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. 1986 Jul;83(13):4594–4598. doi: 10.1073/pnas.83.13.4594

Nucleotide sequences for the gene junctions of human respiratory syncytial virus reveal distinctive features of intergenic structure and gene order.

P L Collins, L E Dickens, A Buckler-White, R A Olmsted, M K Spriggs, E Camargo, K V Coelingh
PMCID: PMC323787  PMID: 3460060

Abstract

Complete sequences for the intergenic regions of the genome of human respiratory syncytial virus were obtained by dideoxynucleotide sequencing using synthetic oligonucleotides. These experiments established that the 10 respiratory syncytial viral genes are arranged, without additional intervening genes, in the order 3' 1C-1B-N-P-M-1A-G-F-22K-L 5'. For the first nine genes, the exact gene boundaries were identified by comparison of the genomic sequences with previously determined mRNA sequences. The intergenic regions varied in length from 1 to 52 nucleotides and lacked any obvious conserved features of primary or secondary structure except that each sequence ended (3' to 5') with an adenosine residue. The exact start site of the 10th gene, the L gene, was not determined. However, RNA blot hybridization using a synthetic oligonucleotide designed from the genomic sequence mapped the L gene to within 54 nucleotides of the end of the penultimate 22K gene. The lack of conservation of chain length and nucleotide sequence for the respiratory syncytial viral intergenic regions, together with the complexity of the genetic map, contrasts with previous observations for other nonsegmented negative-strand viruses.

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Selected References

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

  1. Ball L. A., Wertz G. W. VSV RNA synthesis: how can you be positive? Cell. 1981 Oct;26(2 Pt 2):143–144. doi: 10.1016/0092-8674(81)90297-x. [DOI] [PubMed] [Google Scholar]
  2. Banerjee A. D., Abraham G., Colonno R. J. Vesicular stomatitis virus: mode of transcription. J Gen Virol. 1977 Jan;34(1):1–8. doi: 10.1099/0022-1317-34-1-1. [DOI] [PubMed] [Google Scholar]
  3. Blumberg B., Giorgi C., Roux L., Raju R., Dowling P., Chollet A., Kolakofsky D. Sequence determination of the Sendai virus HN gene and its comparison to the influenza virus glycoproteins. Cell. 1985 May;41(1):269–278. doi: 10.1016/0092-8674(85)90080-7. [DOI] [PubMed] [Google Scholar]
  4. Collins P. L., Anderson K., Langer S. J., Wertz G. W. Correct sequence for the major nucleocapsid protein mRNA of respiratory syncytial virus. Virology. 1985 Oct 15;146(1):69–77. doi: 10.1016/0042-6822(85)90053-4. [DOI] [PubMed] [Google Scholar]
  5. Collins P. L., Huang Y. T., Wertz G. W. Identification of a tenth mRNA of respiratory syncytial virus and assignment of polypeptides to the 10 viral genes. J Virol. 1984 Feb;49(2):572–578. doi: 10.1128/jvi.49.2.572-578.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Collins P. L., Huang Y. T., Wertz G. W. Nucleotide sequence of the gene encoding the fusion (F) glycoprotein of human respiratory syncytial virus. Proc Natl Acad Sci U S A. 1984 Dec;81(24):7683–7687. doi: 10.1073/pnas.81.24.7683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Collins P. L., Wertz G. W. Nucleotide sequences of the 1B and 1C nonstructural protein mRNAs of human respiratory syncytial virus. Virology. 1985 Jun;143(2):442–451. doi: 10.1016/0042-6822(85)90384-8. [DOI] [PubMed] [Google Scholar]
  8. Collins P. L., Wertz G. W. The 1A protein gene of human respiratory syncytial virus: nucleotide sequence of the mRNA and a related polycistronic transcript. Virology. 1985 Mar;141(2):283–291. doi: 10.1016/0042-6822(85)90259-4. [DOI] [PubMed] [Google Scholar]
  9. Collins P. L., Wertz G. W. The envelope-associated 22K protein of human respiratory syncytial virus: nucleotide sequence of the mRNA and a related polytranscript. J Virol. 1985 Apr;54(1):65–71. doi: 10.1128/jvi.54.1.65-71.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Collins P. L., Wertz G. W. cDNA cloning and transcriptional mapping of nine polyadenylylated RNAs encoded by the genome of human respiratory syncytial virus. Proc Natl Acad Sci U S A. 1983 Jun;80(11):3208–3212. doi: 10.1073/pnas.80.11.3208. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Dickens L. E., Collins P. L., Wertz G. W. Transcriptional mapping of human respiratory syncytial virus. J Virol. 1984 Nov;52(2):364–369. doi: 10.1128/jvi.52.2.364-369.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dowling P. C., Giorgi C., Roux L., Dethlefsen L. A., Galantowicz M. E., Blumberg B. M., Kolakofsky D. Molecular cloning of the 3'-proximal third of Sendai virus genome. Proc Natl Acad Sci U S A. 1983 Sep;80(17):5213–5216. doi: 10.1073/pnas.80.17.5213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Elango N., Satake M., Venkatesan S. mRNA sequence of three respiratory syncytial virus genes encoding two nonstructural proteins and a 22K structural protein. J Virol. 1985 Jul;55(1):101–110. doi: 10.1128/jvi.55.1.101-110.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Florkiewicz R. Z., Rose J. K. A cell line expressing vesicular stomatitis virus glycoprotein fuses at low pH. Science. 1984 Aug 17;225(4663):721–723. doi: 10.1126/science.6087454. [DOI] [PubMed] [Google Scholar]
  15. Giorgi C., Blumberg B. M., Kolakofsky D. Sendai virus contains overlapping genes expressed from a single mRNA. Cell. 1983 Dec;35(3 Pt 2):829–836. doi: 10.1016/0092-8674(83)90115-0. [DOI] [PubMed] [Google Scholar]
  16. Gupta K. C., Kingsbury D. W. Complete sequences of the intergenic and mRNA start signals in the Sendai virus genome: homologies with the genome of vesicular stomatitis virus. Nucleic Acids Res. 1984 May 11;12(9):3829–3841. doi: 10.1093/nar/12.9.3829. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gupta K. C., Kingsbury D. W. Conserved polyadenylation signals in two negative-strand RNA virus families. Virology. 1982 Jul 30;120(2):518–523. doi: 10.1016/0042-6822(82)90055-1. [DOI] [PubMed] [Google Scholar]
  18. Gupta K. C., Kingsbury D. W. Polytranscripts of Sendai virus do not contain intervening polyadenylate sequences. Virology. 1985 Feb;141(1):102–109. doi: 10.1016/0042-6822(85)90186-2. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Hsu C. H., Re G. G., Gupta K. C., Portner A., Kingsbury D. W. Expression of Sendai virus defective-interfering genomes with internal deletions. Virology. 1985 Oct 15;146(1):38–49. doi: 10.1016/0042-6822(85)90051-0. [DOI] [PubMed] [Google Scholar]
  21. Huang Y. T., Collins P. L., Wertz G. W. Characterization of the 10 proteins of human respiratory syncytial virus: identification of a fourth envelope-associated protein. Virus Res. 1985 Mar;2(2):157–173. doi: 10.1016/0168-1702(85)90246-1. [DOI] [PubMed] [Google Scholar]
  22. Huang Y. T., Wertz G. W. The genome of respiratory syncytial virus is a negative-stranded RNA that codes for at least seven mRNA species. J Virol. 1982 Jul;43(1):150–157. doi: 10.1128/jvi.43.1.150-157.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Iverson L. E., Rose J. K. Localized attenuation and discontinuous synthesis during vesicular stomatitis virus transcription. Cell. 1981 Feb;23(2):477–484. doi: 10.1016/0092-8674(81)90143-4. [DOI] [PubMed] [Google Scholar]
  24. Masters P. S., Samuel C. E. Detection of in vivo synthesis of polycistronic mRNAs of vesicular stomatitis virus. Virology. 1984 Apr 30;134(2):277–286. doi: 10.1016/0042-6822(84)90297-6. [DOI] [PubMed] [Google Scholar]
  25. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  26. Paterson R. G., Harris T. J., Lamb R. A. Analysis and gene assignment of mRNAs of a paramyxovirus, simian virus 5. Virology. 1984 Oct 30;138(2):310–323. doi: 10.1016/0042-6822(84)90354-4. [DOI] [PubMed] [Google Scholar]
  27. Paterson R. G., Harris T. J., Lamb R. A. Fusion protein of the paramyxovirus simian virus 5: nucleotide sequence of mRNA predicts a highly hydrophobic glycoprotein. Proc Natl Acad Sci U S A. 1984 Nov;81(21):6706–6710. doi: 10.1073/pnas.81.21.6706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Richardson C. D., Berkovich A., Rozenblatt S., Bellini W. J. Use of antibodies directed against synthetic peptides for identifying cDNA clones, establishing reading frames, and deducing the gene order of measles virus. J Virol. 1985 Apr;54(1):186–193. doi: 10.1128/jvi.54.1.186-193.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Rose J. K. Complete intergenic and flanking gene sequences from the genome of vesicular stomatitis virus. Cell. 1980 Feb;19(2):415–421. doi: 10.1016/0092-8674(80)90515-2. [DOI] [PubMed] [Google Scholar]
  30. Satake M., Elango N., Venkatesan S. Sequence analysis of the respiratory syncytial virus phosphoprotein gene. J Virol. 1984 Dec;52(3):991–994. doi: 10.1128/jvi.52.3.991-994.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Satake M., Venkatesan S. Nucleotide sequence of the gene encoding respiratory syncytial virus matrix protein. J Virol. 1984 Apr;50(1):92–99. doi: 10.1128/jvi.50.1.92-99.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. 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]
  33. 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]
  34. Wertz G. W., Collins P. L., Huang Y., Gruber C., Levine S., Ball L. A. Nucleotide sequence of the G protein gene of human respiratory syncytial virus reveals an unusual type of viral membrane protein. Proc Natl Acad Sci U S A. 1985 Jun;82(12):4075–4079. doi: 10.1073/pnas.82.12.4075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Zimmern D., Kaesberg P. 3'-terminal nucleotide sequence of encephalomyocarditis virus RNA determined by reverse transcriptase and chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4257–4261. doi: 10.1073/pnas.75.9.4257. [DOI] [PMC free article] [PubMed] [Google Scholar]

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