A and B viruses NS1 proteins: do they play a role in viral mRNA export? Vaccine 27, 6312–6316 (2009).

    Article  CAS  PubMed  Google Scholar 

  46. Vreede, F. T., Jung, T. E. & Brownlee, G. G. Model suggesting that replication of influenza virus is regulated by stabilization of replicative intermediates. J. Virol. 78, 9568–9572 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. York, A., Hengrung, N., Vreede, F. T., Huiskonen, J. T. & Fodor, E. Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus. Proc. Natl Acad. Sci. USA 110, E4238–E4245 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Deng, T. et al. Role of ran binding protein 5 in nuclear import and assembly of the influenza virus RNA polymerase complex. J. Virol. 80, 11911–11919 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Manzoor, R. et al. Heat shock protein 70 modulates Influenza A virus polymerase activity. J. Biol. Chem. http://dx.doi.org/10.1074/jbc.M113.507798 (2014).

  50. Momose, F. et al. Identification of Hsp90 as a stimulatory host factor involved in influenza virus RNA synthesis. J. Biol. Chem. 277, 45306–45314 (2002).

    Article  CAS  PubMed  Google Scholar 

  51. Naito, T., Momose, F., Kawaguchi, A. & Nagata, K. Involvement of Hsp90 in assembly and nuclear import of influenza virus RNA polymerase subunits. J. Virol. 81, 1339–1349 (2007).

    Article  CAS  PubMed  Google Scholar 

  52. Engelhardt, O. G., Smith, M. & Fodor, E. Association of the influenza A virus RNA-dependent RNA polymerase with cellular RNA polymerase II. J. Virol. 79, 5812–5818 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Llompart, C. M., Nieto, A. & Rodriguez-Frandsen, A. Specific residues of PB2 and PA influenza virus polymerase subunits confer the ability for RNA polymerase II degradation and virus pathogenicity in mice. J. Virol. 88, 3455–3463 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Landeras-Bueno, S., Jorba, N., Perez-Cidoncha, M. & Ortin, J. The splicing factor proline-glutamine rich (SFPQ/PSF) is involved in influenza virus transcription. PLoS Pathog. 7, e1002397 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Jorba, N. et al. Analysis of the interaction of influenza virus polymerase complex with human cell factors. Proteomics 8, 2077–2088 (2008).

    Article  CAS  PubMed  Google Scholar 

  56. Kawaguchi, A. & Nagata, K. De novo replication of the influenza virus RNA genome is regulated by DNA replicative helicase, MCM. EMBO J. 26, 4566–4575 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Naito, T. et al. An influenza virus replicon system in yeast identified Tat-SF1 as a stimulatory host factor for viral RNA synthesis. Proc. Natl Acad. Sci. USA 104, 18235–18240 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  58. Momose, F. et al. Cellular splicing factor RAF-2p48/NPI-5/BAT1/UAP56 interacts with the influenza virus nucleoprotein and enhances viral RNA synthesis. J. Virol. 75, 1899–1908 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Kawaguchi, A., Momose, F. & Nagata, K. Replication-coupled and host factor-mediated encapsidation of the influenza virus genome by viral nucleoprotein. J. Virol. 85, 6197–6204 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Zhou, Z. et al. Fragile X mental retardation protein stimulates ribonucleoprotein assembly of influenza A virus. Nature Commun. 5, 3259 (2014).

    Article  CAS  Google Scholar 

  61. Perez-Gonzalez, A., Rodriguez, A., Huarte, M., Salanueva, I. J. & Nieto, A. hCLE/CGI-99, a human protein that interacts with the influenza virus polymerase, is a mRNA transcription modulator. J. Mol. Biol. 362, 887–900 (2006).

    Article  CAS  PubMed  Google Scholar 

  62. Rodriguez, A., Perez-Gonzalez, A. & Nieto, A. Cellular human CLE/C14orf166 protein interacts with influenza virus polymerase and is required for viral replication. J. Virol. 85, 12062–12066 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Hudjetz, B. & Gabriel, G. Human-like PB2 627K influenza virus polymerase activity is regulated by importin-α1 and -α7. PLoS Pathog. 8, e1002488 (2012). This paper showed that IMPα1 and IMPα7 are positive regulators of human-like, but not avian-like, influenza polymerase activity, independent of IMP nuclear import activities, which suggests that IMPs regulate IAV transmission between reservoir species and humans.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Resa-Infante, P. et al. The host-dependent interaction of α-importins with influenza PB2 polymerase subunit is required for virus RNA replication. PLoS ONE 3, e3904 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Shinya, K. et al. PB2 amino acid at position 627 affects replicative efficiency, but not cell tropism, of Hong Kong H5N1 influenza A viruses in mice. Virology 320, 258–266 (2004).

    Article  CAS  PubMed  Google Scholar 

  66. Hatta, M., Gao, P., Halfmann, P. & Kawaoka, Y. Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses. Science 293, 1840–1842 (2001).

    Article  CAS  PubMed  Google Scholar 

  67. Li, Z. et al. Molecular basis of replication of duck H5N1 influenza viruses in a mammalian mouse model. J. Virol. 79, 12058–12064 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Subbarao, E. K., London, W. & Murphy, B. R. A single amino acid in the PB2 gene of influenza A virus is a determinant of host range. J. Virol. 67, 1761–1764 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Manz, B., Schwemmle, M. & Brunotte, L. Adaptation of avian influenza A virus polymerase in mammals to overcome the host species barrier. J. Virol. 87, 7200–7209 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Shapira, S. D. et al. A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139, 1255–1267 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  71. Tafforeau, L. et al. Generation and comprehensive analysis of an influenza virus polymerase cellular interaction network. J. Virol. 85, 13010–13018 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Bradel-Tretheway, B. G. et al. Comprehensive proteomic analysis of influenza virus polymerase complex reveals a novel association with mitochondrial proteins and RNA polymerase accessory factors. J. Virol. 85, 8569–8581 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Ma, K., Roy, A. M. & Whittaker, G. R. Nuclear export of influenza virus ribonucleoproteins: identification of an export intermediate at the nuclear periphery. Virology 282, 215–220 (2001).

    Article  CAS  PubMed  Google Scholar 

  74. Elton, D. et al. Interaction of the influenza virus nucleoprotein with the cellular CRM1-mediated nuclear export pathway. J. Virol. 75, 408–419 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Watanabe, K. et al. Inhibition of nuclear export of ribonucleoprotein complexes of influenza virus by leptomycin B. Virus Res. 77, 31–42 (2001).

    Article  CAS  PubMed  Google Scholar 

  76. Bui, M., Wills, E. G., Helenius, A. & Whittaker, G. R. Role of the influenza virus M1 protein in nuclear export of viral ribonucleoproteins. J. Virol. 74, 1781–1786 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Chase, G. P. et al. Influenza virus ribonucleoprotein complexes gain preferential access to cellular export machinery through chromatin targeting. PLoS Pathog. 7, e1002187 (2011). This paper describes a strong association between influenza vRNPs and cellular chromatin, which precedes vRNP nuclear export in late-stage infection. The authors hypothesize that influenza virus uses this mechanism to gain preferential access to nuclear export machinery to promote vRNP nuclear export and, ultimately, replicative ability.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Kurokawa, M., Ochiai, H., Nakajima, K. & Niwayama, S. Inhibitory effect of protein kinase C inhibitor on the replication of influenza type A virus. J. General Virol. 71, 2149–2155 (1990).

    Article  CAS  Google Scholar 

  79. Cao, S. et al. A nuclear export signal in the matrix protein of Influenza A virus is required for efficient virus replication. J. Virol. 86, 4883–4891 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Sakaguchi, A., Hirayama, E., Hiraki, A., Ishida, Y. & Kim, J. Nuclear export of influenza viral ribonucleoprotein is temperature-dependently inhibited by dissociation of viral matrix protein. Virology 306, 244–253 (2003).

    Article  CAS  PubMed  Google Scholar 

  81. Zhirnov, O. P. & Klenk, H. D. Histones as a target for influenza virus matrix protein M1. Virology 235, 302–310 (1997).

    Article  CAS  PubMed  Google Scholar 

  82. Whittaker, G., Bui, M. & Helenius, A. Nuclear trafficking of influenza virus ribonuleoproteins in heterokaryons. J. Virol. 70, 2743–2756 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. O'Neill, R. E., Talon, J. & Palese, P. The influenza virus NEP (NS2 protein) mediates the nuclear export of viral ribonucleoproteins. EMBO J. 17, 288–296 (1998). This paper was the first to establish that the influenza NEP protein regulates vRNP nuclear export and identify a region of the NEP protein that functions as a nuclear export signal.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Neumann, G., Hughes, M. T. & Kawaoka, Y. Influenza A virus NS2 protein mediates vRNP nuclear export through NES-independent interaction with hCRM1. EMBO J. 19, 6751–6758 (2000). This paper established the importance of the NEP protein in the nuclear export of vRNPs in the context of viral infection and identified the most crucial residues of the NEP nuclear export signal.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Huang, S. et al. A second CRM1-dependent nuclear export signal in the influenza A virus NS2 protein contributes to the nuclear export of viral ribonucleoproteins. J. Virol. 87, 767–778 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Akarsu, H. et al. Crystal structure of the M1 protein-binding domain of the influenza A virus nuclear export protein (NEP/NS2). EMBO J. 22, 4646–4655 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Imai, M., Watanabe, S. & Odagiri, T. Influenza B virus NS2, a nuclear export protein, directly associates with the viral ribonucleoprotein complex. Arch. Virol. 148, 1873–1884 (2003).

    Article  CAS  PubMed  Google Scholar 

  88. Robb, N. C., Smith, M., Vreede, F. T. & Fodor, E. NS2/NEP protein regulates transcription and replication of the influenza virus RNA genome. J. General Virol. 90, 1398–1407 (2009).

    Article  CAS  Google Scholar 

  89. Brunotte, L. et al. The nuclear export protein of H5N1 Influenza A viruses recruits matrix 1 (M1) protein to the viral ribonucleoprotein to mediate nuclear export. J. Biol. Chem. 289, 20067–20077 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Shimizu, T., Takizawa, N., Watanabe, K., Nagata, K. & Kobayashi, N. Crucial role of the influenza virus NS2 (NEP) C-terminal domain in M1 binding and nuclear export of vRNP. FEBS lett. 585, 41–46 (2011).

    Article  CAS  PubMed  Google Scholar 

  91. Yu, M. et al. Identification and characterization of three novel nuclear export signals in the influenza A virus nucleoprotein. J. Virol. 86, 4970–4980 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Pleschka, S. et al. Influenza virus propagation is impaired by inhibition of the Raf/MEK/ERK signalling cascade. Nature Cell Biol. 3, 301–305 (2001). This paper established the importance of the RAF–MEK–ERK pathway to efficient influenza virus replication and identified the nuclear export of influenza vRNPs as the life cycle step that is affected by inhibition of RAF–MEK–ERK signalling, which indicates that cellular kinase pathways are required for vRNP nuclear export.

    Article  CAS  PubMed  Google Scholar 

  93. Kumar, N., Liang, Y. & Parslow, T. G. Receptor tyrosine kinase inhibitors block multiple steps of influenza A virus replication. J. Virol. 85, 2818–2827 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Alamares-Sapuay, J. G. et al. Serum- and glucocorticoid-regulated kinase 1 is required for nuclear export of the ribonucleoprotein of influenza A virus. J. Virol. 87, 6020–6026 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Marjuki, H. et al. Membrane accumulation of influenza A virus hemagglutinin triggers nuclear export of the viral genome via protein kinase Cα-mediated activation of ERK signaling. J. Biol. Chem. 281, 16707–16715 (2006).

    Article  CAS  PubMed  Google Scholar 

  96. Marjuki, H. et al. Higher polymerase activity of a human influenza virus enhances activation of the hemagglutinin-induced Raf/MEK/ERK signal cascade. Virol. J. 4, 134 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Reinhardt, J. & Wolff, T. The influenza A virus M1 protein interacts with the cellular receptor of activated C kinase (RACK) 1 and can be phosphorylated by protein kinase C. Veterinary Microbiol. 74, 87–100 (2000).

    Article  CAS  Google Scholar 

  98. Petri, T. & Dimmock, N. J. Phosphorylation of influenza virus nucleoprotein in vivo. J. Gen. Virol. 57, 185–190 (1981).

    Article  CAS  PubMed  Google Scholar 

  99. Kistner, O., Muller, K. & Scholtissek, C. Differential phosphorylation of the nucleoprotein of influenza A viruses. J. Gen. Virol. 70, 2421–2431 (1989).

    Article  CAS  PubMed  Google Scholar 

  100. Richardson, J. C. & Akkina, R. K. NS2 protein of influenza virus is found in purified virus and phosphorylated in infected cells. Arch. Virol. 116, 69–80 (1991).

    Article  CAS  PubMed  Google Scholar 

  101. Hutchinson, E. C. et al. Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry. PLoS Pathog. 8, e1002993 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Takizawa, N., Kumakura, M., Takeuchi, K., Kobayashi, N. & Nagata, K. Sorting of influenza A virus RNA genome segments after nuclear export. Virology 401, 248–256 (2010).

    Article  CAS  PubMed  Google Scholar 

  103. Leser, G. P. & Lamb, R. A. Influenza virus assembly and budding in raft-derived microdomains: a quantitative analysis of the surface distribution of HA, NA and M2 proteins. Virology 342, 215–227 (2005).

    Article  CAS  PubMed  Google Scholar 

  104. Momose, F., Kikuchi, Y., Komase, K. & Morikawa, Y. Visualization of microtubule-mediated transport of influenza viral progeny ribonucleoprotein. Microbes Infect. 9, 1422–1433 (2007).

    Article  CAS  PubMed  Google Scholar 

  105. Amorim, M. J. et al. A Rab11- and microtubule-dependent mechanism for cytoplasmic transport of influenza A virus viral RNA. J. Virol. 85, 4143–4156 (2011). This paper was the first to identify overlap between the RAB11 recycling endosome compartment and the localization of cytoplasmic vRNPs in late-stage influenza virus infection. In addition, the PB2 protein of the polymerase complex was shown to form a direct interaction with the RAB11 protein.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Momose, F. et al. Apical transport of influenza A virus ribonucleoprotein requires Rab11-positive recycling endosome. PLoS ONE 6, e21123 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Avilov, S. V., Moisy, D., Naffakh, N. & Cusack, S. Influenza A virus progeny vRNP trafficking in live infected cells studied with the virus-encoded fluorescently tagged PB2 protein. Vaccine 30, 7411–7417 (2012).

    Article  CAS  PubMed  Google Scholar 

  108. Vale, R. D., Reese, T. S. & Sheetz, M. P. Identification of a novel force-generating protein, kinesin, involved in microtubule-based motility. Cell 42, 39–50 (1985).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Rietdorf, J. et al. Kinesin-dependent movement on microtubules precedes actin-based motility of vaccinia virus. Nature Cell Biol. 3, 992–1000 (2001).

    Article  CAS  PubMed  Google Scholar 

  110. Eisfeld, A. J., Kawakami, E., Watanabe, T., Neumann, G. & Kawaoka, Y. RAB11A is essential for transport of the influenza virus genome to the plasma membrane. J. Virol. 85, 6117–6126 (2011). This paper established a clear and tight relationship between RAB11 vesicle trafficking and the trafficking of nuclear-exported influenza vRNPs between the MTOC and the plasma membrane in late-stage infection. In addition, RAB11 expression and functional GTPase activity were shown to be crucial for influenza vRNP cytoplasmic transport.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Shaw, M. L., Stone, K. L., Colangelo, C. M., Gulcicek, E. E. & Palese, P. Cellular proteins in influenza virus particles. PLoS Pathog. 4, e1000085 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Kawaguchi, A., Matsumoto, K. & Nagata, K. YB-1 functions as a porter to lead influenza virus ribonucleoprotein complexes to microtubules. J. Virol. 86, 11086–11095 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. de Lucas, S., Peredo, J., Marion, R. M., Sanchez, C. & Ortin, J. Human Staufen1 protein interacts with influenza virus ribonucleoproteins and is required for efficient virus multiplication. J. Virol. 84, 7603–7612 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Chaineau, M., Danglot, L., Proux-Gillardeaux, V. & Galli, T. Role of HRB in clathrin-dependent endocytosis. J. Biol. Chem. 283, 34365–34373 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Pryor, P. R. et al. Molecular basis for the sorting of the SNARE VAMP7 into endocytic clathrin-coated vesicles by the ArfGAP Hrb. Cell 134, 817–827 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Eisfeld, A. J., Neumann, G. & Kawaoka, Y. Human immunodeficiency virus rev-binding protein is essential for influenza A virus replication and promotes genome trafficking in late-stage infection. J. Virol. 85, 9588–9598 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. McCown, M. F. & Pekosz, A. The influenza A virus M2 cytoplasmic tail is required for infectious virus production and efficient genome packaging. J. Virol. 79, 3595–3605 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Iwatsuki-Horimoto, K. et al. The cytoplasmic tail of the influenza A virus M2 protein plays a role in viral assembly. J. Virol. 80, 5233–5240 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Chen, B. J., Leser, G. P., Jackson, D. & Lamb, R. A. The influenza virus M2 protein cytoplasmic tail interacts with the M1 protein and influences virus assembly at the site of virus budding. J. Virol. 82, 10059–10070 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Noda, T. et al. Architecture of ribonucleoprotein complexes in influenza A virus particles. Nature 439, 490–492 (2006). This paper was the first to describe the organization pattern of influenza vRNPs in virus particles and provided strong support for the selective vRNP packaging model.

    Article  CAS  PubMed  Google Scholar 

  121. Chou, Y. Y. et al. One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis. Proc. Natl Acad. Sci. USA 109, 9101–9106 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  122. Fujii, Y., Goto, H., Watanabe, T., Yoshida, T. & Kawaoka, Y. Selective incorporation of influenza virus RNA segments into virions. Proc. Natl Acad. Sci. USA 100, 2002–2007 (2003). This paper was the first to identify segment-specific packaging signals for an influenza vRNP, which supported the selective incorporation model of vRNP packaging.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Watanabe, T., Watanabe, S., Noda, T., Fujii, Y. & Kawaoka, Y. Exploitation of nucleic acid packaging signals to generate a novel influenza virus-based vector stably expressing two foreign genes. J. Virol. 77, 10575–10583 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Ozawa, M. et al. Contributions of two nuclear localization signals of influenza A virus nucleoprotein to viral replication. J. Virol. 81, 30–41 (2007).

    Article  CAS  PubMed  Google Scholar 

  125. Liang, Y., Hong, Y. & Parslow, T. G. cis-acting packaging signals in the influenza virus PB1, PB2, and PA genomic RNA segments. J. Virol. 79, 10348–10355 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Liang, Y., Huang, T., Ly, H. & Parslow, T. G. Mutational analyses of packaging signals in influenza virus PA, PB1, and PB2 genomic RNA segments. J. Virol. 82, 229–236 (2008).

    Article  CAS  PubMed  Google Scholar 

  127. Hutchinson, E. C., Curran, M. D., Read, E. K., Gog, J. R. & Digard, P. Mutational analysis of cis-acting RNA signals in segment 7 of influenza A virus. J. Virol. 82, 11869–11879 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Gog, J. R. et al. Codon conservation in the influenza A virus genome defines RNA packaging signals. Nucleic Acids Res. 35, 1897–1907 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Muramoto, Y. et al. Hierarchy among viral RNA (vRNA) segments in their role in vRNA incorporation into influenza A virions. J. Virol. 80, 2318–2325 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Marsh, G. A., Hatami, R. & Palese, P. Specific residues of the influenza A virus hemagglutinin viral RNA are important for efficient packaging into budding virions. J. Virol. 81, 9727–9736 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Noda, T. et al. Three-dimensional analysis of ribonucleoprotein complexes in influenza A virus. Nature Commun. 3, 639 (2012). This paper was the first to describe the three-dimensional structure of influenza vRNPs within virus particles. The data suggest that inter-segment vRNP–vRNP interactions occur within virions and that vRNPs are incorporated into progeny virus particles in a specific pattern.

    Article  CAS  Google Scholar 

  132. Fournier, E. et al. A supramolecular assembly formed by influenza A virus genomic RNA segments. Nucleic Acids Res. 40, 2197–2209 (2012).

    Article  CAS  PubMed  Google Scholar 

  133. Fournier, E. et al. Interaction network linking the human H3N2 influenza A virus genomic RNA segments. Vaccine 30, 7359–7367 (2012).

    Article  CAS  PubMed  Google Scholar 

  134. Gavazzi, C. et al. An in vitro network of intermolecular interactions between viral RNA segments of an avian H5N2 influenza A virus: comparison with a human H3N2 virus. Nucleic Acids Res. 41, 1241–1254 (2013).

    Article  CAS  PubMed  Google Scholar 

  135. Essere, B. et al. Critical role of segment-specific packaging signals in genetic reassortment of influenza A viruses. Proc. Natl Acad. Sci. USA 110, E3840–E3848 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  136. Gavazzi, C. et al. A functional sequence-specific interaction between influenza A virus genomic RNA segments. Proc. Natl Acad. Sci. USA 110, 16604–16609 (2013). This paper provides an intriguing set of experiments that suggest the existence of a bona fide inter-segment vRNA–vRNA interaction that occurs in IAV-infected cells.

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors are grateful to S. Watson for scientific editing of the manuscript. This work was supported by grants-in-aid from the Ministry of Health, Labour, and Welfare, Japan, by ERATO (Japan Science and Technology Agency) and by National Institute of Allergy and Infectious Diseases Public Health Service research grants.

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Eisfeld, A., Neumann, G. & Kawaoka, Y. At the centre: influenza A virus ribonucleoproteins. Nat Rev Microbiol 13, 28–41 (2015). https://doi.org/10.1038/nrmicro3367

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