1887

Abstract

Philosophy of genome sequence studies. For the past four years I have been working on nucleotide sequence analyses of animal virus genetic material. During this time my attention has been more on the establishment and development of techniques than on the pursuit of analysis of one virus genome. Thus, I have worked on the genome RNAs and messenger RNAs of vesicular stomatitis virus and other rhabdoviruses, and also on the genome DNA of herpes simplex virus. It is evident that these form a rather disperse set of data on which to base this essay. Eventually, I decided to use the occasion to attempt to clear my own mind on the role of sequence analysis in research on animal viruses. I have from time to time encountered opinions hostile to or sceptical of such analysis. I have heard, often enough for it to stick, the term ‘mindless sequencing’.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-55-1-1
1981-07-01
2024-12-06
Loading full text...

Full text loading...

/deliver/fulltext/jgv/55/1/JV0550010001.html?itemId=/content/journal/jgv/10.1099/0022-1317-55-1-1&mimeType=html&fmt=ahah

References

  1. Akusjärvi G., Pettersson U. 1979; Sequence analysis of adenovirus DNA: complete nucleotide sequence of the spliced 5′ non-coding region of adenovirus 2 hexon messenger RNA. Cell 16:841–850
    [Google Scholar]
  2. Arrand J. R., Roberts R. J. 1979; The nucleotide sequences at the termini of adenovirus-2 DNA. Journal of Molecular Biology 128:577–594
    [Google Scholar]
  3. Atkins J. F., Steitz J. A., Anderson C. W., Model P. 1979; Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function. Cell 18:247–56
    [Google Scholar]
  4. Ayala F. J., Kiger J. A. 1980 Modern Genetics pp 48–49 California: Benjamin/Cummings;
    [Google Scholar]
  5. Ball L. A., White C. N. 1976; Order of transcription of genes of vesicular stomatitis virus. Proceedings of the National Academy of Sciences of the United States of America 73:442–446
    [Google Scholar]
  6. Banerjee A. K., Abraham G., Colonno R. J. 1977; Vesicular stomatitis virus: mode of transcription. Journal of General Virology 34:1–8
    [Google Scholar]
  7. Barrell B. G., Air G. M., Hutchinson C. A. 1976; Overlapping genes in bacteriophage ϕ X174. Nature, London 264:34–41
    [Google Scholar]
  8. Benoist C., O’Hare K., Breathnach R., Chambon P. 1980; The ovalbumin gene-sequence of putative control regions. Nucleic Acids Research 8:127–142
    [Google Scholar]
  9. Beremond M. N., Blumenthal T. 1979; Overlapping genes in RNA phage: a new protein implicated in lysis. Cell 18:257–266
    [Google Scholar]
  10. Bishop D. H. L., Aaslestad H. G., Clark H. F., Flamand A., Obijeski J. F., Repik P., Roy P. 1975; Evidence for the sequence homology and genome size of rhabdovirus RNAs. In Negative Strand Viruses vol 1 pp 259–292 Edited by Mahy B. W. J. Barry R. D. London: Academic Press;
    [Google Scholar]
  11. Busslinger M., Portmann R., Irminger J. C., Birnstiel M. L. 1980; Ubiquitous and gene-specific regulatory 5′ sequences in a sea urchin histone DNA clone coding for histone protein variants. Nucleic Acids Research 8:957–977
    [Google Scholar]
  12. Chargaff E. 1955; Isolation and composition of deoxypentose nucleic acids. In The Nucleic Acids vol 1 pp 368–369 Edited by Chargaff E., Davidson J. N. New York: Academic Press;
    [Google Scholar]
  13. Charnay P., Mondart E., Hampe A., Fitoussi F., Tiollais P., Galibert F. 1979; Localization on the viral genome and nucleotide sequence of the gene coding for the two major polypeptides of the hepatitis B surface antigen (HBs Ag). Nucleic Acids Research 7:335–346
    [Google Scholar]
  14. Chou P. Y., Fasman G. D. 1978; Empirical predictions of protein conformation. Annual Review of Biochemistry 47:251–276
    [Google Scholar]
  15. Clements J. B., McLauchlan J., McGeoch D. J. 1979; Orientation of herpes simplex virus type 1 immediate early mRNAs. Nucleic Acids Research 7:77–91
    [Google Scholar]
  16. Colbere-Garapin F., Chousterman S., Horodniceanu F., Kourilsky P., Garapin A. C. 1979; Cloning of the active thymidine kinase gene of herpes simplex virus type 1 in Escherichia coli K-12. Proceedings of the National Academy of Sciences of the United States ofAmerica 76:3755–3759
    [Google Scholar]
  17. Colonno R. J., Banerjee A. K. 1976; A unique RNA species involved in initiation of vesicular stomatitis virus RNA transcription in vitro . Cell 8:197–204
    [Google Scholar]
  18. Colonno R. J., Banerjee A. K. 1978a; Complete nucleotide sequence of the leader RNA synthesized in vitro by vesicular stomatitis virus. Cell 15:93–101
    [Google Scholar]
  19. Colonno R. J., Banerjee A. K. 1978b; Nucleotide sequence of the leader RNA of the New Jersey serotype of vesicular stomatitis virus. Nucleic Acids Research 5:4165–4176
    [Google Scholar]
  20. Czernilofsky A. P., Levinson A. D., Varmus H. E., Bishop J. M., Tischer E., Goodman H. M. 1980; Nucleotide sequence of an avian sarcoma virus oncogene (src) and proposed amino acid sequence for gene product. Nature, London 287:198–203
    [Google Scholar]
  21. Deininger P. L., Esty A., Laporte P., Hsu H., Friedmann T. 1980; The nucleotide sequence and restriction enzyme sites of the polyoma genome. Nucleic Acids Research 8:855–860
    [Google Scholar]
  22. Delius H., Clements J. B. 1976; A partial denaturation map of herpes simplex virus type 1 DNA: evidence for inversions of the unique DNA regions. Journal of General Virology 33:125–133
    [Google Scholar]
  23. Donis-Keller H., Maxam A., Gilbert W. 1977; Mapping adenines, guanines and pyrimidines in RNA. Nucleic Acids Research 4:2527–2538
    [Google Scholar]
  24. Enquist L. W., Vande Woude G. F., Wagner M., Smiley J. R., Summers W. C. 1979; Construction and characterization of a recombinant plasmid encoding the gene for the thymidine kinase of Herpes simplex type 1 virus. Gene 7:335–342
    [Google Scholar]
  25. Fiers W., Contreras R., Duerinck F., Haegeman G., Iserentant D., Merregaert J., Min Jou W., Molemans F., Raeymakers A., van Den Berghe A., Volkaert G., Ysebaert M. 1976; Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature, London 260:500–507
    [Google Scholar]
  26. Fiers W., Contreras R., Haegeman G., Rogiers R., van De Voorde A., van Heuverswyn H., van Herreweghe J., Volkaert G., Ysebaert M. 1978; Complete nucleotide sequence of SV40 DNA. Nature, London 273:113–120
    [Google Scholar]
  27. Freeman G. J., Rao D. D., Huang A. S. 1979; RNA synthesis of vesicular stomatitis virus. VIII. Oligonucleotides of the structural genes and mRNA. Gene 5:141–157
    [Google Scholar]
  28. Ghosh P. K., Reddy V. B., Swinscoe J., Lebowitz P., Weissman S. M. 1978; Heterogeneity and 5′-terminal structures of the late mRNAs of simian virus 40. Journal of Molecular Biology 126:813–846
    [Google Scholar]
  29. Gronenborn B., Messing J. 1978; Methylation of single-stranded DNA in vitro introduces new restriction endonuclease cleavage sites. Nature, London 272:375–377
    [Google Scholar]
  30. Herisse J., Courtois G., Galibert F. 1980; Nucleotide sequence of the Eco RI D fragment of adenovirus 2 genome. Nucleic Acids Research 8:2173–2192
    [Google Scholar]
  31. Herman R. C., Adler S., Lazzarini A., Colonno R. J., Banerjee A. K., Westphal H. 1978; Intervening polyadenylate sequences in RNA transcripts of vesicular stomatitis virus. Cell 15:587–596
    [Google Scholar]
  32. Holley R. W., Apgar J., Everett G. A., Madison J. T., Marquisee M., Merrill S. H., Penswick J. R., Zamir A. 1965; Structure of a ribonucleic acid. Science 147:1462–1465
    [Google Scholar]
  33. Keene J. D., Schubert M., Lazzarini R. A., Rosenberg M. 1978; Nucleotide sequence homology at the 3′ termini of RNA from vesicular stomatitis virus and its defective interfering particles. Proceedings of the National Academy of Sciences of the United States of America 75:3225–3229
    [Google Scholar]
  34. Kieff E. D., Bachenheimer S. L., Roizman B. 1971; Size, composition and structure of the deoxyribonucleic acid of herpes simplex virus subtypes 1 and 2. Journal of Virology 8:125–132
    [Google Scholar]
  35. Lamb R. A., Lai C. J. 1980; Sequence of interrupted and uninterrupted mRNAs and cloned DNA coding for the two overlapping nonstructural proteins of influenza virus. Cell 21:475–485
    [Google Scholar]
  36. McGeoch D. J. 1979; Structure of the gene N: gene NS intercistronic junction in the genome of vesicular stomatitis virus. Cell 17:673–681
    [Google Scholar]
  37. McGeoch D. J., Dolan A. 1979; Sequence of 200 nucleotides at the 3′-terminus of the genome RNA of vesicular stomatitis virus. Nucleic Acids Research 6:3199–3211
    [Google Scholar]
  38. McGeoch D. J., Turnbull N. T. 1978; Analysis of the 3′-terminal nucleotide sequence of vesicular stomatitis virus N protein mRNA. Nucleic Acids Research 5:4007–4024
    [Google Scholar]
  39. Mcgeoch D. J., Dolan A., Pringle C. R. 1980; Comparisons of nucleotide sequences in the genomes of the New Jersey and Indiana serotypes of vesicular stomatitis virus. Journal of Virology 33:69–77
    [Google Scholar]
  40. Maxam A. M., Gilbert W. 1977; A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America 74:560–564
    [Google Scholar]
  41. Maxam A. M., Gilbert W. 1980; Sequencing end-labeled DNA with base specific chemical cleavages. Methods in Enzymology 65:499–560
    [Google Scholar]
  42. Merregaert J., van Emmelo J., Devos R., Porter A., Fellner P., Fiers W. 1978; The 3′-terminal nucleotide sequence of encephalomyocarditis virus RNA. European Journal of Biochemistry 82:55–63
    [Google Scholar]
  43. Min Jou W., Verhoeyen M., Devos R., Saman E., Fang R., Huylebroek D., Fiers W., Threlfall G., Barber C., Carey N., Emtage S. 1980; Complete structure of the hemagglutinin gene from the human influenza A/Victoria/3/75 (H3N2) strain as determined from cloned DNA. Cell 19:683–696
    [Google Scholar]
  44. Nichols J. L., Hay A. J., Joklik W. K. 1972; 5′-terminal nucleotide sequence of reovirus mRNA synthesized in vitro . Nature New Biology 235:105–107
    [Google Scholar]
  45. Obijeski J. F., McCauley J., Skehel J. J. 1980; Nucleotide sequences at the termini of La Crosse virus RNAs. Nucelic Acids Research 8:2431–2438
    [Google Scholar]
  46. Ohe K., Weissman S. M. 1970; Nucleotide sequence of an RNA from cells infected with adenovirus 2. Science 167:879–881
    [Google Scholar]
  47. Pasek M., Goto T., Gilbert W., Zink B., Schaller H., MacKay P., Leadbetter G., Murray K. 1979; Hepatitis B virus genes and their expression in E. coli . Nature, London 282:575–579
    [Google Scholar]
  48. Peattie D. A. 1979; Direct chemical method for sequencing RNA. Proceedings of the National Academy of Sciences of the United States of America 76:1760–1764
    [Google Scholar]
  49. Porter A. G., Barber C., Carey N. H., Hallewell R. A., Threlfall G., Emtage J. S. 1979; Complete nucleotide sequence of an influenza virus haemagglutinin gene from cloned DNA. Nature, London 282:471–477
    [Google Scholar]
  50. Porter A. G., Smith J. C., Emtage J. S. 1980; Nucleotide sequence of influenza virus RNA segment 8 indicates that coding regions for NS1 and NS2 proteins overlap. Proceedings of the National Academy of Sciences of the United States of America 77:5074–5078
    [Google Scholar]
  51. Preston C. M. 1979; Control of herpes simplex virus type 1 mRNA synthesis in cells infected with wild-type virus or the temperature-sensitive mutant tsK . Journal of Virology 29:275–284
    [Google Scholar]
  52. Preston C. M., McGeoch D. J. 1981; Identification and mapping of two polypeptides encoded by the HSV-1 thymidine kinase gene. Journal of Virology (in press)
    [Google Scholar]
  53. Proudfoot N. J., Brownlee G. G. 1976; 3′ non-coding sequences in eukaryotic messenger RNA. Nature, London 263:211–214
    [Google Scholar]
  54. Reddy V. B., Thimmappaya B., Dhar R., Subramanian K. N., Zain S., Pan J., Ghosh P. K., Celma M. L., Weissman S. M. 1978; The genome of simian virus 40. Science 200:494–502
    [Google Scholar]
  55. Robertson H. D., Barrell B. G., Weith H. L., Donelson J. E. 1973; Isolation and sequence analysis of a ribosome-protected fragment from bacteriophage ϕ X 174 DNA. Nature New Biology 241:38–40
    [Google Scholar]
  56. Rose J. K. 1978; Complete sequences of the ribosome recognition sites in vesicular stomatitis virus mRNAs: recognition by the 40S and 80S complexes. Cell 14:345–353
    [Google Scholar]
  57. Rose J. K. 1980; Complete intergenic and flanking gene sequences from the genome of vesicular stomatitis virus. Cell 19:415–421
    [Google Scholar]
  58. Sanger F., Coulson A. R. 1975; A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology 94:441–448
    [Google Scholar]
  59. Sanger F., Brownlee G. G., Barrell B. G. 1965; A two-dimensional fractionation procedure for radioactive nucleotides. Journal of Molecular Biology 13:373–398
    [Google Scholar]
  60. Sanger F., Donelson J. E., Coulson A. R., Kössel H., Fischer D. 1973; Use of DNA polymerase I primed by a synthetic oligonucleotide to determine a nucleotide sequence in phage fl DNA. Proceedings of the National Academy of Sciences of the United States of America 70:1209–1213
    [Google Scholar]
  61. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America 74:5463–5467
    [Google Scholar]
  62. Sanger F., Coulson A. R., Barrell B. G., Smith A. J. H., Roe B. A. 1980; Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. Journal of Molecular Biology 143:161–178
    [Google Scholar]
  63. Schreier P. H., Cortese R. 1979; A fast and simple method for sequencing DNA cloned in the single-stranded bacteriophage M13. Journal of Molecular Biology 129:169–172
    [Google Scholar]
  64. Schubert M., Keene J. D., Herman R. C., Lazzarini R. A. 1980; Site on the vesicular stomatitis virus genome specifying polyadenylation and the end of the L gene mRNA. Journal of Virology 34:550–559
    [Google Scholar]
  65. Semler B. L., Perrault J., Abelson J., Holland J. J. 1978; Sequence of a RNA templated by the 3′-OH RNA terminus of defective interfering particles of vesicular stomatitis virus. Proceedings of the National Academy of Sciences of the United States of America 75:4704–4708
    [Google Scholar]
  66. Sheldrick P., Berthelot N. 1974; Inverted repetitions in the chromosome of herpes simplex virus. Cold Spring Harbor Symposia on Quantitative Biology 39:667–679
    [Google Scholar]
  67. Simoncsits A., Brownlee G. G., Brown R. S., Rubin J. R., Guilley H. 1977; New rapid gel sequencing method for RNA. Nature, London 269:833–836
    [Google Scholar]
  68. Skehel J. J., Hay A. J. 1978; Nucleotide sequences at the 5′ termini of influenza RNAs and their transcripts. Nucleic Acids Research 5:1207–1219
    [Google Scholar]
  69. Smiley J. R., Wagner M. J., Summers W. P., Summers W. C. 1980; Genetic and physical evidence for the polarity of transcription of the thymidine kinase gene of herpes simplex virus. Virology 102:83–93
    [Google Scholar]
  70. Soeda E., Arrand J. R., Smolar N., Walsh J. E., Griffin B. E. 1980; Coding potential and regulatory signals of the polyoma virus genome. Nature, London 283:445–453
    [Google Scholar]
  71. Steenbergh P. H., Sussenbach J. S., Roberts R. J., Jansz H. S. 1975; The 3′-terminal sequences of adenovirus types 2 and 5 DNA. Journal of Virology 15:268–272
    [Google Scholar]
  72. Sutcliffe J. G., Shinnick T. M., Verma I. M., Lerner R. A. 1980; Nucleotide sequence of Moloney leukemia virus: 3′ end reveals details of replication, analogy to bacterial transposons, and an unexpected gene. Proceedings of the National Academy of Sciences of the United States of America 77:3302–3306
    [Google Scholar]
  73. Testa D., Chanda P. K., Banerjee A. K. 1980; Unique mode of transcription in vitro by vesicular stomatitis virus. Cell 21:267–275
    [Google Scholar]
  74. Valenzuela P., Gray P., Quiroga M., Zaldivar J., Goodman H. M., Rutter W. J. 1979; Nucleotide sequence of the gene coding for the major protein of hepatitis B virus surface antigen. Nature, London 280:815–819
    [Google Scholar]
  75. van Ormondt H., Maat J., van Beveren C. P. 1980; The nucleotide sequence of the transforming early region El of adenovirus type 5 DNA. Gene 11:299–309
    [Google Scholar]
  76. Wigler M., Silverstein S., Lee L.-S., Pellicer A., Cheng Y., Axel R. 1977; Transfer of purified herpes virus thymidine kinase gene to cultured mouse cells. Cell 11:223–232
    [Google Scholar]
  77. Wilkie N. M., Davison A., Chartrand P., Stow N. D., Preston V. G., Timbury M. C. 1978; Recombination in herpes simplex virus: mapping of mutations and analysis of intertypic recombinants. Cold Spring Harbor Symposia on Quantitative Biology 43:827–840
    [Google Scholar]
  78. Wilkie N. M., Clements J. B., Boll W., Mantei N., Lonsdale D., Weissmann C. 1979; Hybrid plasmids containing an active thymidine kinase gene of Herpes simplex virus 1. Nucleic Acids Research 7:859–877
    [Google Scholar]
  79. Wilkie N. M., Eglin R. P., Sanders P. G., Clements J. B. 1980; The association of herpes simplex virus with squamous carcinoma of the cervix, and studies of the virus thymidine kinase gene. Proceedings of the Royal Society B 210:411–421
    [Google Scholar]
  80. Winter G., Fields S. 1980; Cloning of influenza cDNA into M13: the sequence of the RNA segment encoding the A/PR/8/34 matrix protein. Nucleic Acids Research 8:1965–1974
    [Google Scholar]
  81. Yang R. C. A., Wu R. 1979; BK virus DNA: complete nucleotide sequence of a human tumor virus. Science 206:456–462
    [Google Scholar]
  82. Ziff E. B., Sedat I. W., Galibert F. 1973; Determination of the nucleotide sequence of a fragment of bacteriophage ϕ X174 DNA. Nature New Biology 241:34–37
    [Google Scholar]
/content/journal/jgv/10.1099/0022-1317-55-1-1
Loading
/content/journal/jgv/10.1099/0022-1317-55-1-1
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error