1887

Abstract

The arterivirus family (order ) of single-stranded, positive-sense RNA viruses includes porcine respiratory and reproductive syndrome virus and equine arteritis virus (EAV). Their replicative enzymes are translated from their genomic RNA, while their seven structural proteins are encoded by a set of small, partially overlapping genes in the genomic 3′-proximal region. The latter are expressed via synthesis of a set of subgenomic mRNAs that, in general, are functionally monocistronic (except for a bicistronic mRNA encoding the E and GP2 proteins). ORF5, which encodes the major glycoprotein GP5, has been used extensively for phylogenetic analyses. However, an in-depth computational analysis now reveals the arterivirus-wide conservation of an additional AUG-initiated ORF, here termed ORF5a, that overlaps the 5′ end of ORF5. The pattern of substitutions across sequence alignments indicated that ORF5a is subject to functional constraints at the amino acid level, while an analysis of substitutions at synonymous sites in ORF5 revealed a greatly reduced frequency of substitution in the portion of ORF5 that is overlapped by ORF5a. The 43–64 aa ORF5a protein and GP5 are probably expressed from the same subgenomic mRNA, via a translation initiation mechanism involving leaky ribosomal scanning. Inactivation of ORF5a expression by reverse genetics yielded a severely crippled EAV mutant, which displayed lower titres and a tiny plaque phenotype. These defects, which could be partially complemented in ORF5a-expressing cells, indicate that the novel protein, which may be the eighth structural protein of arteriviruses, is expressed and important for arterivirus infection.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.029264-0
2011-05-01
2019-12-11
Loading full text...

Full text loading...

/deliver/fulltext/jgv/92/5/1097.html?itemId=/content/journal/jgv/10.1099/vir.0.029264-0&mimeType=html&fmt=ahah

References

  1. Agapov E. V. , Frolov I. , Lindenbach B. D. , Prágai B. M. , Schlesinger S. , Rice C. M. . ( 1998; ). Noncytopathic Sindbis virus RNA vectors for heterologous gene expression. . Proc Natl Acad Sci U S A 95:, 12989–12994. [CrossRef] [PubMed]
    [Google Scholar]
  2. Allende R. , Lewis T. L. , Lu Z. , Rock D. L. , Kutish G. F. , Ali A. , Doster A. R. , Osorio F. A. . ( 1999; ). North American and European porcine reproductive and respiratory syndrome viruses differ in non-structural protein coding regions. . J Gen Virol 80:, 307–315.[PubMed]
    [Google Scholar]
  3. Altschul S. F. , Gish W. , Miller W. , Myers E. W. , Lipman D. J. . ( 1990; ). Basic local alignment search tool. . J Mol Biol 215:, 403–410.[PubMed] [CrossRef]
    [Google Scholar]
  4. Balasuriya U. B. , Snijder E. J. , van Dinten L. C. , Heidner H. W. , Wilson W. D. , Hedges J. F. , Hullinger P. J. , MacLachlan N. J. . ( 1999; ). Equine arteritis virus derived from an infectious cDNA clone is attenuated and genetically stable in infected stallions. . Virology 260:, 201–208. [CrossRef] [PubMed]
    [Google Scholar]
  5. Balasuriya U. B. , Snijder E. J. , Heidner H. W. , Zhang J. , Zevenhoven-Dobbe J. C. , Boone J. D. , McCollum W. H. , Timoney P. J. , MacLachlan N. J. . ( 2007; ). Development and characterization of an infectious cDNA clone of the virulent Bucyrus strain of Equine arteritis virus. . J Gen Virol 88:, 918–924. [CrossRef] [PubMed]
    [Google Scholar]
  6. Bendtsen J. D. , Nielsen H. , von Heijne G. , Brunak S. . ( 2004; ). Improved prediction of signal peptides: SignalP 3.0. . J Mol Biol 340:, 783–795. [CrossRef] [PubMed]
    [Google Scholar]
  7. Chung B. Y. , Miller W. A. , Atkins J. F. , Firth A. E. . ( 2008; ). An overlapping essential gene in the Potyviridae . . Proc Natl Acad Sci U S A 105:, 5897–5902. [CrossRef] [PubMed]
    [Google Scholar]
  8. Collins J. E. , Benfield D. A. , Christianson W. T. , Harris L. , Hennings J. C. , Shaw D. P. , Goyal S. M. , McCullough S. , Morrison R. B. et al. ( 1992; ). Isolation of swine infertility and respiratory syndrome virus (isolate ATCC VR-2332) in North America and experimental reproduction of the disease in gnotobiotic pigs. . J Vet Diagn Invest 4:, 117–126.[PubMed] [CrossRef]
    [Google Scholar]
  9. den Boon J. A. , Snijder E. J. , Chirnside E. D. , de Vries A. A. F. , Horzinek M. C. , Spaan W. J. M. . ( 1991; ). Equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily. . J Virol 65:, 2910–2920.[PubMed]
    [Google Scholar]
  10. de Vries A. A. F. , Chirnside E. D. , Horzinek M. C. , Rottier P. J. M. . ( 1992; ). Structural proteins of equine arteritis virus. . J Virol 66:, 6294–6303.[PubMed]
    [Google Scholar]
  11. de Vries A. A. F. , Glaser A. L. , Raamsman M. J. B. , de Haan C. A. M. , Sarnataro S. , Godeke G. J. , Rottier P. J. M. . ( 2000; ). Genetic manipulation of equine arteritis virus using full-length cDNA clones: separation of overlapping genes and expression of a foreign epitope. . Virology 270:, 84–97. [CrossRef] [PubMed]
    [Google Scholar]
  12. de Vries A. A. F. , Glaser A. L. , Raamsman M. J. , Rottier P. J. . ( 2001; ). Recombinant equine arteritis virus as an expression vector. . Virology 284:, 259–276. [CrossRef] [PubMed]
    [Google Scholar]
  13. Dobbe J. C. , van der Meer Y. , Spaan W. J. M. , Snijder E. J. . ( 2001; ). Construction of chimeric arteriviruses reveals that the ectodomain of the major glycoprotein is not the main determinant of equine arteritis virus tropism in cell culture. . Virology 288:, 283–294. [CrossRef] [PubMed]
    [Google Scholar]
  14. Faaberg K. S. , Plagemann P. G. W. . ( 1995; ). The envelope proteins of lactate dehydrogenase-elevating virus and their membrane topography. . Virology 212:, 512–525. [CrossRef] [PubMed]
    [Google Scholar]
  15. Fang Y. , Snijder E. J. . ( 2010; ). The PRRSV replicase: exploring the multifunctionality of an intriguing set of nonstructural proteins. . Virus Res 154:, 61–76. [CrossRef] [PubMed]
    [Google Scholar]
  16. Firth A. E. , Atkins J. F. . ( 2009; ). A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1′ may derive from ribosomal frameshifting. . Virol J 6:, 14. [CrossRef] [PubMed]
    [Google Scholar]
  17. Firth A. E. , Brown C. M. . ( 2006; ). Detecting overlapping coding sequences in virus genomes. . BMC Bioinformatics 7:, 75. [CrossRef] [PubMed]
    [Google Scholar]
  18. Firth A. E. , Chung B. Y. , Fleeton M. N. , Atkins J. F. . ( 2008; ). Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma. . Virol J 5:, 108. [CrossRef] [PubMed]
    [Google Scholar]
  19. Godeny E. K. , de Vries A. A. F. , Wang X. C. , Smith S. L. , de Groot R. J. . ( 1998; ). Identification of the leader-body junctions for the viral subgenomic mRNAs and organization of the simian hemorrhagic fever virus genome: evidence for gene duplication during arterivirus evolution. . J Virol 72:, 862–867.[PubMed]
    [Google Scholar]
  20. Gorbalenya A. E. , Enjuanes L. , Ziebuhr J. , Snijder E. J. . ( 2006; ). Nidovirales: evolving the largest RNA virus genome. . Virus Res 117:, 17–37. [CrossRef] [PubMed]
    [Google Scholar]
  21. Han W. , Wu J. J. , Deng X. Y. , Cao Z. , Yu X. L. , Wang C. B. , Zhao T. Z. , Chen N. H. , Hu H. H. et al. ( 2009; ). Molecular mutations associated with the in vitro passage of virulent porcine reproductive and respiratory syndrome virus. . Virus Genes 38:, 276–284. [CrossRef] [PubMed]
    [Google Scholar]
  22. Hedges J. F. , Demaula C. D. , Moore B. D. , McLaughlin B. E. , Simon S. I. , MacLachlan N. J. . ( 2001; ). Characterization of equine E-selectin. . Immunology 103:, 498–504. [CrossRef] [PubMed]
    [Google Scholar]
  23. Johnson C. R. , Griggs T. F. , Gnanandarajah J. S. , Murtaugh M. P. . ( 2011; ). Novel structural protein in porcine reproductive and respiratory syndrome virus encoded in an alternative open reading frame 5 present in all arteriviruses. . J Gen Virol 92:, 1107–1116 [CrossRef] [PubMed].
    [Google Scholar]
  24. Käll L. , Krogh A. , Sonnhammer E. L. . ( 2004; ). A combined transmembrane topology and signal peptide prediction method. . J Mol Biol 338:, 1027–1036. [CrossRef] [PubMed]
    [Google Scholar]
  25. Kozak M. . ( 2002; ). Pushing the limits of the scanning mechanism for initiation of translation. . Gene 299:, 1–34. [CrossRef] [PubMed]
    [Google Scholar]
  26. Larkin M. A. , Blackshields G. , Brown N. P. , Chenna R. , McGettigan P. A. , McWilliam H. , Valentin F. , Wallace I. M. , Wilm A. et al. ( 2007; ). clustal w and clustal_x version 2.0. . Bioinformatics 23:, 2947–2948. [CrossRef] [PubMed]
    [Google Scholar]
  27. Lin Y. C. , Chang R. Y. , Chueh L. L. . ( 2002; ). Leader-body junction sequence of the viral subgenomic mRNAs of porcine reproductive and respiratory syndrome virus isolated in Taiwan. . J Vet Med Sci 64:, 961–965. [CrossRef] [PubMed]
    [Google Scholar]
  28. Maclachlan N. J. , Balasuriya U. B. , Murtaugh M. P. , Barthold S. W. , Lowenstine L. J. . ( 2007; ). Arterivirus pathogenesis and immune response. . In Nidoviruses, pp. 325–337. Edited by Perlman S. , Gallagher T. , Snijder E. J. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  29. Matsuda D. , Dreher T. W. . ( 2006; ). Close spacing of AUG initiation codons confers dicistronic character on a eukaryotic mRNA. . RNA 12:, 1338–1349. [CrossRef] [PubMed]
    [Google Scholar]
  30. Meulenberg J. J. M. , Petersen-den Besten A. , De Kluyver E. P. , Moormann R. J. M. , Schaaper W. M. M. , Wensvoort G. . ( 1995; ). Characterization of proteins encoded by ORFs 2 to 7 of Lelystad virus. . Virology 206:, 155–163. [CrossRef] [PubMed]
    [Google Scholar]
  31. Molenkamp R. , van Tol H. , Rozier B. C. D. , van der Meer Y. , Spaan W. J. M. , Snijder E. J. . ( 2000; ). The arterivirus replicase is the only viral protein required for genome replication and subgenomic mRNA transcription. . J Gen Virol 81:, 2491–2496.[PubMed]
    [Google Scholar]
  32. Nedialkova D. D. , Gorbalenya A. E. , Snijder E. J. . ( 2010; ). Arterivirus Nsp1 modulates the accumulation of minus-strand templates to control the relative abundance of viral mRNAs. . PLoS Pathog 6:, e1000772. [CrossRef] [PubMed]
    [Google Scholar]
  33. Pasternak A. O. , Gultyaev A. P. , Spaan W. J. M. , Snijder E. J. . ( 2000; ). Genetic manipulation of arterivirus alternative mRNA leader-body junction sites reveals tight regulation of structural protein expression. . J Virol 74:, 11642–11653. [CrossRef] [PubMed]
    [Google Scholar]
  34. Pasternak A. O. , Spaan W. J. M. , Snijder E. J. . ( 2006; ). Nidovirus transcription: how to make sense...?. J Gen Virol 87:, 1403–1421. [CrossRef] [PubMed]
    [Google Scholar]
  35. Rice P. , Longden I. , Bleasby A. . ( 2000; ). EMBOSS: the European molecular biology open software suite. . Trends Genet 16:, 276–277. [CrossRef] [PubMed]
    [Google Scholar]
  36. Sawicki S. G. , Sawicki D. L. , Siddell S. G. . ( 2007; ). A contemporary view of coronavirus transcription. . J Virol 81:, 20–29. [CrossRef] [PubMed]
    [Google Scholar]
  37. Shi M. , Lam T. T. , Hon C. C. , Hui R. K. , Faaberg K. S. , Wennblom T. , Murtaugh M. P. , Stadejek T. , Leung F. C. . ( 2010; ). Molecular epidemiology of PRRSV: a phylogenetic perspective. . Virus Res 154:, 7–17. [CrossRef] [PubMed]
    [Google Scholar]
  38. Simmonds P. , Karakasiliotis I. , Bailey D. , Chaudhry Y. , Evans D. J. , Goodfellow I. G. . ( 2008; ). Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses. . Nucleic Acids Res 36:, 2530–2546. [CrossRef] [PubMed]
    [Google Scholar]
  39. Snijder E. J. , Meulenberg J. J. M. . ( 1998; ). The molecular biology of arteriviruses. . J Gen Virol 79:, 961–979.[PubMed]
    [Google Scholar]
  40. Snijder E. J. , Spaan W. J. M. . ( 2006; ). Arteriviruses. . In Fields Virology , , 5th edn., pp. 1337–1355. Edited by Knipe D. M. , Howley P. M. . . Philadelphia, PA:: Lippincott, Williams & Wilkins;.
    [Google Scholar]
  41. Snijder E. J. , van Tol H. , Pedersen K. W. , Raamsman M. J. B. , de Vries A. A. F. . ( 1999; ). Identification of a novel structural protein of arteriviruses. . J Virol 73:, 6335–6345.[PubMed]
    [Google Scholar]
  42. Snijder E. J. , Dobbe J. C. , Spaan W. J. M. . ( 2003; ). Heterodimerization of the two major envelope proteins is essential for arterivirus infectivity. . J Virol 77:, 97–104. [CrossRef] [PubMed]
    [Google Scholar]
  43. Suárez P. , Zardoya R. , Martín M. J. , Prieto C. , Dopazo J. , Solana A. , Castro J. M. . ( 1996; ). Phylogenetic relationships of European strains of porcine reproductive and respiratory syndrome virus (PRRSV) inferred from DNA sequences of putative ORF-5 and ORF-7 genes. . Virus Res 42:, 159–165. [CrossRef] [PubMed]
    [Google Scholar]
  44. Van Breedam W. , Delputte P. L. , Van Gorp H. , Misinzo G. , Vanderheijden N. , Duan X. , Nauwynck H. J. . ( 2010; ). Porcine reproductive and respiratory syndrome virus entry into the porcine macrophage. . J Gen Virol 91:, 1659–1667. [CrossRef] [PubMed]
    [Google Scholar]
  45. van der Meer Y. , van Tol H. , Locker J. K. , Snijder E. J. . ( 1998; ). ORF1a-encoded replicase subunits are involved in the membrane association of the arterivirus replication complex. . J Virol 72:, 6689–6698.[PubMed]
    [Google Scholar]
  46. van Dinten L. C. , den Boon J. A. , Wassenaar A. L. M. , Spaan W. J. M. , Snijder E. J. . ( 1997; ). An infectious arterivirus cDNA clone: identification of a replicase point mutation that abolishes discontinuous mRNA transcription. . Proc Natl Acad Sci U S A 94:, 991–996. [CrossRef] [PubMed]
    [Google Scholar]
  47. Wensvoort G. , Terpstra C. , Pol J. M. , ter Laak E. A. , Bloemraad M. , de Kluyver E. P. , Kragten C. , van Buiten L. , den Besten A. et al. ( 1991; ). Mystery swine disease in The Netherlands: the isolation of Lelystad virus. . Vet Q 13:, 121–130.[PubMed] [CrossRef]
    [Google Scholar]
  48. Wieringa R. , de Vries A. A. F. , van der Meulen J. , Godeke G. J. , Onderwater J. J. M. , van Tol H. , Koerten H. K. , Mommaas A. M. , Snijder E. J. , Rottier P. J. . ( 2004; ). Structural protein requirements in equine arteritis virus assembly. . J Virol 78:, 13019–13027. [CrossRef] [PubMed]
    [Google Scholar]
  49. Wissink E. H. J. , Kroese M. V. , van Wijk H. A. R. , Rijsewijk F. A. M. , Meulenberg J. J. M. , Rottier P. J. M. . ( 2005; ). Envelope protein requirements for the assembly of infectious virions of porcine reproductive and respiratory syndrome virus. . J Virol 79:, 12495–12506. [CrossRef] [PubMed]
    [Google Scholar]
  50. Zevenhoven-Dobbe J. C. , Greve S. , van Tol H. , Spaan W. J. M. , Snijder E. J. . ( 2004; ). Rescue of disabled infectious single-cycle (DISC) equine arteritis virus by using complementing cell lines that express minor structural glycoproteins. . J Gen Virol 85:, 3709–3714. [CrossRef] [PubMed]
    [Google Scholar]
  51. Zhang J. , Timoney P. J. , Shuck K. M. , Seoul G. , Go Y. Y. , Lu Z. , Powell D. G. , Meade B. J. , Balasuriya U. B. . ( 2010; ). Molecular epidemiology and genetic characterization of equine arteritis virus isolates associated with the 2006-2007 multi-state disease occurrence in the USA. . J Gen Virol 91:, 2286–2301. [CrossRef] [PubMed]
    [Google Scholar]
  52. Zhou L. , Yang H. . ( 2010; ). Porcine reproductive and respiratory syndrome in China. . Virus Res 154:, 31–37. [CrossRef] [PubMed]
    [Google Scholar]
  53. Ziebuhr J. , Snijder E. J. , Gorbalenya A. E. . ( 2000; ). Virus-encoded proteinases and proteolytic processing in the Nidovirales. . J Gen Virol 81:, 853–879.[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.029264-0
Loading
/content/journal/jgv/10.1099/vir.0.029264-0
Loading

Data & Media loading...

Most Cited This Month

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