1887

Abstract

Toscana virus (TOSV) is an arthropod-borne phlebovirus within the family in the order . It seems to be an important agent of human meningoencephalitis in the warm season in the Mediterranean area. Because the polymerase of lacks a capping activity, it cleaves short-capped RNA leaders derived from the host cell, and uses them to initiate viral mRNA synthesis. To determine the size and nucleotide composition of the host-derived RNA leaders, and to elucidate the first steps of TOSV transcription initiation, we performed a high-throughput sequencing of the 5′ end of TOSV mRNAs in infected cells at different times post-infection. Our results indicated that the viral polymerase cleaved the host-capped RNA leaders within a window of 11–16 nucleotides. A single population of cellular mRNAs could be cleaved at different sites to prime the synthesis of several viral mRNA species. The majority of the mRNA resulted from direct priming, but we observed mRNAs resulting from several rounds of prime-and-realign events. Our data suggest that the different rounds of the prime-and-realign mechanism result from the blocking of the template strand in a static position in the active site, leading to the slippage of the nascent strand by two nucleotides when the growing duplex is sorted out from the active site. To minimize this rate-limiting step, TOSV polymerase cleaves preferentially capped RNA leaders after GC, so as to greatly reduce the number of cycles of priming and realignment, and facilitate the separation of the growing duplex.

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2017-11-01
2019-12-09
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References

  1. Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL et al. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017). Arch Virol 2017;162:2505–2538 [CrossRef][PubMed]
    [Google Scholar]
  2. Verani P, Ciufolini MG, Nicoletti L, Balducci M, Sabatinelli G et al. [Ecological and epidemiological studies of Toscana virus, an arbovirus isolated from Phlebotomus]. Ann Ist Super Sanita 1982;18:397–399[PubMed]
    [Google Scholar]
  3. Verani P, Nicoletti L, Ciufolini MG. Antigenic and biological characterization of Toscana virus, a new Phlebotomus fever group virus isolated in Italy. Acta Virol 1984;28:39–47[PubMed]
    [Google Scholar]
  4. Verani P, Ciufolini MG, Caciolli S, Renzi A, Nicoletti L et al. Ecology of viruses isolated from sand flies in Italy and characterized of a new Phlebovirus (Arabia virus). Am J Trop Med Hyg 1988;38:433–439 [CrossRef][PubMed]
    [Google Scholar]
  5. Charrel RN, Izri A, Temmam S, de Lamballerie X, Parola P. Toscana virus RNA in Sergentomyia minuta files. Emerg Infect Dis 2006;12:1299–1300 [CrossRef][PubMed]
    [Google Scholar]
  6. Charrel RN, Bichaud L, de Lamballerie X. Emergence of Toscana virus in the mediterranean area. World J Virol 2012;1:135–141 [CrossRef][PubMed]
    [Google Scholar]
  7. Elliott RM. Emerging viruses: the Bunyaviridae. Mol Med 1997;3:572–577[PubMed]
    [Google Scholar]
  8. Giorgi C, Accardi L, Nicoletti L, Gro MC, Takehara K et al. Sequences and coding strategies of the S RNAs of Toscana and rift valley fever viruses compared to those of Punta toro, sicilian sandfly fever, and Uukuniemi viruses. Virology 1991;180:738–753 [CrossRef][PubMed]
    [Google Scholar]
  9. di Bonito P, Mochi S, Grò MC, Fortini D, Giorgi C. Organization of the M genomic segment of Toscana phlebovirus. J Gen Virol 1997;78:77–81 [CrossRef][PubMed]
    [Google Scholar]
  10. Suzich JA, Kakach LT, Collett MS. Expression strategy of a phlebovirus: biogenesis of proteins from the Rift Valley fever virus M segment. J Virol 1990;64:1549–1555[PubMed]
    [Google Scholar]
  11. Gerrard SR, Nichol ST. Synthesis, proteolytic processing and complex formation of N-terminally nested precursor proteins of the Rift Valley fever virus glycoproteins. Virology 2007;357:124–133 [CrossRef][PubMed]
    [Google Scholar]
  12. Accardi L, Grò MC, di Bonito P, Giorgi C. Toscana virus genomic L segment: molecular cloning, coding strategy and amino acid sequence in comparison with other negative strand RNA viruses. Virus Res 1993;27:119–131 [CrossRef][PubMed]
    [Google Scholar]
  13. Amroun A, Priet S, Lamballerie de X, Querat G. Structure Bunyaviridae Rdrps: motifs, and RNA synthesis machinery. Crit Rev Microbiol 2017;1–26
    [Google Scholar]
  14. Shatkin AJ, Manley JL. The ends of the affair: capping and polyadenylation. Nat Struct Biol 2000;7:838–842 [CrossRef][PubMed]
    [Google Scholar]
  15. Moteki S, Price D. Functional coupling of capping and transcription of mRNA. Mol Cell 2002;10:599–609 [CrossRef][PubMed]
    [Google Scholar]
  16. Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res 2016;44:7511–7526 [CrossRef][PubMed]
    [Google Scholar]
  17. Bouloy M, Plotch SJ, Krug RM. Globin mRNAs are primers for the transcription of influenza viral RNA in vitro. Proc Natl Acad Sci USA 1978;75:4886–4890 [CrossRef][PubMed]
    [Google Scholar]
  18. Plotch SJ, Bouloy M, Ulmanen I, Krug RM. A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell 1981;23:847–858 Epub 1981/03/01 [CrossRef][PubMed]
    [Google Scholar]
  19. Raju R, Raju L, Hacker D, Garcin D, Compans R et al. Nontemplated bases at the 5′ ends of Tacaribe virus mRNAs. Virology 1990;174:53–59 Epub 1990/01/01 [CrossRef][PubMed]
    [Google Scholar]
  20. Huiet L, Feldstein PA, Tsai JH, Falk BW. The maize stripe virus major noncapsid protein messenger RNA transcripts contain heterogeneous leader sequences at their 5′ termini. Virology 1993;197:808–812 [CrossRef][PubMed]
    [Google Scholar]
  21. Walia JJ, Falk BW. Fig mosaic virus mRNAs show generation by cap-snatching. Virology 2012;426:162–166 [CrossRef][PubMed]
    [Google Scholar]
  22. Morin B, Coutard B, Lelke M, Ferron F, Kerber R et al. The N-terminal domain of the arenavirus L protein is an RNA endonuclease essential in mRNA transcription. PLoS Pathog 2010;6:e1001038 [CrossRef][PubMed]
    [Google Scholar]
  23. Dias A, Bouvier D, Crépin T, Mccarthy AA, Hart DJ et al. The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit. Nature 2009;458:914–918 [CrossRef][PubMed]
    [Google Scholar]
  24. Reguera J, Weber F, Cusack S. Bunyaviridae RNA polymerases (L-protein) have an N-terminal, influenza-like endonuclease domain, essential for viral cap-dependent transcription. PLoS Pathog 2010;6:e1001101 [CrossRef][PubMed]
    [Google Scholar]
  25. Bouloy M, Pardigon N, Vialat P, Gerbaud S, Girard M. Characterization of the 5' and 3' ends of viral messenger RNAs isolated from BHK21 cells infected with Germiston virus (Bunyavirus). Virology 1990;175:50–58 [CrossRef][PubMed]
    [Google Scholar]
  26. Jin H, Elliott RM. Characterization of Bunyamwera virus S RNA that is transcribed and replicated by the L protein expressed from recombinant vaccinia virus. J Virol 1993;67:1396–1404[PubMed]
    [Google Scholar]
  27. Garcin D, Lezzi M, Dobbs M, Elliott RM, Schmaljohn C et al. The 5' ends of Hantaan virus (Bunyaviridae) RNAs suggest a prime-and-realign mechanism for the initiation of RNA synthesis. J Virol 1995;69:5754–5762[PubMed]
    [Google Scholar]
  28. Simons JF, Pettersson RF. Host-derived 5' ends and overlapping complementary 3' ends of the two mRNAs transcribed from the ambisense S segment of Uukuniemi virus. J Virol 1991;65:4741–4748[PubMed]
    [Google Scholar]
  29. Coupeau D, Claine F, Wiggers L, Martin B, Kirschvink N et al. Characterization of messenger RNA termini in Schmallenberg virus and related Simbuviruses. J Gen Virol 2013;94:2399–2405 [CrossRef][PubMed]
    [Google Scholar]
  30. Bishop DH, Gay ME, Matsuoko Y. Nonviral heterogeneous sequences are present at the 5' ends of one species of snowshoe hare bunyavirus S complementary RNA. Nucleic Acids Res 1983;11:6409–6418 Epub 1983/09/24 [CrossRef][PubMed]
    [Google Scholar]
  31. Dhar R, Chanock RM, Lai CJ. Nonviral oligonucleotides at the 5' terminus of cytoplasmic influenza viral mRNA deduced from cloned complete genomic sequences. Cell 1980;21:495–500 [CrossRef][PubMed]
    [Google Scholar]
  32. Sikora D, Rocheleau L, Brown EG, Pelchat M. Deep sequencing reveals the eight facets of the influenza A/HongKong/1/1968 (H3N2) virus cap-snatching process. Sci Rep 2014;4:6181 [CrossRef][PubMed]
    [Google Scholar]
  33. Duijsings D, Kormelink R, Goldbach R. Alfalfa mosaic virus RNAs serve as cap donors for tomato spotted wilt virus transcription during coinfection of Nicotiana benthamiana. J Virol 1999;73:5172–5175[PubMed]
    [Google Scholar]
  34. Duijsings D, Kormelink R, Goldbach R. In vivo analysis of the TSWV cap-snatching mechanism: single base complementarity and primer length requirements. EMBO J 2001;20:2545–2552 Epub 2001/05/15 [CrossRef][PubMed]
    [Google Scholar]
  35. Shimizu T, Toriyama S, Takahashi M, Akutsu K, Yoneyama K. Non-viral sequences at the 5' termini of mRNAs derived from virus-sense and virus-complementary sequences of the ambisense RNA segments of rice stripe tenuivirus. J Gen Virol 1996;77:541–546 [CrossRef][PubMed]
    [Google Scholar]
  36. Jin H, Elliott RM. Non-viral sequences at the 5' ends of Dugbe nairovirus S mRNAs. J Gen Virol 1993;74:2293–2297 [CrossRef][PubMed]
    [Google Scholar]
  37. Yao M, Zhang T, Zhou T, Zhou Y, Zhou X et al. Repetitive prime-and-realign mechanism converts short capped RNA leaders into longer ones that may be more suitable for elongation during rice stripe virus transcription initiation. J Gen Virol 2012;93:194–202 [CrossRef][PubMed]
    [Google Scholar]
  38. van Knippenberg I, Lamine M, Goldbach R, Kormelink R. Tomato spotted wilt virus transcriptase in vitro displays a preference for cap donors with multiple base complementarity to the viral template. Virology 2005;335:122–130 [CrossRef][PubMed]
    [Google Scholar]
  39. Grò MC, di Bonito P, Accardi L, Giorgi C. Analysis of 3' and 5' ends of N and NSs messenger RNAs of Toscana Phlebovirus. Virology 1992;191:435–438 Epub 1992/11/01 [CrossRef][PubMed]
    [Google Scholar]
  40. Hagen M, Tiley L, Chung TD, Krystal M. The role of template-primer interactions in cleavage and initiation by the influenza virus polymerase. J Gen Virol 1995;76:603–611 [CrossRef][PubMed]
    [Google Scholar]
  41. Rao P, Yuan W, Krug RM. Crucial role of CA cleavage sites in the cap-snatching mechanism for initiating viral mRNA synthesis. EMBO J 2003;22:1188–1198 [CrossRef][PubMed]
    [Google Scholar]
  42. Geerts-Dimitriadou C, Goldbach R, Kormelink R. Preferential use of RNA leader sequences during influenza A transcription initiation in vivo. Virology 2011;409:27–32 [CrossRef][PubMed]
    [Google Scholar]
  43. Geerts-Dimitriadou C, Zwart MP, Goldbach R, Kormelink R. Base-pairing promotes leader selection to prime in vitro influenza genome transcription. Virology 2011;409:17–26 [CrossRef][PubMed]
    [Google Scholar]
  44. Liu X, Xiong G, Qiu P, du Z, Kormelink R et al. Inherent properties not conserved in other tenuiviruses increase priming and realignment cycles during transcription of Rice stripe virus. Virology 2016;496:287–298 [CrossRef][PubMed]
    [Google Scholar]
  45. Koppstein D, Ashour J, Bartel DP. Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation. Nucleic Acids Res 2015;43:5052–5064 Epub 2015/04/23 [CrossRef][PubMed]
    [Google Scholar]
  46. Shih SR, Krug RM. Surprising function of the three influenza viral polymerase proteins: selective protection of viral mRNAs against the cap-snatching reaction catalyzed by the same polymerase proteins. Virology 1996;226:430–435 [CrossRef][PubMed]
    [Google Scholar]
  47. Reguera J, Gerlach P, Cusack S. Towards a structural understanding of RNA synthesis by negative strand RNA viral polymerases. Curr Opin Struct Biol 2016;36:75–84 [CrossRef][PubMed]
    [Google Scholar]
  48. Gerlach P, Malet H, Cusack S, Reguera J. Structural insights into Bunyavirus replication and its regulation by the vRNA promoter. Cell 2015;161:1267–1279 Epub 2015/05/26 [CrossRef][PubMed]
    [Google Scholar]
  49. Reich S, Guilligay D, Pflug A, Malet H, Berger I et al. Structural insight into cap-snatching and RNA synthesis by influenza polymerase. Nature 2014;516:361–366 Epub 2014/11/20 [CrossRef][PubMed]
    [Google Scholar]
  50. Gong P, Peersen OB. Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase. Proc Natl Acad Sci USA 2010;107:22505–22510 [CrossRef][PubMed]
    [Google Scholar]
  51. Prehaud C, Lopez N, Blok MJ, Obry V, Bouloy M. Analysis of the 3' terminal sequence recognized by the Rift Valley fever virus transcription complex in its ambisense S segment. Virology 1997;227:189–197 [CrossRef][PubMed]
    [Google Scholar]
  52. Kranzusch PJ, Schenk AD, Rahmeh AA, Radoshitzky SR, Bavari S et al. Assembly of a functional Machupo virus polymerase complex. Proc Natl Acad Sci USA 2010;107:20069–20074 [CrossRef][PubMed]
    [Google Scholar]
  53. Kolakofsky D. dsRNA-ended genomes in orthobunyavirus particles and infected cells. Virology 2016;489:192–193 [CrossRef][PubMed]
    [Google Scholar]
  54. Varani G, Mcclain WH. The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep 2000;1:18–23 [CrossRef][PubMed]
    [Google Scholar]
  55. Xu D, Landon T, Greenbaum NL, Fenley MO. The electrostatic characteristics of G.U wobble base pairs. Nucleic Acids Res 2007;35:3836–3847 [CrossRef][PubMed]
    [Google Scholar]
  56. Marklewitz M, Zirkel F, Kurth A, Drosten C, Junglen S. Evolutionary and phenotypic analysis of live virus isolates suggests arthropod origin of a pathogenic RNA virus family. Proc Natl Acad Sci USA 2015;112:7536–7541 Epub 2015/06/04 [CrossRef][PubMed]
    [Google Scholar]
  57. Bichaud L, Dachraoui K, Piorkowski G, Chelbi I, Moureau G et al. Toscana virus isolated from sandflies, Tunisia. Emerg Infect Dis 2013;19:322–324 [CrossRef][PubMed]
    [Google Scholar]
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