Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 Jul 25;11(14):4689–4701. doi: 10.1093/nar/11.14.4689

Nucleotide sequence of the gene encoding the serotype-specific glycoprotein of UK bovine rotavirus.

T C Elleman, P A Hoyne, M L Dyall-Smith, I H Holmes, A A Azad
PMCID: PMC326079  PMID: 6308556

Abstract

The nucleotide sequence of the gene which encodes the major outer-shell glycoprotein of UK bovine rotavirus has been determined. The dsRNA genome segment encoding this protein was converted into ds cDNA and cloned into pBR322 for sequence studies. The gene is 1062 base pairs in length and contains a single, long, open reading-frame capable of coding for a protein of 326 amino-acids. This would leave 5' and 3' non-coding regions of 48 and 36 nucleotides in the mRNA. The predicted amino-acid sequence contains three possible glycosylation sites of the type Asn-X-Ser Thr, and an extremely hydrophobic N-terminal region. This sequence is discussed in the light of the known properties and functions of the protein.

Full text

PDF
4689

Images in this article

4693Image
on p.4693

Selected References

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

  1. Alton N. K., Vapnek D. Nucleotide sequence analysis of the chloramphenicol resistance transposon Tn9. Nature. 1979 Dec 20;282(5741):864–869. doi: 10.1038/282864a0. [DOI] [PubMed] [Google Scholar]
  2. Alwine J. C., Kemp D. J., Parker B. A., Reiser J., Renart J., Stark G. R., Wahl G. M. Detection of specific RNAs or specific fragments of DNA by fractionation in gels and transfer to diazobenzyloxymethyl paper. Methods Enzymol. 1979;68:220–242. doi: 10.1016/0076-6879(79)68017-5. [DOI] [PubMed] [Google Scholar]
  3. Anderson S., Gait M. J., Mayol L., Young I. G. A short primer for sequencing DNA cloned in the single-stranded phage vector M13mp2. Nucleic Acids Res. 1980 Apr 25;8(8):1731–1743. doi: 10.1093/nar/8.8.1731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Asbeck F., Beyreuther K., Köhler H., von Wettstein G., Braunitzer G. Virusproteine, IV. Die Konstitution des Hüllproteins des Phagen fd. Hoppe Seylers Z Physiol Chem. 1969 Sep;350(9):1047–1066. [PubMed] [Google Scholar]
  5. Bastardo J. W., McKimm-Breschkin J. L., Sonza S., Mercer L. D., Holmes I. H. Preparation and characterization of antisera to electrophoretically purified SA11 virus polypeptides. Infect Immun. 1981 Dec;34(3):641–647. doi: 10.1128/iai.34.3.641-647.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bentley D. L., Rabbitts T. H. Human immunoglobulin variable region genes--DNA sequences of two V kappa genes and a pseudogene. Nature. 1980 Dec 25;288(5792):730–733. doi: 10.1038/288730a0. [DOI] [PubMed] [Google Scholar]
  7. Bernstein J. M., Hruska J. F. Characterization of RNA polymerase products of Nebraska calf diarrhea virus and SA11 rotavirus. J Virol. 1981 Mar;37(3):1071–1074. doi: 10.1128/jvi.37.3.1071-1074.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Blobel G., Walter P., Chang C. N., Goldman B. M., Erickson A. H., Lingappa V. R. Translocation of proteins across membranes: the signal hypothesis and beyond. Symp Soc Exp Biol. 1979;33:9–36. [PubMed] [Google Scholar]
  9. Bonitz S. G., Coruzzi G., Thalenfeld B. E., Tzagoloff A., Macino G. Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase. J Biol Chem. 1980 Dec 25;255(24):11927–11941. [PubMed] [Google Scholar]
  10. Casadaban M. J., Cohen S. N. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179–207. doi: 10.1016/0022-2836(80)90283-1. [DOI] [PubMed] [Google Scholar]
  11. Cohen J., Laporte J., Charpilienne A., Scherrer R. Activation of rotavirus RNA polymerase by calcium chelation. Arch Virol. 1979;60(3-4):177–186. doi: 10.1007/BF01317489. [DOI] [PubMed] [Google Scholar]
  12. Duckworth M. L., Gait M. J., Goelet P., Hong G. F., Singh M., Titmas R. C. Rapid synthesis of oligodeoxyribonucleotides VI. Efficient, mechanised synthesis of heptadecadeoxyribonucleotides by an improved solid phase phosphotriester route. Nucleic Acids Res. 1981 Apr 10;9(7):1691–1706. doi: 10.1093/nar/9.7.1691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Dyall-Smith M. L., Azad A. A., Holmes I. H. Gene mapping of rotavirus double-stranded RNA segments by northern blot hybridization: application to segments 7, 8, and 9. J Virol. 1983 Apr;46(1):317–320. doi: 10.1128/jvi.46.1.317-320.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dyall-Smith M. L., Holmes I. H. Gene-coding assignments of rotavirus double-stranded RNA segments 10 and 11. J Virol. 1981 Jun;38(3):1099–1103. doi: 10.1128/jvi.38.3.1099-1103.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ericson B. L., Graham D. Y., Mason B. B., Estes M. K. Identification, synthesis, and modifications of simian rotavirus SA11 polypeptides in infected cells. J Virol. 1982 Jun;42(3):825–839. doi: 10.1128/jvi.42.3.825-839.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Fitzgerald M., Shenk T. The sequence 5'-AAUAAA-3'forms parts of the recognition site for polyadenylation of late SV40 mRNAs. Cell. 1981 Apr;24(1):251–260. doi: 10.1016/0092-8674(81)90521-3. [DOI] [PubMed] [Google Scholar]
  17. Flewett T. H., Thouless M. E., Pilfold J. N., Bryden A. S., Candeias J. A. More serotypes of human rotavirus. Lancet. 1978 Sep 16;2(8090):632–632. doi: 10.1016/s0140-6736(78)92854-4. [DOI] [PubMed] [Google Scholar]
  18. Grantham R., Gautier C., Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980 May 10;8(9):1893–1912. doi: 10.1093/nar/8.9.1893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Grantham R., Gautier C., Gouy M., Mercier R., Pavé A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980 Jan 11;8(1):r49–r62. doi: 10.1093/nar/8.1.197-c. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Greenberg H. B., Kalica A. R., Wyatt R. G., Jones R. W., Kapikian A. Z., Chanock R. M. Rescue of noncultivatable human rotavirus by gene reassortment during mixed infection with ts mutants of a cultivatable bovine rotavirus. Proc Natl Acad Sci U S A. 1981 Jan;78(1):420–424. doi: 10.1073/pnas.78.1.420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Grunstein M., Hogness D. S. Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc Natl Acad Sci U S A. 1975 Oct;72(10):3961–3965. doi: 10.1073/pnas.72.10.3961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Holmes I. H. Viral gastroenteritis. Prog Med Virol. 1979;25:1–36. [PubMed] [Google Scholar]
  23. Hopp T. P., Woods K. R. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3824–3828. doi: 10.1073/pnas.78.6.3824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Hudspeth M. E., Ainley W. M., Shumard D. S., Butow R. A., Grossman L. I. Location and structure of the var1 gene on yeast mitochondrial DNA: nucleotide sequence of the 40.0 allele. Cell. 1982 Sep;30(2):617–626. doi: 10.1016/0092-8674(82)90258-6. [DOI] [PubMed] [Google Scholar]
  25. Imai M., Richardson M. A., Ikegami N., Shatkin A. J., Furuichi Y. Molecular cloning of double-stranded RNA virus genomes. Proc Natl Acad Sci U S A. 1983 Jan;80(2):373–377. doi: 10.1073/pnas.80.2.373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kalica A. R., Greenberg H. B., Wyatt R. G., Flores J., Sereno M. M., Kapikian A. Z., Chanock R. M. Genes of human (strain Wa) and bovine (strain UK) rotaviruses that code for neutralization and subgroup antigens. Virology. 1981 Jul 30;112(2):385–390. doi: 10.1016/0042-6822(81)90285-3. [DOI] [PubMed] [Google Scholar]
  27. Killen H. M., Dimmock N. J. Identification of a neutralization-specific antigen of a calf rotavirus. J Gen Virol. 1982 Oct;62(Pt 2):297–311. doi: 10.1099/0022-1317-62-2-297. [DOI] [PubMed] [Google Scholar]
  28. Kozak M. How do eukaryotic ribosomes recognize the unique AUG initiator codon in messenger RNA? Biochem Soc Symp. 1982;47:113–128. [PubMed] [Google Scholar]
  29. Kupersztoch Y. M., Helinski D. R. A catenated DNA molecule as an intermediate in the replication of the resistance transfer factor R6K in Escherichia coli. Biochem Biophys Res Commun. 1973 Oct 15;54(4):1451–1459. doi: 10.1016/0006-291x(73)91149-2. [DOI] [PubMed] [Google Scholar]
  30. 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]
  31. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. McCrae M. A., Faulkner-Valle G. P. Molecular biology of rotaviruses. I. Characterization of basic growth parameters and pattern of macromolecular synthesis. J Virol. 1981 Aug;39(2):490–496. doi: 10.1128/jvi.39.2.490-496.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. McCrae M. A., McCorquodale J. G. The molecular biology of rotaviruses. II. Identification of the protein-coding assignments of calf rotavirus genome RNA species. Virology. 1982 Mar;117(2):435–443. doi: 10.1016/0042-6822(82)90482-2. [DOI] [PubMed] [Google Scholar]
  34. McMaster G. K., Carmichael G. G. Analysis of single- and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4835–4838. doi: 10.1073/pnas.74.11.4835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  36. Petrie B. L., Graham D. Y., Estes M. K. Identification of rotavirus particle types. Intervirology. 1981;16(1):20–28. doi: 10.1159/000149243. [DOI] [PubMed] [Google Scholar]
  37. Petrie B. L., Graham D. Y., Hanssen H., Estes M. K. Localization of rotavirus antigens in infected cells by ultrastructural immunocytochemistry. J Gen Virol. 1982 Dec;63(2):457–467. doi: 10.1099/0022-1317-63-2-457. [DOI] [PubMed] [Google Scholar]
  38. Radloff R., Bauer W., Vinograd J. A dye-buoyant-density method for the detection and isolation of closed circular duplex DNA: the closed circular DNA in HeLa cells. Proc Natl Acad Sci U S A. 1967 May;57(5):1514–1521. doi: 10.1073/pnas.57.5.1514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  40. Rodger S. M., Schnagl R. D., Holmes I. H. Further biochemical characterization, including the detection of surface glycoproteins, of human, calf, and simian rotaviruses. J Virol. 1977 Oct;24(1):91–98. doi: 10.1128/jvi.24.1.91-98.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]
  42. Sato K., Inaba Y., Miura Y., Tokuhisa S., Matumoto M. Antigenic relationships between rotaviruses from different species as studied by neutralization and immunofluorescence. Arch Virol. 1982;73(1):45–50. doi: 10.1007/BF01341726. [DOI] [PubMed] [Google Scholar]
  43. Schreier P. H., Cortese R. A fast and simple method for sequencing DNA cloned in the single-stranded bacteriophage M13. J Mol Biol. 1979 Mar 25;129(1):169–172. doi: 10.1016/0022-2836(79)90068-8. [DOI] [PubMed] [Google Scholar]
  44. Seed B. Diazotizable arylamine cellulose papers for the coupling and hybridization of nucleic acids. Nucleic Acids Res. 1982 Mar 11;10(5):1799–1810. doi: 10.1093/nar/10.5.1799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Smilowitz H., Carson J., Robbins P. W. Association of newly synthesized major f1 coat protein with infected host cell inner membrane. J Supramol Struct. 1972;1(1):8–18. doi: 10.1002/jss.400010103. [DOI] [PubMed] [Google Scholar]
  46. Smith M. L., Lazdins I., Holmes I. H. Coding assignments of double-stranded RNA segments of SA 11 rotavirus established by in vitro translation. J Virol. 1980 Mar;33(3):976–982. doi: 10.1128/jvi.33.3.976-982.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Staden R., McLachlan A. D. Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res. 1982 Jan 11;10(1):141–156. doi: 10.1093/nar/10.1.141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Wain-Hobson S., Nussinov R., Brown R. J., Sussman J. L. Preferential codon usage in genes. Gene. 1981 May;13(4):355–364. doi: 10.1016/0378-1119(81)90015-9. [DOI] [PubMed] [Google Scholar]
  49. Wiley D. C., Wilson I. A., Skehel J. J. Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature. 1981 Jan 29;289(5796):373–378. doi: 10.1038/289373a0. [DOI] [PubMed] [Google Scholar]
  50. Winter G., Fields S. Cloning of influenza cDNA ino M13: the sequence of the RNA segment encoding the A/PR/8/34 matrix protein. Nucleic Acids Res. 1980 May 10;8(9):1965–1974. doi: 10.1093/nar/8.9.1965. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Wyatt R. G., Greenberg H. B., James W. D., Pittman A. L., Kalica A. R., Flores J., Chanock R. M., Kapikian A. Z. Definition of human rotavirus serotypes by plaque reduction assay. Infect Immun. 1982 Jul;37(1):110–115. doi: 10.1128/iai.37.1.110-115.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES