Krammer, F. et al. Influenza. Nat. Rev. Dis. Primers 4, 3 (2018).
Fodor, E. & Te Velthuis, A. J. W. Structure and function of the influenza virus transcription and replication machinery. Cold Spring Harb. Perspect. Med. 10, a038398 (2019).
Wandzik, J. M., Kouba, T. & Cusack, S. Structure and function of influenza polymerase. Cold Spring Harb. Perspect. Med. 10, a038372 (2020).
Long, J. S. et al. Species difference in ANP32A underlies influenza A virus polymerase host restriction. Nature 529, 101–104 (2016).
Walker, A. P. & Fodor, E. Interplay between influenza virus and the host RNA polymerase II transcriptional machinery. Trends Microbiol. 27, 398–407 (2019).
Peacock, T. P., Sheppard, C. M., Staller, E. & Barclay, W. S. Host determinants of influenza RNA synthesis. Annu. Rev. Virol. 6, 215–233 (2019).
Staller, E. et al. ANP32 proteins are essential for influenza virus replication in human cells. J. Virol. 93, e00217-19 (2019).
Zhang, H. et al. Fundamental contribution and host range determination of ANP32A and ANP32B in influenza A virus polymerase activity. J. Virol. 93, e00174-19 (2019).
Huyton, T. & Wolberger, C. The crystal structure of the tumor suppressor protein pp32 (Anp32a): structural insights into Anp32 family of proteins. Protein Sci. 16, 1308–1315 (2007).
Hengrung, N. et al. Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Nature 527, 114–117 (2015).
Thierry, E. et al. Influenza polymerase can adopt an alternative configuration involving a radical repacking of PB2 domains. Mol. Cell 61, 125–137 (2016).
Fan, H. et al. Structures of influenza A virus RNA polymerase offer insight into viral genome replication. Nature 573, 287–290 (2019).
Pflug, A., Guilligay, D., Reich, S. & Cusack, S. Structure of influenza A polymerase bound to the viral RNA promoter. Nature 516, 355–360 (2014).
Peng, Q. et al. Structural insight into RNA synthesis by influenza D polymerase. Nat. Microbiol. 4, 1750–1759 (2019).
Wandzik, J.M. et al. A structure-based model for the complete transcription cycle of influenza polymerase. Cell 181, 877–893 (2020).
Chang, S. et al. Cryo-EM structure of influenza virus RNA polymerase complex at 4.3 Å resolution. Mol. Cell 57, 925–935 (2015).
Long, J. S. et al. Species specific differences in use of ANP32 proteins by influenza A virus. eLife 8, e45066 (2019).
Bi, Z. et al. Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Emerg. Microbes Infect. 8, 1465–1478 (2019).
Zhang, H. et al. A unique feature of swine ANP32A provides susceptibility to avian influenza virus infection in pigs. PLoS Pathog. 16, e1008330 (2020).
Baker, S.F., Ledwith, M.P. & Mehle, A. Differential splicing of ANP32A in birds alters its ability to stimulate rna synthesis by restricted influenza polymerase. Cell Rep. 24, 2581–2588 (2018).
Camacho-Zarco, A. R. et al. Molecular basis of host-adaptation interactions between influenza virus polymerase PB2 subunit and ANP32A. Nat. Commun. 11, 3656 (2020).
Mistry, B. et al. Elucidating the interactions between influenza virus polymerase and host factor ANP32A. J. Virol. 94, e01353-19 (2020).
Domingues, P. & Hale, B. G. Functional insights into ANP32A-dependent influenza A virus polymerase host restriction. Cell Rep. 20, 2538–2546 (2017).
Mehle, A. & Doudna, J. A. Adaptive strategies of the influenza virus polymerase for replication in humans. Proc. Natl Acad. Sci. USA 106, 21312–21316 (2009).
Yamada, S. et al. Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog. 6, e1001034 (2010).
Chin, A. W. H. et al. Influenza A viruses with different amino acid residues at PB2-627 display distinct replication properties in vitro and in vivo: revealing the sequence plasticity of PB2-627 position. Virology 468–470, 545–555 (2014).
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).
Nilsson, B. E., Te Velthuis, A. J. W. & Fodor, E. Role of the PB2 627 domain in influenza A virus polymerase function. J. Virol. 91, e02467-16 (2017).
Mänz, B., Brunotte, L., Reuther, P. & Schwemmle, M. Adaptive mutations in NEP compensate for defective H5N1 RNA replication in cultured human cells. Nat. Commun. 3, 802 (2012).
Sugiyama, K., Kawaguchi, A., Okuwaki, M. & Nagata, K. pp32 and APRIL are host cell-derived regulators of influenza virus RNA synthesis from cRNA. eLife 4, e08939 (2015).
Pan, J. et al. Structure of the human metapneumovirus polymerase phosphoprotein complex. Nature 577, 275–279 (2020).
Lukarska, M. et al. Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Nature 541, 117–121 (2017).
Serna Martin, I. et al. A mechanism for the activation of the influenza virus transcriptase. Mol. Cell 70, 1101–1110 (2018).
Chen, K. Y., Santos Afonso, E. D., Enouf, V., Isel, C. & Naffakh, N. Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. PLoS Pathog. 15, e1008034 (2019).
Killip, M. J., Fodor, E. & Randall, R. E. Influenza virus activation of the interferon system. Virus Res. 209, 11–22 (2015).
Bieniossek, C., Imasaki, T., Takagi, Y. & Berger, I. MultiBac: expanding the research toolbox for multiprotein complexes. Trends Biochem. Sci. 37, 49–57 (2012).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
Naydenova, K. & Russo, C. J. Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy. Nat. Commun. 8, 629 (2017).
Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
Jakobi, A. J., Wilmanns, M. & Sachse, C. Model-based local density sharpening of cryo-EM maps. eLife 6, e27131 (2017).
Burnley, T. Introducing the Proceedings of the CCP-EM Spring Symposium. Acta Crystallogr. D 73, 467–468 (2017).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007).
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46 (W1), W296–W303 (2018).
Crescenzo-Chaigne, B., Naffakh, N. & van der Werf, S. Comparative analysis of the ability of the polymerase complexes of influenza viruses type A, B and C to assemble into functional RNPs that allow expression and replication of heterotypic model RNA templates in vivo. Virology 265, 342–353 (1999).
Tang, Y. S., Lo, C. Y., Mok, C. K., Chan, P. K. & Shaw, P. C. The extended C-terminal region of influenza C virus nucleoprotein is important for nuclear import and ribonucleoprotein activity. J. Virol. 93, e02048-18 (2019).
Fodor, E. et al. A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs. J. Virol. 76, 8989–9001 (2002).
Fodor, E. et al. Rescue of influenza A virus from recombinant DNA. J. Virol. 73, 9679–9682 (1999).
Paterson, D., te Velthuis, A. J., Vreede, F. T. & Fodor, E. Host restriction of influenza virus polymerase activity by PB2 627E is diminished on short viral templates in a nucleoprotein-independent manner. J. Virol. 88, 339–344 (2014).
Robb, N. C., Smith, M., Vreede, F. T. & Fodor, E. NS2/NEP protein regulates transcription and replication of the influenza virus RNA genome. J. Gen. Virol. 90, 1398–1407 (2009).
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).
Vreede, F. T. & Brownlee, G. G. Influenza virion-derived viral ribonucleoproteins synthesize both mRNA and cRNA in vitro. J. Virol. 81, 2196–2204 (2007).
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
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).
Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, W320–W324 (2014).