1887

Abstract

A novel coronavirus is the causative agent of the current epidemic of severe acute respiratory syndrome (SARS). Coronaviruses are exceptionally large RNA viruses and employ complex regulatory mechanisms to express their genomes. Here, we determined the sequence of SARS coronavirus (SARS-CoV), isolate Frankfurt 1, and characterized key RNA elements and protein functions involved in viral genome expression. Important regulatory mechanisms, such as the (discontinuous) synthesis of eight subgenomic mRNAs, ribosomal frameshifting and post-translational proteolytic processing, were addressed. Activities of three SARS coronavirus enzymes, the helicase and two cysteine proteinases, which are known to be critically involved in replication, transcription and/or post-translational polyprotein processing, were characterized. The availability of recombinant forms of key replicative enzymes of SARS coronavirus should pave the way for high-throughput screening approaches to identify candidate inhibitors in compound libraries.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.19424-0
2003-09-01
2024-03-19
Loading full text...

Full text loading...

/deliver/fulltext/jgv/84/9/vir842305.html?itemId=/content/journal/jgv/10.1099/vir.0.19424-0&mimeType=html&fmt=ahah

References

  1. Anand K., Palm G. J., Mesters J. R., Siddell S. G., Ziebuhr J., Hilgenfeld R. 2002; Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J 21:3213–3224
    [Google Scholar]
  2. Anand K., Ziebuhr J., Wadhwani P., Mesters J. R., Hilgenfeld R. 2003; Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science 300:1763–1767
    [Google Scholar]
  3. Baker S. C., Shieh C. K., Soe L. H., Chang M. F., Vannier D. M., Lai M. M. 1989; Identification of a domain required for autoproteolytic cleavage of murine coronavirus gene A polyprotein. J Virol 63:3693–3699
    [Google Scholar]
  4. Bonilla P. J., Hughes S. A., Weiss S. R. 1997; Characterization of a second cleavage site and demonstration of activity in trans by the papain-like proteinase of the murine coronavirus mouse hepatitis virus strain A59. J Virol 71:900–909
    [Google Scholar]
  5. Bost A. G., Carnahan R. H., Lu X. T., Denison M. R. 2000; Four proteins processed from the replicase gene polyprotein of mouse hepatitis virus colocalize in the cell periphery and adjacent to sites of virion assembly. J Virol 74:3379–3387
    [Google Scholar]
  6. Brierley I. 1995; Ribosomal frameshifting viral RNAs. J Gen Virol 76:1885–1892
    [Google Scholar]
  7. Brierley I., Digard P., Inglis S. C. 1989; Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot. Cell 57:537–547
    [Google Scholar]
  8. de Haan C. A., Masters P. S., Shen X., Weiss S., Rottier P. J. 2002; The group-specific murine coronavirus genes are not essential, but their deletion, by reverse genetics, is attenuating in the natural host. Virology 296:177–189
    [Google Scholar]
  9. Drosten C., Gunther S., Preiser W. 23 other authors 2003; Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 348:1967–1976
    [Google Scholar]
  10. Eleouet J. F., Rasschaert D., Lambert P., Levy L., Vende P., Laude H. 1995; Complete sequence (20 kilobases) of the polyprotein-encoding gene 1 of transmissible gastroenteritis virus. Virology 206:817–822
    [Google Scholar]
  11. Fouchier R. A., Kuiken T., Schutten M. 7 other authors 2003; Aetiology: Koch's postulates fulfilled for SARS virus. Nature 423:240
    [Google Scholar]
  12. Gorbalenya A. E. 2001; Big nidovirus genome. When count and order of domains matter. Adv Exp Med Biol 494:1–17
    [Google Scholar]
  13. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1989a; Coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis. Nucleic Acids Res 17:4847–4861
    [Google Scholar]
  14. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1989b; Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res 17:4713–4730
    [Google Scholar]
  15. Gorbalenya A. E., Koonin E. V., Lai M. M. 1991; Putative papain-related thiol proteases of positive-strand RNA viruses. Identification of rubi- and aphthovirus proteases and delineation of a novel conserved domain associated with proteases of rubi-, alpha- and coronaviruses. FEBS Lett 288:201–205
    [Google Scholar]
  16. Hegyi A., Ziebuhr J. 2002; Conservation of substrate specificities among coronavirus main proteases. J Gen Virol 83:595–599
    [Google Scholar]
  17. Hegyi A., Friebe A., Gorbalenya A. E., Ziebuhr J. 2002; Mutational analysis of the active centre of coronavirus 3C-like proteases. J Gen Virol 83:581–593
    [Google Scholar]
  18. Herold J., Raabe T., Schelle-Prinz B., Siddell S. G. 1993; Nucleotide sequence of the human coronavirus 229E RNA polymerase locus. Virology 195:680–691
    [Google Scholar]
  19. Herold J., Gorbalenya A. E., Thiel V., Schelle B., Siddell S. G. 1998; Proteolytic processing at the amino terminus of human coronavirus 229E gene 1-encoded polyproteins: identification of a papain-like proteinase and its substrate. J Virol 72:910–918
    [Google Scholar]
  20. Heusipp G., Harms U., Siddell S. G., Ziebuhr J. 1997; Identification of an ATPase activity associated with a 71-kilodalton polypeptide encoded in gene 1 of the human coronavirus 229E. J Virol 71:5631–5634
    [Google Scholar]
  21. Kanjanahaluethai A., Baker S. C. 2000; Identification of mouse hepatitis virus papain-like proteinase 2 activity. J Virol 74:7911–7921
    [Google Scholar]
  22. Kocherhans R., Bridgen A., Ackermann M., Tobler K. 2001; Completion of the porcine epidemic diarrhoea coronavirus (PEDV) genome sequence. Virus Genes 23:137–144
    [Google Scholar]
  23. Ksiazek T. G., Erdman D., Goldsmith C. S. 23 other authors 2003; A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 348:1953–1966
    [Google Scholar]
  24. Lai M. M. C., Holmes K. V. 2001; Coronaviridae : the viruses and their replication. In Fields Virology , 4th edn. pp  1163–1185 Edited by Knipe D. M., Howley P. M. Philadelphia: Lippincott Williams & Wilkins;
    [Google Scholar]
  25. Lim K. P., Ng L. F., Liu D. X. 2000; Identification of a novel cleavage activity of the first papain-like proteinase domain encoded by open reading frame 1a of the coronavirus avian infectious bronchitis virus and characterization of the cleavage products. J Virol 74:1674–1685
    [Google Scholar]
  26. Liu D. X., Tibbles K. W., Cavanagh D., Brown T. D., Brierley I. 1995; Involvement of viral and cellular factors in processing of polyprotein encoded by ORF1a of the coronavirus IBV. Adv Exp Med Biol 380:413–421
    [Google Scholar]
  27. Marra M. A., Jones S. J., Astell C. R. 56 other authors 2003; The genome sequence of the SARS-associated coronavirus. Science 300:1399–1404
    [Google Scholar]
  28. Pasternak A. O., van den Born E., Spaan W. J., Snijder E. J. 2001; Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis. EMBO J 20:7220–7228
    [Google Scholar]
  29. Peiris J. S., Chu C. M., Cheng V. C. 14 other authors 2003a; Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study. Lancet 361:1767–1772
    [Google Scholar]
  30. Peiris J. S., Lai S. T., Poon L. L. 13 other authors 2003b; Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 361:1319–1325
    [Google Scholar]
  31. Rota P. A., Oberste M. S., Monroe S. S. 32 other authors 2003; Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300:1394–1399
    [Google Scholar]
  32. Ruan Y. J., Wei C. L., Ee A. L. 17 other authors 2003; Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet 361:1779–1785
    [Google Scholar]
  33. Sawicki S. G., Sawicki D. L. 1998; A new model for coronavirus transcription. Adv Exp Med Biol 440:215–219
    [Google Scholar]
  34. Schneider T. D., Stephens R. M. 1990; Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18:6097–6100
    [Google Scholar]
  35. Seybert A., Ziebuhr J., Siddell S. G. 1997; Expression and characterization of a recombinant murine coronavirus 3C-like proteinase. J Gen Virol 78:71–75
    [Google Scholar]
  36. Seybert A., Hegyi A., Siddell S. G., Ziebuhr J. 2000a; The human coronavirus 229E superfamily 1 helicase has RNA and DNA duplex-unwinding activities with 5′-to-3′ polarity. RNA 6:1056–1068
    [Google Scholar]
  37. Seybert A., van Dinten L. C., Snijder E. J., Ziebuhr J. 2000b; Biochemical characterization of the equine arteritis virus helicase suggests a close functional relationship between arterivirus and coronavirus helicases. J Virol 74:9586–9593
    [Google Scholar]
  38. Siddell S. G. 1995 The Coronaviridae New York: Plenum Press;
    [Google Scholar]
  39. Snijder E. J., Bredenbeek P. J., Dobbe J. C. 7 other authors 2003; Unique and conserved features of genome and proteome of SARS coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol (in press
  40. Thiel V., Siddell S. G. 1994; Internal ribosome entry in the coding region of murine hepatitis virus mRNA 5. J Gen Virol 75:3041–3046
    [Google Scholar]
  41. Thiel V., Rashtchian A., Herold J., Schuster D. M., Guan N., Siddell S. G. 1997; Effective amplification of 20-kb DNA by reverse transcription PCR. Anal Biochem 252:62–70
    [Google Scholar]
  42. Thiel V., Herold J., Schelle B., Siddell S. G. 2001; Infectious RNA transcribed in vitro from a cDNA copy of the human coronavirus genome cloned in vaccinia virus. J Gen Virol 82:1273–1281
    [Google Scholar]
  43. van Dinten L. C., van Tol H., Gorbalenya A. E., Snijder E. J. 2000; The predicted metal-binding region of the arterivirus helicase protein is involved in subgenomic mRNA synthesis, genome replication, and virion biogenesis. J Virol 74:5213–5223
    [Google Scholar]
  44. van Vliet A. L., Smits S. L., Rottier P. J., de Groot R. J. 2002; Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus. EMBO J 21:6571–6580
    [Google Scholar]
  45. Walker J. E., Saraste M., Runswick M. J., Gay N. J. 1982; Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1:945–951
    [Google Scholar]
  46. Yao Z., Jones D. H., Grose C. 1992; Site-directed mutagenesis of herpesvirus glycoprotein phosphorylation sites by recombination polymerase chain reaction. PCR Methods Appl 1:205–207
    [Google Scholar]
  47. Ziebuhr J., Siddell S. G. 1999; Processing of the human coronavirus 229E replicase polyproteins by the virus-encoded 3C-like proteinase: identification of proteolytic products and cleavage sites common to pp1a and pp1ab. J Virol 73:177–185
    [Google Scholar]
  48. Ziebuhr J., Herold J., Siddell S. G. 1995; Characterization of a human coronavirus (strain 229E) 3C-like proteinase activity. J Virol 69:4331–4338
    [Google Scholar]
  49. Ziebuhr J., Heusipp G., Siddell S. G. 1997; Biosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase. J Virol 71:3992–3997
    [Google Scholar]
  50. Ziebuhr J., Snijder E. J., Gorbalenya A. E. 2000; Virus-encoded proteinases and proteolytic processing in the Nidovirales . J Gen Virol 81:853–879
    [Google Scholar]
  51. Ziebuhr J., Thiel V., Gorbalenya A. E. 2001; The autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond. J Biol Chem 276:33220–33232
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.19424-0
Loading
/content/journal/jgv/10.1099/vir.0.19424-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error