Cited by 32Influenza Virus Research StudiesVirology and Viral DiseasesViral Infectious Diseases and Gene Expression in Insects

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Phosphorylation controls RNA binding and transcription by the influenza virus polymerase

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Abstract

The influenza virus polymerase transcribes and replicates the viral genome. The proper timing and balance of polymerase activity is important for successful replication. Genome replication is controlled in part by phosphorylation of NP that regulates assembly of the replication machinery. However, it remains unclear whether phosphorylation directly regulated polymerase activity. Here we identified polymerase phosphosites that control its function. Mutating phosphosites in the catalytic subunit PB1 altered polymerase activity and virus replication. Biochemical analyses revealed phosphorylation events that disrupted global polymerase function by blocking the NTP entry channel or preventing RNA binding. We also identified a regulatory site that split polymerase function by specifically suppressing transcription. These experiments show that host kinases phospho-regulate viral RNA synthesis directly by modulating polymerase activity and indirectly by controlling assembly of replication machinery. Further, they suggest polymerase phosphorylation may bias replication versus transcription at discrete times or locations during the infectious cycle.

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Research works printed but not linked: 61

  1. N Biedenkopf, 2016, Dynamic Phosphorylation of VP30 Is Essential for Ebola Virus Life Cycle, J Virol, 90, 4914, 10.1128/JVI.03257-15 · DOI
  2. B Tigabu, 2018, Phosphorylated VP30 of Marburg Virus Is a Repressor of Transcription, J Virol, 92, e00426, 10.1128/JVI.00426-18 · DOI
  3. TL Cartee, 2001, Respiratory Syncytial Virus M2-1 Protein Requires Phosphorylation for Efficient Function and Binds Viral RNA during Infection, J Virol, 75, 12188 LP, 10.1128/JVI.75.24.12188-12197.2001 · DOI
  4. C-A Richard, 2018, RSV hijacks cellular protein phosphatase 1 to regulate M2-1 phosphorylation and viral transcription, PLOS Pathog, 14, e1006920, 10.1371/journal.ppat.1006920 · DOI
  5. L Chen, 2013, N-terminal phosphorylation of phosphoprotein of vesicular stomatitis virus is required for preventing nucleoprotein from binding to cellular RNAs and for functional template formation, J Virol, 87, 3177, 10.1128/JVI.02761-12 · DOI
  6. A Mondal, 2014, Newly Identified Phosphorylation Site in the Vesicular Stomatitis Virus P Protein Is Required for Viral RNA Synthesis, J Virol, 88, 1461, 10.1128/JVI.02384-13 · DOI
  7. R Arranz, 2012, The structure of native influenza virion ribonucleoproteins, Science (80-), 338, 1634, 10.1126/science.1228172 · DOI
  8. K Klumpp, 1997, Roles of the influenza virus polymerase and nucleoprotein in forming a functional RNP structure, EMBO J, 16, 1248, 10.1093/emboj/16.6.1248 · DOI
  9. A Moeller, 2012, Organization of the influenza virus replication machinery, Science (80-), 338, 1631, 10.1126/science.1227270 · DOI
  10. MW Pons, 1969, Isolation and characterization of the ribonucleoprotein of influenza virus, Virology, 39, 250, 10.1016/0042-6822(69)90045-2 · DOI
  11. C Herz, 1981, Influenza virus, an RNA virus, synthesizes its messenger RNA in the nucleus of infected cells, Cell, 26, 391, 10.1016/0092-8674(81)90208-7 · DOI
  12. DA Jackson, 1982, Influenza virus RNA is synthesized at fixed sites in the nucleus, Nature, 296, 366, 10.1038/296366a0 · DOI
  13. M Bouloy, 1978, Globin mRNAs are primers for the transcription of influenza viral RNA in vitro, Proc Natl Acad Sci, 75, 4886, 10.1073/pnas.75.10.4886 · DOI
  14. SJ Plotch, 1979, Transfer of 5’-terminal cap of globin mRNA to influenza viral complementary RNA during transcription in vitro, Proc Natl Acad Sci, 76, 1618, 10.1073/pnas.76.4.1618 · DOI
  15. AJ Hay, 1977, Transcription of the influenza virus genome, Virology, 83, 337, 10.1016/0042-6822(77)90179-9 · DOI
  16. FT Vreede, 2004, Model Suggesting that Replication of Influenza Virus Is Regulated by Stabilization of Replicative Intermediates, J Virol, 78, 9568, 10.1128/JVI.78.17.9568-9572.2004 · DOI
  17. N Jorba, 2009, Genetic trans-complementation establishes a new model for influenza virus RNA transcription and replication, PLoS Pathog, 5, e1000462, 10.1371/journal.ppat.1000462 · DOI
  18. H Fan, 2019, Structures of influenza A virus RNA polymerase offer insight into viral genome replication, Nature
  19. A York, 2013, Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus, Proc Natl Acad Sci U S A, 110, E4238, 10.1073/pnas.1315068110 · DOI
  20. S Chang, 2015, Cryo-EM structure of influenza virus RNA polymerase complex at 4.3 Å resolution, Mol Cell, 57, 925, 10.1016/j.molcel.2014.12.031 · DOI
  21. Q Peng, 2019, Structural insight into RNA synthesis by influenza D polymerase, Nat Microbiol, 4, 1750, 10.1038/s41564-019-0487-5 · DOI
  22. JT Perez, 2010, Influenza A virus-generated small RNAs regulate the switch from transcription to replication, Proc Natl Acad Sci U S A
  23. NC Robb, 2009, NS2/NEP protein regulates transcription and replication of the influenza virus RNA genome, J Gen Virol, 90, 1398, 10.1099/vir.0.009639-0 · DOI
  24. AR Dawson, 2018, Flu’s cues: Exploiting host post-translational modifications to direct the influenza virus replication cycle, PLoS Pathog, 14, e1007205, 10.1371/journal.ppat.1007205 · DOI
  25. AR Dawson, 2020, Post-Translation Regulation of Influenza Virus Replication, Annu Rev Virol
  26. A Mondal, 2015, Phosphorylation at the homotypic interface regulates nucleoprotein oligomerization and assembly of the influenza virus replication machinery, PLoS Pathog, 11, e1004826, 10.1371/journal.ppat.1004826 · DOI
  27. A Mondal, 2017, Influenza virus recruits host protein kinase C to control assembly and activity of its replication machinery, Elife, 6, e26910, 10.7554/eLife.26910 · DOI
  28. L Cui, 2018, CDC25B promotes influenza A virus replication by regulating the phosphorylation of nucleoprotein, Virology, 525, 40, 10.1016/j.virol.2018.09.005 · DOI
  29. Q Yang, 2019, The Role of Tyrosine Phosphorylation of Protein Kinase C Delta in Infection and Inflammation, Int J Mol Sci, 20
  30. J Durgan, 2007, Novel phosphorylation site markers of protein kinase C delta activation, FEBS Lett, 581, 3377, 10.1016/j.febslet.2007.06.035 · DOI
  31. M Blass, 2002, Tyrosine phosphorylation of protein kinase Cdelta is essential for its apoptotic effect in response to etoposide, Mol Cell Biol, 22, 182, 10.1128/MCB.22.1.182-195.2002 · DOI
  32. TA DeVries, 2002, Nuclear import of PKCdelta is required for apoptosis: identification of a novel nuclear import sequence, EMBO J, 21, 6050, 10.1093/emboj/cdf606 · DOI
  33. L Turrell, 2013, The role and assembly mechanism of nucleoprotein in influenza A virus ribonucleoprotein complexes, Nat Commun, 4, 1511, 10.1038/ncomms2589 · DOI
  34. S Reich, 2014, Structural insight into cap-snatching and RNA synthesis by influenza polymerase, Nature, 516, 361, 10.1038/nature14009 · DOI
  35. H Fan, 2019, Structures of influenza A virus RNA polymerase offer insight into viral genome replication, Nature, 573, 287, 10.1038/s41586-019-1530-7 · DOI
  36. JM Wandzik, 2020, A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase, Cell
  37. PS Kerry, 2008, A cluster of conserved basic amino acids near the C-terminus of the PB1 subunit of the influenza virus RNA polymerase is involved in the regulation of viral transcription, Virology, 373, 202, 10.1016/j.virol.2007.11.030 · DOI
  38. E Fodor, 2019, Structure and Function of the Influenza Virus Transcription and Replication Machinery, Cold Spring Harb Perspect Med
  39. T Deng, 2005, In vitro assembly of PB2 with a PB1-PA dimer supports a new model of assembly of influenza A virus polymerase subunits into a functional trimeric complex, J Virol, 79, 8669, 10.1128/JVI.79.13.8669-8674.2005 · DOI
  40. JM Wandzik, 2020, Structure and Function of Influenza Polymerase, Cold Spring Harb Perspect Med
  41. S Reich, 2017, An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase, Nucleic Acids Res, 45, 3353
  42. A Weber, 2019, Phosphoproteome Analysis of Cells Infected with Adapted and Nonadapted Influenza A Virus Reveals Novel Pro- and Antiviral Signaling Networks, J Virol, 93, 10.1128/JVI.00528-19 · DOI
  43. A Pflug, 2014, Structure of influenza A polymerase bound to the viral RNA promoter, Nature, 516, 355, 10.1038/nature14008 · DOI
  44. E Fodor, 2002, 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, 10.1128/JVI.76.18.8989-9001.2002 · DOI
  45. T Kouba, 2019, Structural snapshots of actively transcribing influenza polymerase, Nat Struct Mol Biol, 26, 460, 10.1038/s41594-019-0232-z · DOI
  46. OG Engelhardt, 2005, Association of the influenza A virus RNA-dependent RNA polymerase with cellular RNA polymerase II, J Virol, 79, 5812, 10.1128/JVI.79.9.5812-5818.2005 · DOI
  47. A Mehle, 2008, Inhibitory activity restricts the function of an avian-like influenza polymerase in primate cells, Cell Host Microbe, 4, 111, 10.1016/j.chom.2008.06.007 · DOI
  48. J-W Soh, 2003, Roles of Specific Isoforms of Protein Kinase C in the Transcriptional Control of Cyclin D1 and Related Genes, J Biol Chem, 278, 34709, 10.1074/jbc.M302016200 · DOI
  49. G Neumann, 2005, An improved reverse genetics system for influenza A virus generation and its implications for vaccine production, Proc Natl Acad Sci U S A, 102, 16825, 10.1073/pnas.0505587102 · DOI
  50. E Dos Santos Afonso, 2005, The generation of recombinant influenza A viruses expressing a PB2 fusion protein requires the conservation of a packaging signal overlapping the coding and noncoding regions at the 5′ end of the PB2 segment, Virology, 341, 34, 10.1016/j.virol.2005.06.040 · DOI
  51. JW Yewdell, 1981, Expression of influenza A virus internal antigens on the surface of infected P815 cells, J Immunol, 126, 1814, 10.4049/jimmunol.126.5.1814 · DOI
  52. GP Larson, 2019, EPS8 Facilitates Uncoating of Influenza A Virus, Cell Rep, 29, 2175, 10.1016/j.celrep.2019.10.064 · DOI
  53. SF Baker, 2018, Differential Splicing of ANP32A in Birds Alters Its Ability to Stimulate RNA Synthesis by Restricted Influenza Polymerase, Cell Rep, 24, 2581, 10.1016/j.celrep.2018.08.012 · DOI
  54. J Kirui, 2016, Ubiquitination up-regulates influenza virus polymerase function, J Virol, 90, 10906, 10.1128/JVI.01829-16 · DOI
  55. J Cox, 2011, Andromeda: A peptide search engine integrated into the MaxQuant environment, J Proteome Res, 10, 1794, 10.1021/pr101065j · DOI
  56. JE Elias, 2007, Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry, Nat Methods, 4, 207, 10.1038/nmeth1019 · DOI · Paper page
  57. J Cox, 2014, Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ, Mol Cell Proteomics, 13, 2513, 10.1074/mcp.M113.031591 · DOI · Paper page
  58. Y Zhang, 2017, Influenza Research Database: An integrated bioinformatics resource for influenza virus research, Nucleic Acids Res, 45, D466, 10.1093/nar/gkw857 · DOI
  59. R Fraczkiewicz, 1998, Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules, J Comput Chem, 19, 319, 10.1002/(SICI)1096-987X(199802)19:3<319::AID-JCC6>3.0.CO;2-W · DOI
  60. J Kirui, 2014, Conserved features of the PB2 627 domain impact influenza virus polymerase function and replication, J Virol, 88, 5977, 10.1128/JVI.00508-14 · DOI
  61. FT Vreede, 2011, Stabilization of Influenza Virus Replication Intermediates Is Dependent on the RNA-Binding but Not the Homo-Oligomerization Activity of the Viral Nucleoprotein, J Virol, 85, 12073, 10.1128/JVI.00695-11 · DOI

Metadata

Authors
Dawson, A. R., Wilson, G. M., Freiberger, E. C., Mondal, A., Coon, J. J., & Mehle, A.
Affiliations
University of Wisconsin–Madison (US)
Corresponding author
Mehle, Andrew
Venue
PLOS Pathogens
Published
2020-09-03
Volume
16
Issue
9
Pages
e1008841
ISSN
  • 1553-7366 (ISSN-L)
  • 1553-7374
OpenAlex
W3083493094
Cited by
32
References
2
Citations by year
2026: 4 · 2025: 9 · 2024: 4 · 2023: 9 · 2022: 3 · 2021: 3
FWCI
2.69
Type
journal article
Language
en
Open access
Locations
  • PLoS Pathogens (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Institute of Allergy and Infectious Diseases (R01AI125271, T32AI078985)
  • National Institute of General Medical Sciences (R35GM118110, T32GM008349)
  • Burroughs Wellcome Fund (Investigator in the Pathogenesis of Disease)
Topics
  • Health Sciences › Medicine › Epidemiology › Influenza Virus Research Studies
  • Health Sciences › Medicine › Epidemiology › Virology and Viral Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
Keywords
protein phosphorylation, phosphosites, RNA binding, viral transcription, viral genome replication
MeSH terms
A549 Cells, Animals, Dogs, Humans, Influenza A virus, Phosphorylation, RNA, Viral, Transcription, Genetic, Viral Proteins, Virus Replication, HEK293 Cells, Madin Darby Canine Kidney Cells

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