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. 1990 Jan;64(1):331–338. doi: 10.1128/jvi.64.1.331-338.1990

A 3'-coterminal nested set of independently transcribed mRNAs is generated during Berne virus replication.

E J Snijder 1, M C Horzinek 1, W J Spaan 1
PMCID: PMC249106  PMID: 2293666

Abstract

By using poly(A)-selected RNA from Berne virus (BEV)-infected embryonic mule skin cells as a template, cDNA was prepared and cloned in plasmid pUC9. Recombinants covering a contiguous sequence of about 10 kilobases were identified. Northern (RNA) blot hybridizations with various restriction fragments from these clones showed that the five BEV mRNAs formed a 3'-coterminal nested set. Sequence analysis revealed the presence of four complete open reading frames of 4743, 699, 426, and 480 nucleotides, with initiation codons coinciding with the 5' ends of BEV RNAs 2 through 5, respectively. By using primer extension analysis and oligonucleotide hybridizations, RNA 5 was found to be contiguous on the consensus sequence. The transcription of BEV mRNAs was studied by means of UV mapping. BEV RNAs 1, 2, and 3 were shown to be transcribed independently, which is also likely--although not rigorously proven--for RNAs 4 and 5. Upstream of the AUG codon of each open reading frame a conserved sequence pattern was observed which is postulated to function as a core promoter sequence in subgenomic RNA transcription. In the area surrounding the core promoter region of the two most abundant subgenomic BEV RNAs, a number of homologous sequence motifs were identified.

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Selected References

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

  1. Beards G. M., Hall C., Green J., Flewett T. H., Lamouliatte F., Du Pasquier P. An enveloped virus in stools of children and adults with gastroenteritis that resembles the Breda virus of calves. Lancet. 1984 May 12;1(8385):1050–1052. doi: 10.1016/S0140-6736(84)91454-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Boccara M., Hamilton W. D., Baulcombe D. C. The organisation and interviral homologies of genes at the 3' end of tobacco rattle virus RNA1. EMBO J. 1986 Feb;5(2):223–229. doi: 10.1002/j.1460-2075.1986.tb04202.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  4. French R., Ahlquist P. Characterization and engineering of sequences controlling in vivo synthesis of brome mosaic virus subgenomic RNA. J Virol. 1988 Jul;62(7):2411–2420. doi: 10.1128/jvi.62.7.2411-2420.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Goelet P., Lomonossoff G. P., Butler P. J., Akam M. E., Gait M. J., Karn J. Nucleotide sequence of tobacco mosaic virus RNA. Proc Natl Acad Sci U S A. 1982 Oct;79(19):5818–5822. doi: 10.1073/pnas.79.19.5818. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Goldbach R., Wellink J. Evolution of plus-strand RNA viruses. Intervirology. 1988;29(5):260–267. doi: 10.1159/000150054. [DOI] [PubMed] [Google Scholar]
  7. Gubler U., Hoffman B. J. A simple and very efficient method for generating cDNA libraries. Gene. 1983 Nov;25(2-3):263–269. doi: 10.1016/0378-1119(83)90230-5. [DOI] [PubMed] [Google Scholar]
  8. Hamilton W. D., Boccara M., Robinson D. J., Baulcombe D. C. The complete nucleotide sequence of tobacco rattle virus RNA-1. J Gen Virol. 1987 Oct;68(Pt 10):2563–2575. doi: 10.1099/0022-1317-68-10-2563. [DOI] [PubMed] [Google Scholar]
  9. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  10. Horzinek M. C., Flewett T. H., Saif L. J., Spaan W. J., Weiss M., Woode G. N. A new family of vertebrate viruses: Toroviridae. Intervirology. 1987;27(1):17–24. doi: 10.1159/000149710. [DOI] [PubMed] [Google Scholar]
  11. Horzinek M. C., Weiss M. Toroviridae: a taxonomic proposal. Zentralbl Veterinarmed B. 1984 Oct;31(9):649–659. [PubMed] [Google Scholar]
  12. Jacobs L., Spaan W. J., Horzinek M. C., van der Zeijst B. A. Synthesis of subgenomic mRNA's of mouse hepatitis virus is initiated independently: evidence from UV transcription mapping. J Virol. 1981 Aug;39(2):401–406. doi: 10.1128/jvi.39.2.401-406.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lenstra J. A., de Groot R. J., Jacobs L., Kusters J. G., Niesters H. G., van der Zeijst B. A. Synthesis of long cDNA from viral RNA template. Gene Anal Tech. 1988 May-Jun;5(3):57–61. doi: 10.1016/0735-0651(88)90017-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Marsh L. E., Dreher T. W., Hall T. C. Mutational analysis of the core and modulator sequences of the BMV RNA3 subgenomic promoter. Nucleic Acids Res. 1988 Feb 11;16(3):981–995. doi: 10.1093/nar/16.3.981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Meinkoth J., Wahl G. Hybridization of nucleic acids immobilized on solid supports. Anal Biochem. 1984 May 1;138(2):267–284. doi: 10.1016/0003-2697(84)90808-x. [DOI] [PubMed] [Google Scholar]
  16. Ou J. H., Rice C. M., Dalgarno L., Strauss E. G., Strauss J. H. Sequence studies of several alphavirus genomic RNAs in the region containing the start of the subgenomic RNA. Proc Natl Acad Sci U S A. 1982 Sep;79(17):5235–5239. doi: 10.1073/pnas.79.17.5235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. 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]
  18. Sauerbier W., Hercules K. Gene and transcription unit mapping by radiation effects. Annu Rev Genet. 1978;12:329–363. doi: 10.1146/annurev.ge.12.120178.001553. [DOI] [PubMed] [Google Scholar]
  19. Snijder E. J., Ederveen J., Spaan W. J., Weiss M., Horzinek M. C. Characterization of Berne virus genomic and messenger RNAs. J Gen Virol. 1988 Sep;69(Pt 9):2135–2144. doi: 10.1099/0022-1317-69-9-2135. [DOI] [PubMed] [Google Scholar]
  20. Spaan W., Cavanagh D., Horzinek M. C. Coronaviruses: structure and genome expression. J Gen Virol. 1988 Dec;69(Pt 12):2939–2952. doi: 10.1099/0022-1317-69-12-2939. [DOI] [PubMed] [Google Scholar]
  21. Staden R. The current status and portability of our sequence handling software. Nucleic Acids Res. 1986 Jan 10;14(1):217–231. doi: 10.1093/nar/14.1.217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Strauss J. H., Strauss E. G. Evolution of RNA viruses. Annu Rev Microbiol. 1988;42:657–683. doi: 10.1146/annurev.mi.42.100188.003301. [DOI] [PubMed] [Google Scholar]
  23. Watanabe Y., Meshi T., Okada Y. The initiation site for transcription of the TMV 30-kDa protein messenger RNA. FEBS Lett. 1984 Jul 23;173(1):247–250. doi: 10.1016/0014-5793(84)81056-x. [DOI] [PubMed] [Google Scholar]
  24. Weiss M., Horzinek M. C. The proposed family Toroviridae: agents of enteric infections. Brief review. Arch Virol. 1987;92(1-2):1–15. doi: 10.1007/BF01310058. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Weiss M., Steck F., Horzinek M. C. Purification and partial characterization of a new enveloped RNA virus (Berne virus). J Gen Virol. 1983 Sep;64(Pt 9):1849–1858. doi: 10.1099/0022-1317-64-9-1849. [DOI] [PubMed] [Google Scholar]
  26. Woode G. N., Saif L. J., Quesada M., Winand N. J., Pohlenz J. F., Gourley N. K. Comparative studies on three isolates of Breda virus of calves. Am J Vet Res. 1985 May;46(5):1003–1010. [PubMed] [Google Scholar]
  27. de Groot R. J., ter Haar R. J., Horzinek M. C., van der Zeijst B. A. Intracellular RNAs of the feline infectious peritonitis coronavirus strain 79-1146. J Gen Virol. 1987 Apr;68(Pt 4):995–1002. doi: 10.1099/0022-1317-68-4-995. [DOI] [PubMed] [Google Scholar]
  28. van Berlo M. F., Horzinek M. C., van der Zeijst B. A. Equine arteritis virus-infected cells contain six polyadenylated virus-specific RNAs. Virology. 1982 Apr 30;118(2):345–352. doi: 10.1016/0042-6822(82)90354-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. van Berlo M. F., Rottier P. J., Horzinek M. C., van der Zeijst B. A. Intracellular equine arteritis virus (EAV)-specific RNAs contain common sequences. Virology. 1986 Jul 30;152(2):492–496. doi: 10.1016/0042-6822(86)90154-6. [DOI] [PubMed] [Google Scholar]

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