Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 May 26;15(10):3961–3976. doi: 10.1093/nar/15.10.3961

Nucleotide sequence analysis of the L gene of Newcastle disease virus: homologies with Sendai and vesicular stomatitis viruses.

K Yusoff, N S Millar, P Chambers, P T Emmerson
PMCID: PMC340824  PMID: 3035486

Abstract

The nucleotide sequence of the L gene of the Beaudette C strain of Newcastle disease virus (NDV) has been determined. The L gene is 6704 nucleotides long and encodes a protein of 2204 amino acids with a calculated molecular weight of 248822. Mung bean nuclease mapping of the 5' terminus of the L gene mRNA indicates that the transcription of the L gene is initiated 11 nucleotides upstream of the translational start site. Comparison with the amino acid sequences of the L genes of Sendai virus and vesicular stomatitis virus (VSV) suggests that there are several regions of homology between the sequences. These data provide further evidence for an evolutionary relationship between the Paramyxoviridae and the Rhabdoviridae. A non-coding sequence of 46 nucleotides downstream of the presumed polyadenylation site of the L gene may be part of a negative strand leader RNA.

Full text

PDF
3961

Images in this article

3967Image
on p.3967

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abraham G., Banerjee A. K. Sequential transcription of the genes of vesicular stomatitis virus. Proc Natl Acad Sci U S A. 1976 May;73(5):1504–1508. doi: 10.1073/pnas.73.5.1504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ball L. A., White C. N. Order of transcription of genes of vesicular stomatitis virus. Proc Natl Acad Sci U S A. 1976 Feb;73(2):442–446. doi: 10.1073/pnas.73.2.442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chambers P., Millar N. S., Bingham R. W., Emmerson P. T. Molecular cloning of complementary DNA to Newcastle disease virus, and nucleotide sequence analysis of the junction between the genes encoding the haemagglutinin-neuraminidase and the large protein. J Gen Virol. 1986 Mar;67(Pt 3):475–486. doi: 10.1099/0022-1317-67-3-475. [DOI] [PubMed] [Google Scholar]
  5. Chambers P., Millar N. S., Emmerson P. T. Nucleotide sequence of the gene encoding the fusion glycoprotein of Newcastle disease virus. J Gen Virol. 1986 Dec;67(Pt 12):2685–2694. doi: 10.1099/0022-1317-67-12-2685. [DOI] [PubMed] [Google Scholar]
  6. Chambers P., Millar N. S., Platt S. G., Emmerson P. T. Nucleotide sequence of the gene encoding the matrix protein of Newcastle disease virus. Nucleic Acids Res. 1986 Nov 25;14(22):9051–9061. doi: 10.1093/nar/14.22.9051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chambers P., Samson A. C. Non-structural proteins in Newcastle disease virus-infected cells. J Gen Virol. 1982 Jan;58(Pt 1):1–12. doi: 10.1099/0022-1317-58-1-1. [DOI] [PubMed] [Google Scholar]
  8. Collins P. L., Hightower L. E., Ball L. A. Transcriptional map for Newcastle disease virus. J Virol. 1980 Sep;35(3):682–693. doi: 10.1128/jvi.35.3.682-693.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Emerson S. U., Yu Y. Both NS and L proteins are required for in vitro RNA synthesis by vesicular stomatitis virus. J Virol. 1975 Jun;15(6):1348–1356. doi: 10.1128/jvi.15.6.1348-1356.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fry D. C., Kuby S. A., Mildvan A. S. ATP-binding site of adenylate kinase: mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins. Proc Natl Acad Sci U S A. 1986 Feb;83(4):907–911. doi: 10.1073/pnas.83.4.907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
  12. Gill D. S., Banerjee A. K. Vesicular stomatitis virus NS proteins: structural similarity without extensive sequence homology. J Virol. 1985 Jul;55(1):60–66. doi: 10.1128/jvi.55.1.60-66.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hamaguchi M., Yoshida T., Nishikawa K., Naruse H., Nagai Y. Transcriptive complex of Newcastle disease virus. I. Both L and P proteins are required to constitute an active complex. Virology. 1983 Jul 15;128(1):105–117. doi: 10.1016/0042-6822(83)90322-7. [DOI] [PubMed] [Google Scholar]
  14. Hiebert S. W., Paterson R. G., Lamb R. A. Identification and predicted sequence of a previously unrecognized small hydrophobic protein, SH, of the paramyxovirus simian virus 5. J Virol. 1985 Sep;55(3):744–751. doi: 10.1128/jvi.55.3.744-751.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Horikami S. M., Moyer S. A. Host range mutants of vesicular stomatitis virus defective in in vitro RNA methylation. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7694–7698. doi: 10.1073/pnas.79.24.7694. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hunt D. M., Smith E. F., Buckley D. W. Aberrant polyadenylation by a vesicular stomatitis virus mutant is due to an altered L protein. J Virol. 1984 Nov;52(2):515–521. doi: 10.1128/jvi.52.2.515-521.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ishida N., Taira H., Omata T., Mizumoto K., Hattori S., Iwasaki K., Kawakita M. Sequence of 2,617 nucleotides from the 3' end of Newcastle disease virus genome RNA and the predicted amino acid sequence of viral NP protein. Nucleic Acids Res. 1986 Aug 26;14(16):6551–6564. doi: 10.1093/nar/14.16.6551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jorgensen E. D., Collins P. L., Lomedico P. T. Cloning and nucleotide sequence of Newcastle disease virus hemagglutinin-neuraminidase mRNA: identification of a putative sialic acid binding site. Virology. 1987 Jan;156(1):12–24. doi: 10.1016/0042-6822(87)90431-4. [DOI] [PubMed] [Google Scholar]
  19. Kolakofsky D., Boy de la Tour E., Delius H. Molecular weight determination of Sendai and Newcastle disease virus RNA. J Virol. 1974 Feb;13(2):261–268. doi: 10.1128/jvi.13.2.261-268.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell. 1986 Jan 31;44(2):283–292. doi: 10.1016/0092-8674(86)90762-2. [DOI] [PubMed] [Google Scholar]
  21. Kozak M. Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes. Nucleic Acids Res. 1981 Oct 24;9(20):5233–5252. doi: 10.1093/nar/9.20.5233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kurilla M. G., Stone H. O., Keene J. D. RNA sequence and transcriptional properties of the 3' end of the Newcastle disease virus genome. Virology. 1985 Sep;145(2):203–212. doi: 10.1016/0042-6822(85)90154-0. [DOI] [PubMed] [Google Scholar]
  23. Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. doi: 10.1016/0022-2836(82)90515-0. [DOI] [PubMed] [Google Scholar]
  24. Lamb R. A., Mahy B. W., Choppin P. W. The synthesis of sendai virus polypeptides in infected cells. Virology. 1976 Jan;69(1):116–131. doi: 10.1016/0042-6822(76)90199-9. [DOI] [PubMed] [Google Scholar]
  25. Leppert M., Rittenhouse L., Perrault J., Summers D. F., Kolakofsky D. Plus and minus strand leader RNAs in negative strand virus-infected cells. Cell. 1979 Nov;18(3):735–747. doi: 10.1016/0092-8674(79)90127-2. [DOI] [PubMed] [Google Scholar]
  26. Millar N. S., Chambers P., Emmerson P. T. Nucleotide sequence analysis of the haemagglutinin-neuraminidase gene of Newcastle disease virus. J Gen Virol. 1986 Sep;67(Pt 9):1917–1927. doi: 10.1099/0022-1317-67-9-1917. [DOI] [PubMed] [Google Scholar]
  27. Mizusawa S., Nishimura S., Seela F. Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP. Nucleic Acids Res. 1986 Feb 11;14(3):1319–1324. doi: 10.1093/nar/14.3.1319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Morgan E. M., Rakestraw K. M. Sequence of the Sendai virus L gene: open reading frames upstream of the main coding region suggest that the gene may be polycistronic. Virology. 1986 Oct 15;154(1):31–40. doi: 10.1016/0042-6822(86)90427-7. [DOI] [PubMed] [Google Scholar]
  29. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  30. Queen C., Korn L. J. A comprehensive sequence analysis program for the IBM personal computer. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):581–599. doi: 10.1093/nar/12.1part2.581. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Schubert M., Harmison G. G., Meier E. Primary structure of the vesicular stomatitis virus polymerase (L) gene: evidence for a high frequency of mutations. J Virol. 1984 Aug;51(2):505–514. doi: 10.1128/jvi.51.2.505-514.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Schubert M., Keene J. D., Herman R. C., Lazzarini R. A. Site on the vesicular stomatitis virus genome specifying polyadenylation and the end of the L gene mRNA. J Virol. 1980 May;34(2):550–559. doi: 10.1128/jvi.34.2.550-559.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Schubert M., Lazzarini R. A. In vivo transcription of the 5'-terminal extracistronic region of vesicular stomatitis virus RNA. J Virol. 1981 Apr;38(1):256–262. doi: 10.1128/jvi.38.1.256-262.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Shioda T., Hidaka Y., Kanda T., Shibuta H., Nomoto A., Iwasaki K. Sequence of 3,687 nucleotides from the 3' end of Sendai virus genome RNA and the predicted amino acid sequences of viral NP, P and C proteins. Nucleic Acids Res. 1983 Nov 11;11(21):7317–7330. doi: 10.1093/nar/11.21.7317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Shioda T., Iwasaki K., Shibuta H. Determination of the complete nucleotide sequence of the Sendai virus genome RNA and the predicted amino acid sequences of the F, HN and L proteins. Nucleic Acids Res. 1986 Feb 25;14(4):1545–1563. doi: 10.1093/nar/14.4.1545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Staden R. Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):521–538. doi: 10.1093/nar/12.1part2.521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Thomas D., Newcomb W. W., Brown J. C., Wall J. S., Hainfeld J. F., Trus B. L., Steven A. C. Mass and molecular composition of vesicular stomatitis virus: a scanning transmission electron microscopy analysis. J Virol. 1985 May;54(2):598–607. doi: 10.1128/jvi.54.2.598-607.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Walker J. E., Saraste M., Runswick M. J., Gay N. J. 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. 1982;1(8):945–951. doi: 10.1002/j.1460-2075.1982.tb01276.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wierenga R. K., Terpstra P., Hol W. G. Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint. J Mol Biol. 1986 Jan 5;187(1):101–107. doi: 10.1016/0022-2836(86)90409-2. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES