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The Gene pp 599-633 | Cite as

Viral Genes — Structure and Controls

  • Lawrence S. Dillon
Chapter
  • 497 Downloads

Abstract

Because of their minuteness and relative simplicity, the viruses afford insights into structural arrangements and activities that might long be overlooked in higher, more complex organisms. In many cases, however, these parasites have become degenerate in part by replacement of their original genes and translational products by those of the host cells. The resulting degree of dependency varies with the species, for many, including bacteriophage T4 among numerous others, expend considerable energy synthesizing macromolecules that duplicate or augment metabolic activities already present in its cellular habitat (Schmidt, 1985). By way of illustration, the genome of that T-even phage contains genes that encode one enzyme that cleaves the bacterial tRNAs near the anticodon and another pair that together repair the resulting damage, an altogether fruitless cycle. While useless to the virus, such relict genes are important from a biological point of view in suggesting that these organisms once were more completely supplied with genes and thus were less dependent upon living cellular types for existence. Hence, degeneration and evolutionary conservation have played antagonistic roles in molding the multitudinous diversity of extant viruses from their forebears of billions of years in the past.

Keywords

Mosaic Virus Viral Genome Tobacco Mosaic Virus Cucumber Mosaic Virus Early Promoter 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Reference

  1. Ahlquist, P., Luckow, V., and Kaesberg, P. 1981. Complete nucleotide sequence of brome mosaic virus RNA3. J. Mol. Biol. 153: 23–38.PubMedCrossRefGoogle Scholar
  2. Ahlquist, P., Dasgupta, R., and Kaesberg, P. 1984. Nucleotide sequence of the brome mosaic virus genome and its implications for viral replication. J. Mol. Biol. 172: 369–383.PubMedCrossRefGoogle Scholar
  3. Aleström, P., Akusjärvi, G., Pettersson, M., and Pettersson, U. 1982. DNA sequence analysis of the region encoding the terminal protein and the hypothetical N-gene product of adenovirus type II. J. Biol. Chem. 257: 13492–13498.PubMedGoogle Scholar
  4. Arnheiter, H., Davis, N. L., Wertz, G., Schubert, M., and Lazzarini, R. A. 1985. Role of the nucleocapsid protein in regulating vesicular stomatitis virus RNA synthesis. Cell 41: 259–267.PubMedCrossRefGoogle Scholar
  5. Atkins, J. F., Steitz, J. A., Anderson, C. W., and Model, P. 1979. Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function. Cell 18: 247–256.PubMedCrossRefGoogle Scholar
  6. Backhaus, H., and Petri, J. B. 1984. Sequence analysis of a region from the early right operon in phage P22, including the replication genes 18 and 12. Gene 32: 289–303.CrossRefGoogle Scholar
  7. Bailey, J. N., Klement, J. F., and McAllister, W. T. 1983. Relationship between promoter structure and template specificities exhibited by the bacteriophage T3 and T7 RNA polymerases. Proc. Natl. Acad. Sci. USA 80: 2814–2818.PubMedCrossRefGoogle Scholar
  8. Balâzs, E., Guilley, H., Jonard, G., and Richards, K. 1982. Nucleotide sequence of DNA from an altered-virulence D/H of the cauliflower mosaic virus. Gene 19: 239–249.PubMedCrossRefGoogle Scholar
  9. Baroudy, B. M., Venkateson, S., and Moss, B. 1982. Incompletely base-paired flip-flop terminal loops link the two DNA strands of the vaccinia virus genome into one uninterrupted polynucleotide chain. Cell 28: 315–324.PubMedCrossRefGoogle Scholar
  10. Baty, D., Barrera-Saldana, H. A., Everett, R. D., Vigneron, M., and Chambon, P. 1984. Mutational dissection of the 21 bp repeat region of the SV40 early promoter reveals that it contains overlapping elements of the early-early and late-early promoters. Nucleic Acids Res. 12: 915–932.PubMedCrossRefGoogle Scholar
  11. Beck, E., Sommer, R., Auerswald, E. A., Kürz, C., Zink, B., Osterburg, G., Schaller, H., Sugimoto, K., Sugisaki, H., Okamoto, T., and Takanami, M. 1978. Nucleotide sequence of bacteriophage fd DNA. Nucleic Acids Res. 5: 4495–4503.PubMedCrossRefGoogle Scholar
  12. Benoist, C., and Chambon, P. 1981. In vivo sequence requirements of the SV40 early promoter region. Nature (London) 290: 304–310.Google Scholar
  13. Berget, P. B., Poteete, A. R., and Sauer. R. T. 1983. Control of phage P22 tail protein expression by transcription termination. J. Mol. Biol. 164: 561–572.PubMedCrossRefGoogle Scholar
  14. Blomquist, M. C., Hunt, L. T., and Barker, W. C. 1984. Vaccinia virus 19-kilodalton protein: Relationship to several mammalian proteins including two growth factors. Proc. Natl. Acad. Sci. USA 81: 7363–7367.PubMedCrossRefGoogle Scholar
  15. Bodescot, M., Chambrand, B., Farrell, P., and Perricaudet, M. 1984. Spliced RNA from the IR1–U2 region of Epstein-Barr virus: Presence of an open reading frame for a repetitive polypeptide. EMBO J. 3: 1913–1917.PubMedGoogle Scholar
  16. Boursnell, M. E. G., and Brown, T. D. K. 1984. Sequencing of coronavirus IBV genomic RNA: A 195-base open reading frame encoded by mRNA B. Gene 29: 87–92.PubMedCrossRefGoogle Scholar
  17. Braam, J., Ulmanen, I., and Krug, R. M. 1983. Molecular model of a eucaryotic transcription complex: Functions and movements of influenza P proteins during capped RNA-primed transcription. Cell 34: 609–618.PubMedCrossRefGoogle Scholar
  18. Brady, J., Radonovich, M., Vodkin, M., Natarajan, V., Thoren, M., Das, G., Janik, J., and Salzman, N. P. 1982. Site-specific base substitution and deletion mutations that enhance or suppress transcription of the SV40 major late RNA. Cell 31: 625–633.PubMedCrossRefGoogle Scholar
  19. Brady, J., Radonovich, M., Thoren, M., Das, G., and Salzman, N. P. 1984. Simian virus 40 major late promoter: An upstream DNA sequence required for efficient in vitro transcription. Mol. Cell. Biol. 4: 133–141PubMedGoogle Scholar
  20. Brederode, F. T., Koper-Zwarthoff, E. C., and Bol, J. F. 1980. Complete nucleotide sequence of alfalfa mosaic virus RNA 4. Nucleic Acids Res. 8: 2213–2223.PubMedCrossRefGoogle Scholar
  21. Byrne, B. J., Davis, M. S., Yamaguchi, J., Bergsma, D. J., and Subramanian, K. N. 1983. Definition of the simian virus 40 early promoter region and demonstration of a host range bias in the enhancement effect of the simian virus 40 72-base-pair repeat. Proc. Natl. Acad. Sci. USA 80: 721–725.PubMedCrossRefGoogle Scholar
  22. Callahan, P. L., Mizutani, S., and Colonno, R. J. 1985. Molecular cloning and complete sequence determination of RNA genome of human rhinovirus type 14. Proc. Natl. Acad. Sci. USA 82: 732–736.PubMedCrossRefGoogle Scholar
  23. Campbell, A. 1983. Bacteriophage X. In: Shapiro, J. A., ed., Mobile Genetic Elements, New York, Academic Press, pp. 65–104.Google Scholar
  24. Carroll, A. R., Rowlands, D. J., and Clarke, B. E. 1984. The complete nucleotide sequence of the RNA coding for the primary translation product of foot and mouth disease virus. Nucleic Acids Res. 12: 2461–2472.PubMedCrossRefGoogle Scholar
  25. Cashdollar, L. W., Esparza, J., Hudson, G. R., Chmelo, R., Lee, P. W. K., and Joklic, W. K. 1982. Cloning the double-stranded RNA genes for reovirus: Sequence of the cloned S2 gene. Proc. Natl. Acad. Sci. USA 79: 7644–7648.PubMedCrossRefGoogle Scholar
  26. Cashdollar, L. W., Chmelo, R. A., Wiener, J. R., and Joklik, W. K. 1985. Sequences of the S1 genes of the three serotypes of reovirus. Proc. Natl. Acad. Sci. USA 82: 24–28.PubMedCrossRefGoogle Scholar
  27. Chow, L. T., Broker, T., and Lewis, J. B. 1979. Complex splicing patterns of RNAs from the early regions of adenovirus-2. J. Mol. Biol. 134: 265–303.PubMedCrossRefGoogle Scholar
  28. Christie, G. E., and Calendar, R. 1985. Bacteriophage P2 late promoters. II. Comparison of the four late promoter sequences. J. Mol. Biol. 181: 373–382.PubMedCrossRefGoogle Scholar
  29. Chu, F. K., Maley, G. F., Maley, F., and Belfort, M. 1984. Intervening sequence in the thymidylate synthase gene of bacteriophage T4. Proc. Natl. Acad. Sci. USA 81: 3049–3053.PubMedCrossRefGoogle Scholar
  30. Cochran. M. A., Puckett, C., and Moss. B. 1985. In vitro mutagenesis of the promoter region for a vaccinia virus gene: Evidence for tandem early and late regulatory signals. J. Virol. 54: 30–37.Google Scholar
  31. Concino, M. F., Lee, R. F., Merryweather, J. P., and Weinmann, R. 1984. The adenovirus major late promoter TATA box and initiation site are both necessary for transcription in vitro. Nucleic Acids Res. 12: 7423–7433.CrossRefGoogle Scholar
  32. Conway, L., and Wickens, M. 1985. A sequence of A-A-U-A-A-A is required for formation of simian virus 40 late mRNA3 termini in frog oocytes. Proc. Natl. Acad. Sci. USA 82: 3949–3953.PubMedCrossRefGoogle Scholar
  33. Cornelissen, B. J. C., Brederode, F. T., Moormann, R. J. M., and Bol, J. F. 1983a. A complete nucleotide sequence of alfalfa mosaic virus RNA 1. Nucleic Acids Res. 11: 1253–1265.PubMedCrossRefGoogle Scholar
  34. Cornelissen, B. J. C., Brederode, F. T., Vesneman, G. H., van Boom, J. H., and Bol, J. F. 1983b. Complete nucleotide sequence of alfalfa mosaic virus RNA 2. Nucleic Acids Res. 11: 3019–3025.PubMedCrossRefGoogle Scholar
  35. Comelissen, B. J. C., Janssen, H., Zuidema, D., and Bol, J. F. 1984. Complete nucleotide sequence of tobacco streak RNA 3. Nucleic Acids Res. 12: 2427–2437.CrossRefGoogle Scholar
  36. Costa, R. H., Draper, K. G., Kelly, T. J., and Wagner, E. K. 1985. An unusual spliced herpes simplex virus type 1 transcript with sequence homology to Epstein-Barr virus DNA. J. Virol. 54: 317–328.PubMedGoogle Scholar
  37. Craig, N. L. 1985. Site-specific inversion: Enhancers, recombination proteins, and mechanism. Cell 41: 649–650.PubMedCrossRefGoogle Scholar
  38. Davies, J. W., Stanley, J., and Van Kammen, A. 1979. Sequence homology adjacent to the 3’ terminal poly(A) of cowpea mosaic virus RNAs. Nucleic Acids Res. 7: 493–500.PubMedCrossRefGoogle Scholar
  39. Davies, R. W. 1980. DNA sequence of the int-xis-P1 region of the bacteriophage X: Overlap of the int and xis genes. Nucleic Acids Res. 8: 1765–1782.PubMedCrossRefGoogle Scholar
  40. Haseth, P. L., Goldman, R. A., Cech, C. L., and Caruthers, M. H. 1983. Chemical synthesis and biochemical reactivity of bacteriophage lambda PR promoter. Nucleic Acids Res. 11: 773–787.CrossRefGoogle Scholar
  41. Dekker, B. M. M., and van Ormondt, H. 1984. The nucleotide sequence of fragment HindIII-C of human adenovirus type 5 DNA (map positions 17.1–31.7). Gene 27: 115–120.PubMedCrossRefGoogle Scholar
  42. Dillon, L. S. 1978. The Genetic Mechanism and the Origin of Life, New York, Plenum Press.CrossRefGoogle Scholar
  43. Dixon, L. K., and Hohn, T. 1984. Initiation of translation of the cauliflower mosaic virus genome from a polycistronic mRNA: Evidence from deletion mutagenesis. EMBO J. 3: 2731–2736.PubMedGoogle Scholar
  44. Dunn, J. J., and Studier, F. W. 1983. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166: 477–535.PubMedCrossRefGoogle Scholar
  45. Dyall-Smith, M. L., and Holmes, I. H. 1984. Sequence homology between human and animal rotavirus serotype-specific glycoproteins. Nucleic Acids Res. 12: 3973–3982.PubMedCrossRefGoogle Scholar
  46. Elliott, T., and Geiduschek, E. P. 1984. Defining a bacteriophage T4 late promoter: absence of a “-35” region. Cell 36: 211–219.PubMedCrossRefGoogle Scholar
  47. Emerson, S. U. 1982. Reconstitution studies detect a single polymerase entry site on the vesicular stomatitis virus genome. Cell 31: 635–642.PubMedCrossRefGoogle Scholar
  48. Ernoult-Lange, M., and May, E. 1983. Evidence of transcription from the late region of the integrated simian virus 40 genome in transformed cells: Location of the 5’ ends of late transcripts in cells abortively infected and in cells transformed by simian virus 40. J. Virol. 46: 756–767.PubMedGoogle Scholar
  49. Escarmis, C., and Salas, M. 1982. Nucleotide sequence of the early genes 3 and 4 of bacteriophage 4.29. Nucleic Acids Res. 10: 5785–5798.PubMedCrossRefGoogle Scholar
  50. Everett, R. D., Baty, D., and Chambon, P. 1983. The repeated GC-rich motifs upstream from the TATA box are important elements of the SV40 early promoter. Nucleic Acids Res. 11: 2447–2464.PubMedCrossRefGoogle Scholar
  51. Fiers, W., Contreras, R., Duerinck, F., Haegmean, G., Merregaert, J., Min Jou, W., Raeymakers, A., Volckaert, G., Ysebaert, M., Van de Kerckhove, J., Nolf, F., and Van Montagu, M. 1975. A-protein gene of bacteriophage MS2. Nature (London) 256: 273–278.CrossRefGoogle Scholar
  52. Fiers, W., Contreras, R., Haegeman, G., Rogiers, R., Van deVoorde, A., Van Heuverswyn, H., Van Herreweghe, J., Volckaert, G., and Ysebaert, M. 1978. Complete nucleotide sequence of SV40 DNA. Nature (London) 273: 113–119.CrossRefGoogle Scholar
  53. Franck, A., Guilley, H., Jonard, G., Richards, K., and Hirth, L. 1980. Nucleotide sequence of cauliflower mosaic virus DNA. Cell 21: 285–294.PubMedCrossRefGoogle Scholar
  54. Franssen, H., Leunissen, J., Goldback, R., Lomonossoff, G., and Zimmern, D. 1984. Homologous sequences in non-structural proteins from cowpea mosaic virus and picornaviruses. EMBO J. 3: 655–661.Google Scholar
  55. Fulford, W., and Model, P. 1984. Gene X of bacteriophage fl is required for phage DNA synthesis. Mutagenesis of in-frame overlapping genes. J. Mol. Biol. 178: 137–153.PubMedCrossRefGoogle Scholar
  56. Furuichi, Y. 1978. “Pretranscriptional capping” in the biosynthesis of cytoplasmic polyhedrosis virus mRNA. Proc. Natl. Acad. Sci. USA 75:1086–1090.Google Scholar
  57. Gardner, R. C., Howarth, A. J., Hahn, P., Brown-Leudi, M., Shepherd, R. J., and Messing, J. 1981. The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shot gun sequencing. Nucleic Acids Res. 9: 2871–2887.PubMedCrossRefGoogle Scholar
  58. Gaynor, R. B., and Beck, A. J. 1983. Cis-acting induction of adenovirus transcription. Cell 33: 683–693.PubMedCrossRefGoogle Scholar
  59. Gerald, W. L., and Karam, J. D. 1984. Expression of a DNA replication gene cluster in bacteriophage T4: Genetic linkage and the control of gene product interactions. Genetics 107: 537–549.PubMedGoogle Scholar
  60. Ghosh, P. K., Lebowitz, P., Frisque, R. J., and Gluzman, Y. 1981. Identification of a promoter component involved in positioning the 5’ termini of simian virus 40 early mRNAs. Proc. Natl. Acad. Sci. USA 78: 100–104.PubMedCrossRefGoogle Scholar
  61. Gibson, T., Stockwell, P., Ginsburg, M., and Barrel, B. 1984. Homology between two EBV early genes and HSV ribonucleotide reductase and 38K genes. Nucleic Acids Res. 12: 5087–5099.PubMedCrossRefGoogle Scholar
  62. Giorgi, C., Blumberg, B. M., and Kolakofsky, D. 1983. Sendai virus contains overlapping genes expressed from a single mRNA. Cell 35: 829–836.PubMedCrossRefGoogle Scholar
  63. Goelet, P., Lommossoff, G. P., Butler, P. J. G., Akam, M. E., Gait, M. J., and Kant, J. 1982. Nucleotide sequence of tobacco mosaic virus RNA. Proc. Natl. Acad. Sci. USA 79: 5818–5822.PubMedCrossRefGoogle Scholar
  64. Gomez-Marquez, J., Puga, A., and Notkins, A. L. 1985. Regions of the terminal repetitions of the herpes simplex virus type 1 genome. Relationship to immunoglobulin switch-like DNA sequences. J. Biol. Chem. 260: 3490–3495.PubMedGoogle Scholar
  65. Gram, H., and Rüger, W. 1985. Genes 55, at, 47 and 46 of bacteriophage T4: The genomic organization as deduced by sequence analysis. EMBO J. 4: 257–264.PubMedGoogle Scholar
  66. Greene, J. R., Brennan, S. M., Andrew, D. J., Thompson, C. C., Richards, S. H., Heinrikson, R. L., and Geiduschek, E. P. 1984. Sequence of the bacteriophage SPO 1 gene coding for transcription factor 1, a viral homolog of the bacterial type II DNA-binding proteins. Proc. Natl. Acad. Sci. USA 81: 7031–7035.PubMedCrossRefGoogle Scholar
  67. Griffith, J. D., and Nash, H. A. 1985. Genetic rearrangement of DNA induces knots with a unique topology: Implications for the mechanism of synapsis and crossing-over. Proc. Natl. Acad. Sci. USA 82: 3124–3128.PubMedCrossRefGoogle Scholar
  68. Grinnell, B. W., and Wagner, R. R. 1984. Nucleotide sequence and secondary structure of VSV leader RNA and homologous DNA involved in inhibition of DNA-dependent transcription. Cell 36: 533–543.PubMedCrossRefGoogle Scholar
  69. Gruss, P., Dhar, R., and Khoury, G. 1981. Simian virus 40 tandem repeated sequences as an element of the early promoter. Proc. Natl. Acad. Sci. USA 78: 943–947.PubMedCrossRefGoogle Scholar
  70. Guilfoyle, A., Osheroff, W. P., and Rossini, M. 1985. Two functions encoded by adenovirus early region IA are responsible for the activation and repression of the DNA-binding protein gene. EMBO J. 4: 707–713.PubMedGoogle Scholar
  71. Guilley, H., Jonard, G., Kukla, B., and Richards, K. E. 1979. Sequence of 1000 nucleotides at the 3’ end of tobacco mosaic virus RNA. Nucleic Acids Res. 6: 1287–1308.PubMedCrossRefGoogle Scholar
  72. Guilley, H., Dudley, R. K., Jonard, G., Balks, E., and Richards, K. E. 1982. Transcription of cauliflower mosaic virus DNA: Detection of promoter sequences, and characterization of transcripts. Cell 30: 763–773.PubMedCrossRefGoogle Scholar
  73. Hamilton, W. D. O., Bisaro, D. M., and Buck, K. W. 1982. Identification of novel DNA forms in tomato golden mosaic virus infected tissue. Evidence for a two component viral genome. Nucleic Acids Res. 10: 4901–4912.PubMedCrossRefGoogle Scholar
  74. Hamilton, W. D. O., Stein, V. E., Coutts, R. H. A., and Buck, K. W. 1984. Complete nucleotide sequence of the infectious cloned DNA components of tomato golden mosaic virus: Potential coding regions and regulatory sequences. EMBO J. 3: 2197–2205.PubMedGoogle Scholar
  75. Hattman, S., and Ives, J. 1984. SI nuclease mapping of the phage Mu mom gene promoter: A model for the regulation of mom expression. Gene 29: 185–198.PubMedCrossRefGoogle Scholar
  76. Hen, R. Borrelli, E., Sassone-Corsi, P., and Chambon, P. 1983. An enhancer element is located 340 base pairs upstream from the adenovirus-2 EIA capsite. Nucleic Acids Res. 11: 8747–8760.PubMedCrossRefGoogle Scholar
  77. Hill, D. F., and Petersen, G. B. 1982. Nucleotide sequence of bacteriophage fl DNA. J. Virol. 44: 32–46.PubMedGoogle Scholar
  78. Hiti, A. L., and Nayak, D. P. 1985. Complete nucleotide sequence of the neuraminidase gene of human influenza virus A/WSN/33. J. Virol. 41: 730–734.Google Scholar
  79. Ho, Y. S., Wulff, D. L., and Rosenberg, M. 1983. Bacteriophage X protein cil binds promoters on the opposite face of the DNA from RNA polymerase. Nature (London) 304: 703–708.CrossRefGoogle Scholar
  80. Holder, R. D., and Whiteley, H. R. 1983. In vitro synthesis of late bacteriophage 4 29 RNA. J. Virol. 46: 690–702.Google Scholar
  81. Hoopes, B. C., and McClure, W. R. 1985. A cII-dependent promoter is located within the Q gene of bacteriophage X. Proc. Natl. Acad. Sci. USA 82: 3134–3138.PubMedCrossRefGoogle Scholar
  82. Hoyt, M. A., Knight, D. M., Das, A., Miller, H. I., and Echols, H. 1982. Control of phage X development by stability and synthesis of cII protein: Role of the viral cIII and host hflA, himA, and himD genes. Cell 31: 565–573.PubMedCrossRefGoogle Scholar
  83. Huddleston, J. A., and Brownlee, G. G. 1982. The sequence of the nucleoprotein gene of human influenza A virus, strain A/NT/60/68. Nucleic Acids Res. 10: 1029–1038.PubMedCrossRefGoogle Scholar
  84. Imai, M., Richardson, M. A., Ikegami, N., Shatkin, A. J., and Furuichi, Y. 1983. Molecular cloning of double-stranded RNA virus genomes. Proc. Natl. Acad. Sci. USA 80: 373–377.PubMedCrossRefGoogle Scholar
  85. Inokuchi, Y., Hirashima, A., and Watanabe, I. 1982. Comparison of the nucleotide sequences at the 3’-terminal region of RNAs from RNA coliphages. J. Mol. Biol. 158: 711–730.PubMedCrossRefGoogle Scholar
  86. Jones, M. D., and Griffin, B. E. 1983. Clustered repeat sequences in the genome of Epstein Barr virus. Nucleic Acids Res. 11: 3919–3937.PubMedCrossRefGoogle Scholar
  87. Kahmann, R., Rudt, F., Koch, C., and Mertens, G. 1985. G inversion in bacteriophage Mu DNA is stimulated by a site within the invertase gene and a host factor. Cell 41: 771–780.PubMedCrossRefGoogle Scholar
  88. Kassavetis, G. A., Elliott, T., Rabussay, D. P., and Geiduschek, E. P. 1983. Initiation of transcription at phage T4 late promoters with purified RNA polymerases. Cell 33: 887–897.PubMedCrossRefGoogle Scholar
  89. Katze, M. G., Chen, Y.-T., and Krug, R. M. 1984. Nuclear-cytoplasmic transport and VA1 RNA-independent translation of influenza viral messenger RNAs in late adenovirus-infected cells. Cell 37: 483–490.PubMedCrossRefGoogle Scholar
  90. Keller, J. M., and Alwine, J. C. 1984. Activation of the SV40 late promoter: Direct effects of T antigen in the absence of viral DNA replication. Cell 36: 381–389.PubMedCrossRefGoogle Scholar
  91. Keohavong, P., Gattoni, R., LeMoullec, J. M., Jacob, M., and Stévenin, J. 1982. The orderly splicing of the first three leaders of the adenovirus-2 major late transcript. Nucleic Acids Res. 10: 1215–1229.PubMedCrossRefGoogle Scholar
  92. Kozlov, Y. V., Rupasov, V. V., Adshey, D. M., Belgelkarskaya, S. N., Agranovsky, A. A., Mankin, A. S., Morozov, S. Y., Dolja, V. V., and Atabekov, J. G. 1984. Nucleotide sequence of the 3’-terminal tRNAlike structure in barley stripe mosaic virus genome. Nucleic Acids Res. 12: 4001–4009.PubMedCrossRefGoogle Scholar
  93. Krause, H. M., Rothwell, M. R., and Higgins, N. P. 1983. The early promoter of bacteriophage Mu: Definition of the site of transcript initiation. Nucleic Acids Res. 11: 5483–5495.PubMedCrossRefGoogle Scholar
  94. La Farina, M., and Vitale, M. 1984. Rho-dependence of the terminator active at the end of the I region of transcription of bacteriophage fi. Mol. Gen. Genet. 195: 5–9.PubMedCrossRefGoogle Scholar
  95. Lamb, R. A., and Choppin, P. W. 1979. Segment 8 of the influenza virus genome is unique in coding for two polypeptides. Proc. Natl. Acad. Sci. USA 76: 4908–4912.PubMedCrossRefGoogle Scholar
  96. Lamb, R. A., and Lai, C. J. 1980. Sequence of interrupted and uninterrupted mRNAs and cloned DNA coding for the two overlapping non-structural proteins of influenza virus. Cell 21: 475–485.PubMedCrossRefGoogle Scholar
  97. Lamb, R. A., Choppin, P. W., Chanock, R. M., and Lai, C. J. 1980. Mapping of the two overlapping genes for polypeptides NS, and NS2 on RNA segment 8 of influenza virus genome. Proc. Natl. Acad. Sci. USA 77: 1857–1861.PubMedCrossRefGoogle Scholar
  98. Lamb, R. A., Zebedee, S. L., and Richardson, C. D. 1985. Influenza virus M2 protein is an integral membrane protein expressed on the infected-cell surface. Cell 40: 827–833.CrossRefGoogle Scholar
  99. Lamy, D., Jonard, G., Guilley, H., and Hirth, L. 1975. Comparison between the 3’OH end RNA sequence of two strains of TMV which may be aminoacylated. J. Biol. Chem. 247: 4966–4974.Google Scholar
  100. Langner, K. D., Vardimon, L., Renz, D., and Doerfler, W. 1984. DNA methylation of three 5’ C-C-G-G 3’ sites in the promoter and 5’ region inactivate the Eta gene of adenovirus type 2. Proc. Natl. Acad. Sci. USA 81: 2950–2954.PubMedCrossRefGoogle Scholar
  101. Lee, G., and Pero, J. 1981. Conserved nucleotide sequences in temporally controlled bacteriophage promoters. J. Mol. Biol. 152: 247–265.PubMedCrossRefGoogle Scholar
  102. Lee, D. C., Roeder, R. G., and Wold, W. S. M. 1982. DNA sequences affecting specific initiation of transcription in vitro from the EIII promoter of adenovirus 2. Proc. Natl. Acad. Sci. USA 79: 41–45.PubMedCrossRefGoogle Scholar
  103. Lengyel, J. A., and Calendar, R. 1974. Control of bacteriophage P2 protein and DNA synthesis. Virology 57: 305–313.PubMedCrossRefGoogle Scholar
  104. Luiten, R. G. M., Schoenmakers, J. G. G., and Konings, R. N. H. 1983. Major coat protein gene of the filamentous Pseudomonas aeruginosa phage Pf3: Absence of a N-terminal leader signal sequence. Nucleic Acids Res. 11: 8073–8085.PubMedCrossRefGoogle Scholar
  105. Mathis, D. J., and Chambon, P. 1981. The SV40 early region TATA box is required for accurate in vitro initiation of transcription. Nature (London) 290: 310–315.CrossRefGoogle Scholar
  106. Matsui, T. 1982. In vitro accurate initiation of transcription on the adenovirus type 2 IVa2 gene which does not contain a TATA box. Nucleic Acids Res. 10: 7089–7101.PubMedGoogle Scholar
  107. Meyer, F., Weber, H., and Weissmann, C. 1981. Interactions of Q13 replicase with Q13 RNA. J. Mol. Biol. 153: 631–660.PubMedCrossRefGoogle Scholar
  108. Mills, D. R., Dobkin, C., and Kramer, F. R. 1978. Template-determined variable rate of RNA chain elongation. Cell 15: 541–550.PubMedCrossRefGoogle Scholar
  109. Min Jou, W., and Fiers, W. 1976. Studies on the bacteriophage MS2. XXXIII. Comparison of the nucleotide sequences in related bacteriophage RNAs. J. Mol. Biol. 106: 1047–1060.CrossRefGoogle Scholar
  110. Miura, N., Nakatani, Y., Ishiura, M., Uchida, T., and Okada, Y. 1985. Molecular cloning of a full-length cDNA encoding the hemaglutinin-neuraminidase glycoprotein of Sendai virus. FEBS Lett. 188: 112–116.PubMedCrossRefGoogle Scholar
  111. Moffatt, B. A., Dunn, J. J., and Studier, F. W. 1984. Nucleotide sequence of the gene for bacteriophage T7 RNA polymerase. J. Mol. Biol. 173: 265–269.PubMedCrossRefGoogle Scholar
  112. Morch, M. D., Zagorski, W., and Haenni, A. L. 1982. Proteolytic maturation of the turnip-yellow-mosaic-virus polyprotein coded in vitro occurs by internal catalysis. Eur. J. Biochem. 127: 259–265.PubMedCrossRefGoogle Scholar
  113. Murray, C. L., and Rabinowitz, J. C. 1982. Nucleotide sequences of transcription and translation initiation region in Bacillus phage.4)29 early genes. J. Biol. Chem. 257: 1053–1062.PubMedGoogle Scholar
  114. Murthy, S. C. S., Bhat, G. P., and Thimmoppaya, B. 1985. Adenovirus EIIA early promoter: Transcriptional control elements and induction by the viral pre-early EIA gene, which appears to be sequence independent. Proc. Natl. Acad. Sci. USA 82: 2230–2234.PubMedCrossRefGoogle Scholar
  115. Najarian, R., Caput, D., Gee, W., Potter, S: J., Renard, A., Merryweather, J., Van Nest, G., and Dina, D. 1985. Primary structure and gene organization of human hepatitis A virus. Proc. Natl. Acad. Sci. USA 82: 2627–2631.Google Scholar
  116. Natarajan, V., and Salzman, N. P. 1985. Cis and trans activation of adenovirus IVa2 gene transcription. Nucleic Acids Res. 13: 4067–4083.CrossRefGoogle Scholar
  117. Nishiguchi, M., Kibuchi, S., Kiho, Y., Ohno, T., Meshi, T., and Okada, Y. 1985. Molecular basis of plant viral virulence: The complete nucleotide sequence of an attenuated strain of tobacco mosaic virus. Nucleic Acids Res. 13: 5585–5590.PubMedCrossRefGoogle Scholar
  118. Nishihara, T., Mills, D. R., and Kramer, F. R. 1983. Localization of the Qß replicase recognition site in MDV-1 RNA. J. Biochem. 93: 669–674.PubMedCrossRefGoogle Scholar
  119. Nomoto, A., Omata, T., Toyoda, H., Kuge, S., Hori, H., Kataoka, Y., Genba, Y., Nakano, Y., and Imura, N. 1982. Complete nucleotide sequence of the attenuated poliovirus Sabin 1 strain genome. Proc. Natl. Acad. Sci. USA 79: 5793–5797.PubMedCrossRefGoogle Scholar
  120. Ohno, T., Aoyagi, M., Yamanashi, Y., Saito, H., Ikawa, S., Meshi, T., and Okada, Y. 1984. Nucleotide sequence of the tobacco mosaic virus (tomato strain) genome and comparison with the common strain genome. J. Biochem. 96: 1915–1923.PubMedGoogle Scholar
  121. Osboume, T. F., Gaynor, R. B., and Berk, A. J. 1982. The TATA homology and the mRNA 5’ untranslated sequence are not required for the expression of essential adenovirus EIA functions. Cell 29: 139–148.CrossRefGoogle Scholar
  122. Otsuka, J., and Kunisawa, T. 1982. Characteristic base sequence patterns of promoter and terminator sites in 4X174 and Fd phage DNAs. J. Theor. Biol. 97: 415–436.PubMedCrossRefGoogle Scholar
  123. Peeters, B. P. H., Peters, R. M., Schoenmakers, J. G. G., and Konings, R. N. H. 1985. Nucleotide sequence and genetic organization of the genome of the N-specific filamentous bacteriophage IKe. J. Mol. Biol. 181: 27–39.PubMedCrossRefGoogle Scholar
  124. Pero, J. 1983. A prokaryotic model for the developmental control of gene expression. In: Subtelnig, S., and Kafatos, E. C., eds. Gene Structure and Regulation in Development, New York, Alan R. Liss, pp. 227–233.Google Scholar
  125. Pfeiffer, P., and Hohn, T. 1983. Involvement of reverse transcription in the replication of cauliflower mosaic virus: A detailed model and test of some aspects. Cell 33: 781–789.PubMedCrossRefGoogle Scholar
  126. Plasterk, R. H. A., Vrieling, H., and Van de Putte, 1983. Transcription initiation of Mu mom depends on methylation of the promoter region and a phage-encoded transactivator. Nature (London) 301: 344–347.CrossRefGoogle Scholar
  127. Plasterk, R. H. A., Vollering, M., Brinkman, A., and Van de Putte, P. 1984. Analysis of the methylationregulated Mu mom transcript. Cell 36: 189–196.PubMedCrossRefGoogle Scholar
  128. Plucienniczak, A., Schroeder, E., Zettlmeissl, G., and Streeck, R. E. 1985. Nucleotide sequence of a cluster of early and late genes in a conserved segment of the vaccinia virus genome. Nucleic Acids Res. 13: 985–998.PubMedCrossRefGoogle Scholar
  129. Porter, A. G., Smith, J. C., and Emtage, J. S. 1980. Nucleotide sequence of influenza virus RNA segment 8 indicates that coding regions for NSA and NS2 proteins overlap. Proc. Natl. Acad. Sci. USA 77: 5074–5078.PubMedCrossRefGoogle Scholar
  130. Pribnow, D. 1975. Bacteriophage T7 early promoters. Nucleotide sequences of two RNA polymerase binding sites. J. Mol. Biol. 99: 419–443.PubMedCrossRefGoogle Scholar
  131. Pulitzer, J. F., Colombo, M., and Ciaramella, M. 1985. New control elements of bacteriophage T4 prereplicative transcription. J. Mol. Biol. 182: 249–263.PubMedCrossRefGoogle Scholar
  132. Purohit, S., and Mathews, C. K. 1984. Nucleotide sequence reveals overlap between T4 phage genes encoding dihydrofolate reductase and thymidylate synthase. J. Biol. Chem. 259: 6261–6266.PubMedGoogle Scholar
  133. Rand, K. N., and Gait, M. J. 1984. Sequence and cloning of bacteriophage T4 gene 63 encoding RNA ligase and tail fibre attachment activities. EMBO J. 3: 397–402.PubMedGoogle Scholar
  134. Reddy, V. B., Thimmappaya, B., Dhar, R., Subramanian, K. N., Zain, B. S., Pan, J., Ghosh, P. K., Celma, M. L., and Weissman, S. M. 1978. The genome of simian virus 40. Science 200: 494–502.PubMedCrossRefGoogle Scholar
  135. Rezaian, M. A., Williams, R. H. V., Gordon, K. H. J., Gould, A. R., and Symons, R. H. 1984. Nucleotide sequence of cucumber-mosaic-virus RNA2 reveals a translation product significantly homologous to corresponding proteins of other viruses. Eur. J. Biochem. 143: 277–284.PubMedCrossRefGoogle Scholar
  136. Rezaian, M. A., Williams, R. H. V., and Symons, R. H. 1985. Nucleotide sequence of cucumber mosaic virus RNA I. Presence of a sequence complementary to part of the viral satellite RNA and homologies with other viral RNAs. Eur. J. Biochem. 150: 331–339.PubMedCrossRefGoogle Scholar
  137. Rice, C. M., Lenches, E. M., Eddy, S. R., Shin, S. J., Sheets, R. L., and Strauss, J. H. 1985. Nucleotide sequence of yellow fever virus: Implications for flavivirus gene expression and evolution. Science 229: 726–733.PubMedCrossRefGoogle Scholar
  138. Richardson, M. A., and Furuichi, Y. 1983. Nucleotide sequence of reovirus genome segment S3, encoding nonstructural protein sigma NS. Nucleic Acids Res. 11: 6399–6408.PubMedCrossRefGoogle Scholar
  139. Sanger, F., Air, G. M., Barrell, B. G., Brown, N. L., Coulson, A. R., Fiddes, J. C., Hutchison, C. A., Slocombe, P. M., and Smith, H. 1977. Nucleotide sequence of bacteriophage cfoX174 DNA. Nature (London) 265: 687–695.CrossRefGoogle Scholar
  140. Sanger, F., Coulson, A. R., Friedmann, T., Air, G. M., Barrell, B. G., Brown, N. L., Fiddes, J. C., Hutchison, C. A., Slocombe, P. M., and Smith, M. 1978. The nucleotide sequence of bacteriophage X174. J. Mol. Biol. 125: 225–246.PubMedCrossRefGoogle Scholar
  141. Sanger, F., Coulson, A. R., Hong, G., Hill, D., and Peterson, G. 1982. Nucleotide sequence of bacteriophage X DNA. J. Mol. Biol. 162: 729–774.PubMedCrossRefGoogle Scholar
  142. Sarkar, P., Sengupta, D., Baser, S., and Maitra, U. 1985. Nucleotide sequence of a major class-III phage-T3 RNA-polymerase promoter located at 98.0% of phage-T3 genetic map. Gene 33: 351–355.PubMedCrossRefGoogle Scholar
  143. Sassone-Corsi, P., Hen, R., Borrelli, E., Leff, T., and Chambon, P. 1983. Far upstream sequences are required for efficient transcription from the adenovirus-2 E1A transcription unit. Nucleic Acids Res. 11: 8738–8745.CrossRefGoogle Scholar
  144. Sassone-Corsi, P., Dougherty, J. P., Wasylajk, B., and Chambon, P. 1984. Stimulation of in vitro transcription from heterologous promoters by the simian virus 40 enhancer. Proc. Natl. Acad. Sci. USA 81: 308–312.PubMedCrossRefGoogle Scholar
  145. Schmidt, F. J. 1985. RNA splicing in prokaryotes: Bacteriophage T4 leads the way. Cell 41: 339–340.PubMedCrossRefGoogle Scholar
  146. Schwarz, E., Scherer, G., Hobom, G., and Kössel, H. 1978. Nucleotide sequence of cro, cII and part of the O gene in phage X DNA. Nature (London) 272: 410–414.CrossRefGoogle Scholar
  147. Seif, I., Khowry, G., and Dhar, R. 1979. The genome of human papovavirus BKV. Cell 18: 963–977.PubMedCrossRefGoogle Scholar
  148. Shaw, M. W., Choppin, P. W., and Lamb, R. A. 1983. A previously unrecognized influenza B virus glycoprotein from a bicistronic mRNA that also encodes the viral neuraminidase. Proc. Natl. Acad. Sci. USA 80: 4879–4883.PubMedCrossRefGoogle Scholar
  149. Shih, M. C., and Gussin, G. N. 1983. Mutations affecting two different steps in transcription initiation at the phage X PRM promoter. Proc. Natl. Acad. Sci. USA 80: 496–500.PubMedCrossRefGoogle Scholar
  150. Smits, M. A., Jansen, J., Konings, R. N. H., and Schoenmakers, J. G. G. 1984. Initiation and termination signals for transcription in bacteriophage M13. Nucleic Acids Res. 12: 4071–4081.PubMedCrossRefGoogle Scholar
  151. Spicer, E. K., Noble, J. A., Nossal, N. G., Konigsberg, W. H., and Williams, K. R. 1982. Bacteriophage T4 gene 48. Sequence of the structural gene and its protein product. J. Biol. Chem. 257: 8972–8979.PubMedGoogle Scholar
  152. Stahl, S. J., and Zinn, K. 1981. Nucleotide sequence of the cloned gene for bacteriophage T7 RNA polymerase. J. Mol. Biol. 148: 481–485.PubMedCrossRefGoogle Scholar
  153. Stanley, J., and Van Kammen, A. 1979. Nucleotide sequences adjacent to the proteins covalently linked to the cowpea mosaic virus genome. Eur. J. Biochem. 101: 45–49.PubMedCrossRefGoogle Scholar
  154. Stanway, G., Hughes, P. J., Mountford, R. C., Minor, P. D., and Almond, J. W. 1984. The complete nucleotide sequence of a common cold virus: Human rhinovirus 14. Nucleic Acids Res. 12: 7859–7875.PubMedCrossRefGoogle Scholar
  155. Studier, F. W., and Dunn, J. J. 1983. Organization and expression of bacteriophage T7 DNA. Cold Spring Harbor Symp. Quant. Biol. 47: 999–1007.PubMedCrossRefGoogle Scholar
  156. Tack, L. C., and Heard, P. 1985. Both trans-acting factors and chromatin structure are involved in the regulation of transcription from the early and late promoters in simian virus 40 chromosomes. J. Virol. 54: 207–218.PubMedGoogle Scholar
  157. Takamatsu, N., Ohno, T., Meshi, T., and Okada, Y. 1983. Molecular cloning and nucleotide sequence of the 30K and the coat protein cistron of TMV (tomato strain) genome. Nucleic Acids Res. 11: 3767–3778.PubMedCrossRefGoogle Scholar
  158. Thomsen, D. R., Stenberg, R. M., Goins, W. F., and Stinski, M. F. 1984. Promoter-regulatory region of the major immediate early gene of human cytomegalovirus. Proc. Natl. Acad. Sci. USA 81: 659–665.PubMedCrossRefGoogle Scholar
  159. Toyoda, H., Kohara, M., Kataoka, Y., Suganuma, T., Omata, T., Imura, N., and Nomoto, A. 1984. Complete nucleotide sequences of all three poliovirus serotype genomes. Implications for genetic relationship, gene function and antigenic determinants. J. Mol. Biol. 174: 561–585.PubMedCrossRefGoogle Scholar
  160. Valerie, K., Henderson, E. E., and de Riel, J. K. 1984. Identification, physical map location and sequence of the denV gene from bacteriophage T4. Nucleic Acids Res. 12: 8085–8096.PubMedCrossRefGoogle Scholar
  161. Wezenbeek, P. M. G. F., and Schoenmakers, J. G. G. 1979. Nucleotide sequence of the genes III, VI, and I of bacteriophage M13. Nucleic Acids Res. 6: 2799–2818.PubMedCrossRefGoogle Scholar
  162. Wezenbeek, P. M. G. F., Hulsebos, T. J. M., and Schoenmakers, J. G. G. 1980. Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: Comparisons with phage fd. Gene 11: 129–148.PubMedCrossRefGoogle Scholar
  163. Velcich, A., and Ziff, E. 1985. Adenovirus Ela proteins repress transcription from the SV40 early promoter. Cell 40: 705–716.PubMedCrossRefGoogle Scholar
  164. Virtanen, A., Aleström, P., Persson, H., Katze, M. G., and Pettersson, U. 1982. An adenovirus agnogene. Nucleic Acids Res. 10: 2539–2548.PubMedCrossRefGoogle Scholar
  165. Völker, T. A., Gafner, J., Bickle, T. A., and Showe, M. K. 1982. Gene 67, a new essential bacteriophage T4 head gene codes for a prehead core component, PIP. I. Genetic mapping and DNA sequence. J. Mol. Biol. 161: 479–489.PubMedCrossRefGoogle Scholar
  166. Watanabe, Y., Meshi, T., and Okada, Y. 1984. The initiation site for transcription of the TMV 30-kDa protein messenger RNA. FEBS Lett. 173: 247–250.PubMedCrossRefGoogle Scholar
  167. Wilusz, J., Kurilla, M. G., and Keene, J. D. 1983. A host protein (La) binds to a unique species of minus-sense leader RNA during replication of vesicular stomatitis virus. Proc. Natl. Acad. Sci. USA 80: 5827–5831.PubMedCrossRefGoogle Scholar
  168. Yang, R. C. A., and Wu, R. 1979. BK virus DNA: Complete nucleotide sequence of a human tumor virus. Science 206: 456–462.PubMedCrossRefGoogle Scholar
  169. Zajchowski, D. A., Boeuf, H., and Kédinger, C. 1985. The adenovirus-2 early EIIa transcription unit possesses two overlapping promoters with different sequence requirements for EIa-dependent stimulation. EMBO J. 4: 1293–1300.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1987

Authors and Affiliations

  • Lawrence S. Dillon
    • 1
  1. 1.Texas A&M UniversityCollege StationUSA

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