Comparative analysis of the full genome sequence of European bat lyssavirus type 1 and type 2 with other lyssaviruses and evidence for a conserved transcription termination and polyadenylation motif in the G–L 3′ non-translated region Free

Abstract

We report the first full-length genomic sequences for European bat lyssavirus type-1 (EBLV-1) and type-2 (EBLV-2). The EBLV-1 genomic sequence was derived from a virus isolated from a serotine bat in Hamburg, Germany, in 1968 and the EBLV-2 sequence was derived from a virus isolate from a human case of rabies that occurred in Scotland in 2002. A long-distance PCR strategy was used to amplify the open reading frames (ORFs), followed by standard and modified RACE (rapid amplification of cDNA ends) techniques to amplify the 3′ and 5′ ends. The lengths of each complete viral genome for EBLV-1 and EBLV-2 were 11 966 and 11 930 base pairs, respectively, and follow the standard rhabdovirus genome organization of five viral proteins. Comparison with other lyssavirus sequences demonstrates variation in degrees of homology, with the genomic termini showing a high degree of complementarity. The nucleoprotein was the most conserved, both intra- and intergenotypically, followed by the polymerase (L), matrix and glyco- proteins, with the phosphoprotein being the most variable. In addition, we have shown that the two EBLVs utilize a conserved transcription termination and polyadenylation (TTP) motif, approximately 50 nt upstream of the L gene start codon. All available lyssavirus sequences to date, with the exception of Pasteur virus (PV) and PV-derived isolates, use the second TTP site. This observation may explain differences in pathogenicity between lyssavirus strains, dependent on the length of the untranslated region, which might affect transcriptional activity and RNA stability.

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2007-04-01
2024-03-28
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References

  1. Amengual B., Whitby J. E., King A., Cobo J. S., Bourhy H. 1997; Evolution of European bat lyssaviruses. J Gen Virol 78:2319–2328
    [Google Scholar]
  2. Auewarakul P. 2005; Composition bias and genome polarity of RNA viruses. Virus Res 109:33–37 [CrossRef]
    [Google Scholar]
  3. Badrane H., Bahloul C., Perrin P., Tordo N. 2001; Evidence of two Lyssavirus phylogroups with distinct pathogenicity and immunogenicity. J Virol 75:3268–3276 [CrossRef]
    [Google Scholar]
  4. Banerjee A. K. 1987; Transcription and replication of rhabdoviruses. Microbiol Rev 51:66–87
    [Google Scholar]
  5. Bourhy H., Kissi B., Lafon M., Sacramento D., Tordo N. 1992; Antigenic and molecular characterization of bat rabies virus in Europe. J Clin Microbiol 30:2419–2426
    [Google Scholar]
  6. Calain P., Roux L. 1993; The rule of six, a basic feature for efficient replication of Sendai virus defective interfering RNA. J Virol 67:4822–4830
    [Google Scholar]
  7. Chenik M., Chebli K., Gaudin Y., Blondel D. 1994; In vivo interaction of rabies virus phosphoprotein (P) and nucleoprotein (N) existence of two N-binding sites on P protein. J Gen Virol 75:2889–2896 [CrossRef]
    [Google Scholar]
  8. Chenik M., Schnell M., Conzelmann K. K., Blondel D. 1998; Mapping the interacting domains between the rabies virus polymerase and phosphoprotein. J Virol 72:1925–1930
    [Google Scholar]
  9. Coll J. M. 1995; The glycoprotein G of rhabdoviruses. Arch Virol 140:827–851 [CrossRef]
    [Google Scholar]
  10. Conzelmann K. K., Cox J. H., Schneider L. G., Thiel H. J. 1990; Molecular cloning and complete nucleotide sequence of the attenuated rabies virus SAD B19. Virology 175:485–499 [CrossRef]
    [Google Scholar]
  11. Coulon P., Ternaux J. P., Flamand A., Tuffereau C. 1998; An avirulent mutant of rabies virus is unable to infect motoneurons in vivo and in vitro . J Virol 72:273–278
    [Google Scholar]
  12. Davis P. L., Holmes E. C., Larrous F., Van der Poel W. H., Tjornehoj K., Alonso W. J., Bourhy H. 2005; Phylogeography, population dynamics, and molecular evolution of European bat lyssaviruses. J Virol 79:10487–10497 [CrossRef]
    [Google Scholar]
  13. Dietzschold B., Wunner W. H., Wiktor T. J., Lopes A. D., Lafon M., Smith C. L., Koprowski H. 1983; Characterization of an antigenic determinant of the glycoprotein that correlates with pathogenicity of rabies virus. Proc Natl Acad Sci U S A 80:70–74 [CrossRef]
    [Google Scholar]
  14. Dietzschold B., Lafon M., Wang H., Otvos L. Jr, Celis E., Wunner W. H., Koprowski H. 1987; Localization and immunological characterization of antigenic domains of the rabies virus internal N and NS proteins. Virus Res 8:103–125 [CrossRef]
    [Google Scholar]
  15. Faber M., Pulmanausahakul R., Nagao K., Prosniak M., Rice A. B., Koprowski H., Schnell M. J., Dietzschold B. 2004; Identification of viral genomic elements responsible for rabies virus neuroinvasiveness. Proc Natl Acad Sci U S A 101:16328–16332 [CrossRef]
    [Google Scholar]
  16. Finke S., Conzelmann K. K. 1999; Virus promoters determine interference by defective RNAs selective amplification of mini-RNA vectors and rescue from cDNA by a 3′ copy-back ambisense rabies virus. J Virol 73:3818–3825
    [Google Scholar]
  17. Finke S., Conzelmann K. K. 2003; Dissociation of rabies virus matrix protein functions in regulation of viral RNA synthesis and virus assembly. J Virol 77:12074–12082 [CrossRef]
    [Google Scholar]
  18. Finke S., Mueller-Waldeck R., Conzelmann K.-K. 2003; Rabies virus matrix protein regulates the balance of virus transcription and replication. J Gen Virol 84:1613–1621 [CrossRef]
    [Google Scholar]
  19. Fooks A. 2004; The challenge of new and emerging lyssaviruses. Expert Rev Vaccines 3:333–336 [CrossRef]
    [Google Scholar]
  20. Fooks A. R., Brookes S. M., Johnson N., McElhinney L. M., Hutson A. M. 2003a; European bat lyssaviruses: an emerging zoonosis. Epidemiol Infect 131:1029–1039 [CrossRef]
    [Google Scholar]
  21. Fooks A. R., McElhinney L. M., Pounder D. J., Finnegan C. J., Mansfield K., Johnson N., Brookes S. M., Parsons G., White K. & other authors (2003b). Case report: isolation of a European bat lyssavirus type 2a from a fatal human case of rabies encephalitis. J Med Virol 71:281–289 [CrossRef]
    [Google Scholar]
  22. Fu Z. F., Zheng Y., Wunner W. H., Koprowski H., Dietzschold B. 1994; Both the N- and the C-terminal domains of the nominal phosphoprotein of rabies virus are involved in binding to the nucleoprotein. Virology 200:590–597 [CrossRef]
    [Google Scholar]
  23. Gaudin Y., Ruigrok R. W., Tuffereau C., Knossow M., Flamand A. 1992; Rabies virus glycoprotein is a trimer. Virology 187:627–632 [CrossRef]
    [Google Scholar]
  24. Gill D. S., Banerjee A. K. 1985; Vesicular stomatitis virus NS proteins: structural similarity without extensive sequence homology. J Virol 55:60–66
    [Google Scholar]
  25. Gilmore R. D. Jr, Leong J. A. 1988; The nucleocapsid gene of infectious hematopoietic necrosis virus, a fish rhabdovirus. Virology 167:644–648
    [Google Scholar]
  26. Gould A. R., Kattenbelt J. A., Gumley S. G., Lunt R. A. 2002; Characterisation of an Australian bat lyssavirus variant isolated from an insectivorous bat. Virus Res 89:1–28 [CrossRef]
    [Google Scholar]
  27. Gupta A. K., Blondel D., Choudhary S., Banerjee A. K. 2000; The phosphoprotein of rabies virus is phosphorylated by a unique cellular protein kinase and specific isomers of protein kinase C. J Virol 74:91–98 [CrossRef]
    [Google Scholar]
  28. Harty R. N., Paragas J., Sudol M., Palese P. 1999; A proline-rich motif within the matrix protein of vesicular stomatitis virus and rabies virus interacts with WW domains of cellular proteins: implications for viral budding. J Virol 73:2921–2929
    [Google Scholar]
  29. Harty R. N., Brown M. E., McGettigan J. P., Wang G., Jayakar H. R., Huibregtse J. M., Whitt M. A., Schnell M. J. 2001; Rhabdoviruses and the cellular ubiquitin-proteasome system: a budding interaction. J Virol 75:10623–10629 [CrossRef]
    [Google Scholar]
  30. Inoue K., Shoji Y., Kurane I., Iijima T., Sakai T., Morimoto K. 2003; An improved method for recovering rabies virus from cloned cDNA. J Virol Methods 107:229–236 [CrossRef]
    [Google Scholar]
  31. Irie T., Licata J. M., Jayakar H. R., Whitt M. A., Bell P., Harty R. N. 2004; Functional analysis of late-budding domain activity associated with the PSAP motif within the vesicular stomatitis virus M protein. J Virol 78:7823–7827 [CrossRef]
    [Google Scholar]
  32. Ito N., Kakemizu M., Ito K. A., Yamamoto A., Yoshida Y., Sugiyama M., Minamoto N. 2001; A comparison of complete genome sequences of the attenuated RC-HL strain of rabies virus used for production of animal vaccine in Japan, and the parental Nishigahara strain. Microbiol Immunol 45:51–58 [CrossRef]
    [Google Scholar]
  33. Jacob Y., Real E., Tordo N. 2001; Functional interaction map of lyssavirus phosphoprotein: identification of the minimal transcription domains. J Virol 75:9613–9622 [CrossRef]
    [Google Scholar]
  34. Jayakar H. R., Murti K. G., Whitt M. A. 2000; Mutations in the PPPY motif of vesicular stomatitis virus matrix protein reduce virus budding by inhibiting a late step in virion release. J Virol 74:9818–9827 [CrossRef]
    [Google Scholar]
  35. Johnson N., McElhinney L. M., Smith J., Lowings P., Fooks A. R. 2002; Phylogenetic comparison of the genus Lyssavirus using distal coding sequences of the glycoprotein and nucleoprotein genes. Arch Virol 147:2111–2123 [CrossRef]
    [Google Scholar]
  36. Kassis R., Larrous F., Estaquier J., Bourhy H. 2004; Lyssavirus matrix protein induces apoptosis by a TRAIL-dependent mechanism involving caspase-8 activation. J Virol 78:6543–6555 [CrossRef]
    [Google Scholar]
  37. Keene J. D., Thornton B. J., Emerson S. U. 1981; Sequence-specific contacts between the RNA polymerase of vesicular stomatitis virus and the leader RNA gene. Proc Natl Acad Sci U S A 78:6191–6195 [CrossRef]
    [Google Scholar]
  38. Kissi B., Tordo N., Bourhy H. 1995; Genetic polymorphism in the rabies virus nucleoprotein gene. Virology 209:526–537 [CrossRef]
    [Google Scholar]
  39. Kuzmin I. V., Orciari L. A., Arai Y. T., Smith J. S., Hanlon C. A., Kameoka Y., Rupprecht C. E. 2003; Bat lyssaviruses (Aravan and Khujand) from Central Asia: phylogenetic relationships according to N, P and G gene sequences. Virus Res 97:65–79 [CrossRef]
    [Google Scholar]
  40. Kuzmin I. V., Hughes G. J., Botvinkin A. D., Orciari L. A., Rupprecht C. E. 2005; Phylogenetic relationships of Irkut and West Caucasian bat viruses within the Lyssavirus genus and suggested quantitative criteria based on the N gene sequence for lyssavirus genotype definition. Virus Res 111:28–43 [CrossRef]
    [Google Scholar]
  41. Le Mercier P., Jacob Y., Tordo N. 1997; The complete Mokola virus genome sequence: structure of the RNA-dependent RNA polymerase. J Gen Virol 78:1571–1576
    [Google Scholar]
  42. Lo K. W., Naisbitt S., Fan J. S., Sheng M., Zhang M. 2001; The 8-kDa dynein light chain binds to its targets via a conserved (K/R)XTQT motif. J Biol Chem 276:14059–14066
    [Google Scholar]
  43. Lumio J., Hillbom M., Roine R., Ketonen L., Haltia M., Valle M., Neuvonen E., Lahdevirta J. 1986; Human rabies of bat origin in Europe. Lancet 1:378
    [Google Scholar]
  44. Masters P. S., Banerjee A. K. 1987; Sequences of Chandipura virus N and NS genes: evidence for high mutability of the NS gene within vesiculoviruses. Virology 157:298–306 [CrossRef]
    [Google Scholar]
  45. Mavrakis M., Iseni F., Mazza C., Schoehn G., Ebel C., Gentzel M., Franz T., Ruigrok R. W. H. 2003; Isolation and characterisation of the rabies virus N-P complex produced in insect cells. Virology 305:406–414 [CrossRef]
    [Google Scholar]
  46. Mavrakis M., McCarthy A. A., Roche S., Blondel D., Ruigrok R. W. 2004; Structure and function of the C-terminal domain of the polymerase cofactor of rabies virus. J Mol Biol 343:819–831 [CrossRef]
    [Google Scholar]
  47. Mebatsion T. 2001; Extensive attenuation of rabies virus by simultaneously modifying the dynein light chain binding site in the P protein and replacing Arg333 in the G protein. J Virol 75:11496–11502 [CrossRef]
    [Google Scholar]
  48. Mebatsion T., Konig M., Conzelmann K. K. 1996; Budding of rabies virus particles in the absence of the spike glycoprotein. Cell 84:941–951 [CrossRef]
    [Google Scholar]
  49. Mebatsion T., Weiland F., Conzelmann K. K. 1999; Matrix protein of rabies virus is responsible for the assembly and budding of bullet-shaped particles and interacts with the transmembrane spike glycoprotein G. J Virol 73:242–250
    [Google Scholar]
  50. Morimoto K., Hooper D. C., Spitsin S., Koprowski H., Dietzschold B. 1999; Pathogenicity of different rabies virus variants inversely correlates with apoptosis and rabies virus glycoprotein expression in infected primary neuron cultures. J Virol 73:510–518
    [Google Scholar]
  51. Muller R., Poch O., Delarue M., Bishop D. H., Bouloy M. 1994; Rift Valley fever virus L segment: correction of the sequence and possible functional role of newly identified regions conserved in RNA-dependent polymerases. J Gen Virol 75:1345–1352 [CrossRef]
    [Google Scholar]
  52. Nadin-Davis S. A., Abdel-Malik M., Armstrong J., Wandeler A. I. 2002; Lyssavirus P gene characterisation provides insights into the phylogeny of the genus and identifies structural similarities and diversity within the encoded phosphoprotein. Virology 298:286–305 [CrossRef]
    [Google Scholar]
  53. Nicholas K. B., Nicholas H. B. Jr, Deerfield D. W., II. 1997; GeneDoc: analysis and visualization of genetic variation. EMBnet News 4:1–4 http://www.embnet.org/download/embnetnews/embnet_news_4_2.pdf
    [Google Scholar]
  54. Pattnaik A. K., Hwang L., Li T., Englund N., Mathur M., Das T., Banerjee A. K. 1997; Phosphorylation within the amino-terminal acidic domain I of the phosphoprotein of vesicular stomatitis virus is required for transcription but not for replication. J Virol 71:8167–8175
    [Google Scholar]
  55. Poch O., Tordo N., Keith G. 1988; Sequence of the 3386 3′ nucleotides of the genome of the AVO1 strain rabies virus: structural similarities in the protein regions involved in transcription. Biochimie 70:1019–1029 [CrossRef]
    [Google Scholar]
  56. Poch O., Blumberg B. M., Bougueleret L., Tordo N. 1990; Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains. J Gen Virol 71:1153–1162 [CrossRef]
    [Google Scholar]
  57. Poisson N., Real E., Gaudin Y., Vaney M.-C., King S., Jacob Y., Tordo N., Blondel D. 2001; Molecular basis for the interaction between rabies virus phosphoprotein P and the dynein light chain LC8 dissociation of dynein binding properties and transcriptional functionality of P. J Gen Virol 82:2691–2696
    [Google Scholar]
  58. Prehaud C., Coulon P., LaFay F., Thiers C., Flamand A. 1988; Antigenic site II of the rabies virus glycoprotein: structure and role in viral virulence. J Virol 62:1–7
    [Google Scholar]
  59. Rasalingam P., Rossiter J. P., Mebatsion T., Jackson A. C. 2005; Comparative pathogenesis of the SAD-L16 strain of rabies virus and a mutant modifying the dynein light chain binding site of the rabies virus phosphoprotein in young mice. Virus Res 111:55–60 [CrossRef]
    [Google Scholar]
  60. Ravkov E. V., Smith J. S., Nichol S. T. 1995; Rabies virus glycoprotein gene contains a long 3′ noncoding region which lacks pseudogene properties. Virology 206:718–723 [CrossRef]
    [Google Scholar]
  61. Rodriguez L. L., Pauszek S. J., Bunch T. A., Schumann K. R. 2002; Full-length genome analysis of natural isolates of vesicular stomatitis virus (Indiana 1 serotype) from North, Central and South America. J Gen Virol 83:2475–2483
    [Google Scholar]
  62. Schnell M. J., Conzelmann K. K. 1995; Polymerase activity of in vitro mutated rabies virus L protein. Virology 214:522–530 [CrossRef]
    [Google Scholar]
  63. Seif I., Coulon P., Rollin P. E., Flamand A. 1985; Rabies virulence effect on pathogenicity and sequence characterization of rabies virus mutations affecting antigenic site III of the glycoprotein. J Virol 53:926–934
    [Google Scholar]
  64. Selimov M. A., Tatarov A. G., Botvinkin A. D., Klueva E. V., Kulikova L. G. 1989; Rabies-related Yuli virus; identification with a panel of monoclonal antibodies. Acta Virol 33:542–546
    [Google Scholar]
  65. Sleat D. E., Banerjee A. K. 1993; Transcriptional activity and mutational analysis of recombinant vesicular stomatitis virus RNA polymerase. J Virol 67:1334–1339
    [Google Scholar]
  66. Tordo N., Poch O., Ermine A., Keith G., Rougeon F. 1986; Walking along the rabies genome: is the large G-L intergenic region a remnant gene?. Proc Natl Acad Sci U S A 83:3914–3918 [CrossRef]
    [Google Scholar]
  67. Tordo N., Poch O., Ermine A., Keith G., Rougeon F. 1988; Completion of the rabies virus genome sequence determination: highly conserved domains among the L (polymerase) proteins of unsegmented negative-strand RNA viruses. Virology 165:565–576 [CrossRef]
    [Google Scholar]
  68. Warrilow D., Smith I. L., Harrower B., Smith G. A. 2002; Sequence analysis of an isolate from a fatal human infection of Australian bat lyssavirus. Virology 297:109–119 [CrossRef]
    [Google Scholar]
  69. Yang J., Koprowski H., Dietzschold B., Fu Z. F. 1999; Phosphorylation of rabies virus nucleoprotein regulates viral RNA transcription and replication by modulating leader RNA encapsidation. J Virol 73:1661–1664
    [Google Scholar]
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