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The Structure of Influenza Virus Defective Interfering (DI) RNAs and Their Progenitor Genes

  • Chapter
Genetics of Influenza Viruses

Abstract

The term defective interfering (DI) virus particles was used by Huang and Baltimore [31] to define a class of virus particles which possess the following properties: (a) They are defective, unable to replicate independently; (b) They require the helper function of standard virus for replication; (c) They interfere with the replication of standard virus; (d) They are usually deletion mutants, i.e., the genome of DI particles does not represent the entire genome of standard virions. Although all of the DI genomes studied to date are shorter than the standard viral genome and are deletion mutants, it is possible some DI genome may contain an altered nucleic acid sequence(s) rather than a deletion(s) and become defective as well as interfering. DI particles were first observed by von Magnus [64,65] when he passaged influenza virus serially undiluted in embryonated chicken eggs. He called these particles “incomplete” particles which were both defective and interfering. Subsequently, DI particles have been reported for nearly all animal viruses during high multiphcity passages (for a detailed review see reference no. [32]).

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References

  1. Ada, G. L., Perry, B. T.: Infectivity and nucleic acid content of influenza virus. Nature (Lond.) 175, 209–210 (1955).

    Article  CAS  Google Scholar 

  2. Ada, G. L., Perry, B. T.: Influenza virus nucleic acid relationship between biological characteristics of the vims particle and properties of the nucleic acid. J. Gen. Microbiol. 14, 623 (1956).

    Google Scholar 

  3. Adman, R., Grossman, L.: Template properties of polyribonucleotides containing uracil or modified uracil in the RNA polymerase reaction. J. Mol. Biol. 23, 417–439 (1967).

    Article  PubMed  CAS  Google Scholar 

  4. Amesse, L. S., Pridgen, C.L., Kingsbury, D. W.: Sendai virus DI RNA species with conserved virus genome termini and extensive internal deletions. Virology 118, 17–27 (1982).

    Article  PubMed  CAS  Google Scholar 

  5. Bean, W.J., Simpson, R.W.: Transcription activity and genome conposition of defective influenza vims. J. Virol. 18, 365–369 (1976).

    PubMed  CAS  Google Scholar 

  6. Bennink, J. R., Yewdell, J. W., Gerhard, W.: A viral polymerase involved in recognition of influenza vims-infected cells by a cytotoxic T-cell clone. Nature 296, 75–76 (1982).

    Article  PubMed  CAS  Google Scholar 

  7. Bishop, D. H. L., Huddleston, J. A., Brownlee, G. G.: The complete sequence of RNA segments of influenza A/NT/60/68 and its encoded PI protein. Nucleic Acids Res. 10,1335–1343 (1982).

    Article  PubMed  CAS  Google Scholar 

  8. Bishop, D. H. L., Jones, K. L., Huddleston, J. A., Brownlee, G. G.: Influenza A vims evolution: Complete sequences of influenza A/NT/60/68 RNA segment 3 and its predicted acidic P polypeptide compared with those of influenza A/PR/8/34. Virology 120, 481–489 (1982).

    Article  PubMed  CAS  Google Scholar 

  9. Brown, W. E., Stump, K. H., Kelley, W. S.: Escherichia coh DNA polymerase 1 sequence characterization and secondary stmcture prediction. J. Biol. Chem. 257, 1965–1972 (1982).

    PubMed  CAS  Google Scholar 

  10. Camerini-Otero, R.D., Sollner-Webb, B., Felsenfeld, G.: The stmcture of the nucleosome: Evidence for an arginine rich histone kernel. In: Nucleic Acid-Protein Recognition (Vogel, H.J., ed.), 151–158. New York: Academic Press 1977.

    Google Scholar 

  11. Carter, C. W., Kraut, J.: A proposed model for interaction of polypeptides with RNA. Proc. Natl. Acad. Sci. U.S.A. 71, 283–287 (1974).

    Article  PubMed  CAS  Google Scholar 

  12. Carter, M.J., Mahy, B. W.J.: Incomplete avian influenza vims contains a defective noninterfer- ing component. Arch. Virol. 71, 12–25 (1982).

    Google Scholar 

  13. Carter, M.J., Mahy, B. W.J.: Synthesis of RNA segments 1–3 during generation of incomplete influenza A (Fowl plague) vims. Arch. Virol. 73, 109–119 (1982).

    Article  PubMed  CAS  Google Scholar 

  14. Carter, M.J., Mahy, B.W.J.: Incomplete avian influenza A vims displays anomalous interference. Arch. Virol. 74, 71–76 (1982).

    Article  PubMed  CAS  Google Scholar 

  15. Chamberlin, M., Berg, P.: Mechanism of RNA polymerase action. Characterization of DNA- dependent synthesis of polyadenylic acid. J. Mol. Biol. 8, 708–726 (1964).

    Article  PubMed  CAS  Google Scholar 

  16. Champness, J. N., Bloomer, A. C., Bricogne, G., Butler, P.J. G., Klug, A.: The stmcture of the protein disk of tobacco mosaic vims to 5 Â resolution. Nature 259, 20–24 (1976).

    Article  PubMed  CAS  Google Scholar 

  17. Chanda, P. K., Chambers, T. M., Nayak, D. P.: In vitro transcription of defective interfering particles of influenza virus produces poly(A)-containing complementary RNAs. J. Virol. 45, 55–61 (1983).

    PubMed  CAS  Google Scholar 

  18. Choppin, P. W., Pons, M. W.: The RNAs of infective and incomplete influenza virions grown in MDBK and HeLa cells. Virology 42, 603 (1970).

    Article  PubMed  CAS  Google Scholar 

  19. Chou, P. Y., Adler, A. J., Pasman, G. D.: Conformational prediction and circular dichroism studies on the lac repressor. J. Mol. Biol. 96, 29–45 (1975).

    Article  PubMed  CAS  Google Scholar 

  20. Chou, P. Y., Pasman, G. D.: Empirical predictions of protein conformation. Annu. Rev. Biochem. 47, 251–276 (1978).

    Article  PubMed  CAS  Google Scholar 

  21. Cmmpton, W. M., Dimmock, N. J., Minor, P. D., Avery, R. J.: The RNAs of defective-interfering influenza virus. Virology 90, 370–373 (1978).

    Article  Google Scholar 

  22. Cmmpton, W. M., Clewley, J. P., Dimmock, N. J., Avery, R. J.: Origin of subgenomic RNAs in defective-interfering influenza virus. PEMS Microbiol. Lett. 6, 431–434 (1979).

    Google Scholar 

  23. Cmmpton, W. M., Avery, R. J., Dimmock, N. J.: Influence of the host cell on the genomic and subgenomic RNA content of defective-interfering influenza vims. J. Gen. Virol. 53,173–177 (1981).

    Article  Google Scholar 

  24. Davis, A. R., Nayak, D. P.: Sequence relationships among defective interfering influenza viral RNAs. Proc. Nati. Acad. Sci. U.S.A. 76, 3092–3096 (1979).

    Article  CAS  Google Scholar 

  25. Davis, A. R., Hiti, A. L., Nayak, D. P.: Influenza defective interfering viral RNA is formed by internal deletion of genomic RNA. Proc. Nafl. Acad. Sci. U.S.A. 77, 215–219 (1980).

    Article  CAS  Google Scholar 

  26. Dayhoff, M. O.: Atlas of Protein Sequence and Stmcture, Vol. 5, Suppl. 3. National Biomedical Research Foundation, Georgetown University Medical Center, Washington, DC 20007, U.S.A., 363–373 (1978).

    Google Scholar 

  27. De, B. K., Nayak, D. P.: Defective interfering influenza vimses and host cells: Establishment and maintenance of persistent influenza virus infection in MDBK and HeLa cells. J. Virol. 36, 847–859 (1980).

    PubMed  CAS  Google Scholar 

  28. Fields, S., Winter, G.: Nucleotide sequence heterogeneity and sequence rearrangements in influenza virus cDNA. Gene 15, 207–214 (1981).

    Article  PubMed  CAS  Google Scholar 

  29. Fields, S., Winter, G.: Nucleotide sequences of influenza virus segments 1 and 3 reveal mosaic stmctures of a small viral RNA segment. Cell 28, 303–313 (1982).

    Article  PubMed  CAS  Google Scholar 

  30. Fiers, W., Contreras, R., Duerinck, P., Haigeman, G., Iserentant, D., Merregaert, J., Minjou, W, Molemans, P., Raeymaekers, A., van den Berghe, A., Volckaert, G., Ysebaert, M.: Complete nucleotide sequence of bacterophage MS2 RNA: primary and secondary stmcture of the replicase gene. Nature 260, 500–507 (1976).

    Article  PubMed  CAS  Google Scholar 

  31. Garoff, H., Frischauf, A.M., Simons, K., Lehrach, H., Delius, H.: The capsid protein of Semliki forest vims has clusters of basic amino acids and prolines in its amino terminal region. Proc. Nafl. Acad. Sci. U.S.A. 77, 6376–6380 (1980).

    Article  CAS  Google Scholar 

  32. Hiti, A. L., Davis, A. R., Nayak, D. P.: Complete sequence analysis shows that the hemagglutinins of the HO and H2 subtypes of human influenza vims are closely related. Virology iii, 113–124 (1981).

    Google Scholar 

  33. Hiti, A. L., Nayak, D. P.: Complete nucleotide sequence of the neuraminidase gene of human influenza vims A/WSN/33. J. Virol. 41, 730–734 (1982).

    PubMed  CAS  Google Scholar 

  34. Holland, J. J., Kennedy, S. I. T, Semler, B. L, Jones, C. L., Roux, L., Grabau, E. A.: Defective interfering RNA vimses and the host cell response. In: Comprehensive Virology, Vol. 16 (Fraenkel-Conrat, H., Wagner, R. R., eds.), 137–192. New York: Plenum Press 1980.

    Chapter  Google Scholar 

  35. Huang, A. S., Baltimore, D.: Defective viral particles and viral disease processes. Nature (Lond.) 226, 325 (1970).

    Article  CAS  Google Scholar 

  36. Huang, A. S., Baltimore, D.: Defective interfering animal vimses. In: Comprehensive Virology, Vol. 10 (Frankel-Conrat, H., Wagner, R. R., eds.), 73–116. New York: Plenum 1977.

    Google Scholar 

  37. Irwin, M. J., Nyborg, J., Reid, B. R., Blow, D. M.: The crystal stmcture of tyrosyl-transfer RNA synthetase at 2.7 A resolution. J. Mol. Biol. 105, 577–586 (1976).

    Article  PubMed  CAS  Google Scholar 

  38. Janda, J. M., Nayak, D. P.: Defective influenza viral ribonucleoproteins cause interference. J. Virol. 32, 697–702 (1979).

    PubMed  CAS  Google Scholar 

  39. Janda, J. M., Davis, A. R., Nayak, D. P., De, B. K: Diversity and generation of defective interfering influenza virus particles. Virology 95, 48–58 (1979).

    Article  PubMed  CAS  Google Scholar 

  40. D. P. Nayak and N. Sivasubramanian Kaptein, J., Nayak, D.P.: Complete nucleotide sequence of the polymerase 3 (P3) gene of human influenza vims A/WSN/33. J. Virol. 42, 55–63 (1982).

    PubMed  Google Scholar 

  41. Kavern, N., Kolomietz, L., Rudneva, I.: Incomplete influenza vims. Partial functional complementation as revealed by hemadsorbing cell count test. J. Virol. 34, 506–511 (1980).

    Google Scholar 

  42. Keene, J. D., Chien, I. M., Lazzarini, R. A.: Vesicular Stomatitis defective interfering particle contained a muted, internal leader RNA gene. Proc. Nad. Acad. Sci. U.S.A. 18, 2090–2094 (1981).

    Article  Google Scholar 

  43. King, A. M. Q, McCahon, D., Slade, W. R., Newman, J. W. L: Recombination in RNA. Cell 29, 921–928 (1982).

    Article  PubMed  CAS  Google Scholar 

  44. Kitamura, N., Semer, B.L., Rothberg, P.O., Larsen, G.R., Adler, C.J., Dorner, A.J., Emini, E. A., Hanecak, R., Lee, J. I., Van der Werf, S., Anderson, C. W.,’Wimmer, E.: Primary Stmcture, gene organization and polypeptide expression of polio-vims RNA. Nature 291,547–553 (1981).

    Article  PubMed  CAS  Google Scholar 

  45. Lamb, R. A., Ching-Juh, Lai: Sequence of intermpted and unintermpted mRNAs and cloned DNA coding for the two overlapping nonstmctural proteins of Influenza Vims. Cell 21, 475–485 (1980).

    Article  PubMed  CAS  Google Scholar 

  46. Lazzarini, R. A., Keene, J. D., Schubert, M.: The origins of Defective Interfering Particles of the negative strand RNA vimses. Cell 26, 145–154 (1981).

    Article  PubMed  CAS  Google Scholar 

  47. Lehtovaara, P., Soderlund, H., Keranen, S., Petterson, R. F., Kaarianen, L.: 18 S defective interfering RNA of Semliki forest vims contains a triplicated linear repeat. Proc. Nad. Acad. Sci. U.S.A. 78, 5353–5357 (1981).

    Article  CAS  Google Scholar 

  48. Lenard, J., Compans, R. W.: Polypeptide composition of incomplete influenza vims grown in MDBK cells. Virology 65, 418–426 (1975).

    Article  PubMed  CAS  Google Scholar 

  49. Moss, B. A., Brownlee, G. G.: Sequence of DNA complementary to a small RNA segment of Influenza vims A/NT/60/68. Nucleic Acids Res. 9, 1941–1947 (1981).

    Article  PubMed  CAS  Google Scholar 

  50. Nakajima, K., Ueda, M., Sugiura, A.: Origin of small RNA in von Magnus particles of influenza vims. J. Virol. 29, 1142–1148 (1979).

    PubMed  CAS  Google Scholar 

  51. Nayak, D. P., Baluda, M. A.: Isolation and partial characterization of nucleic acid of influenza vims. J. Virol. 1 (6), 1217–1223 (1967).

    PubMed  CAS  Google Scholar 

  52. Nayak, D.P.: Influenza vimses: stmcture, replication and defectiveness. Fed. Proc. 28, 1858–1865 (1969).

    PubMed  CAS  Google Scholar 

  53. Nayak, D. P.: Defective vims RNA synthesis and production of incomplete influenza vims in chick embryo cells. J. Gen. Virol. 14, 63 (1972).

    Article  PubMed  CAS  Google Scholar 

  54. Nayak, D. P.: Defective interfering influenza vimses. Ann. Rev. Microbiol. 34, 619–644 (1980).

    Article  CAS  Google Scholar 

  55. Nayak, D.P., Tobita, K., Janda, J.M., Davis, A.R., De, B.K.: Homologous interference mediated by defective interfering influenza vims derived from a temperature-sensitive mutant of influenza vims.J. ViroL 28, 375–386 (1978).

    PubMed  CAS  Google Scholar 

  56. Nayak, D.P., Davis, A. R., Cortini, R.: Defective interfering influenza vimses: Complete sequence analysis of a DI RNA. In: Genetic Variation Among Influenza Vimses (Nayak, D. P., ed.), 77–92. New York: Academic Press 1982.

    Google Scholar 

  57. Nayak, D.P., Sivasubramanian, N., Davis, A. R., Cortini, R., Sung, J.: Complete sequence analyses show that two defective interfering influenza viral RNAs contain a single internal deletion ofa polymerase gene. Proc. Nad. Acad. Sci. U.S.A. 79, 2216–2220 (1982).

    Article  CAS  Google Scholar 

  58. Pasek, M., Goto, T., Gilbert, W., Zink, B., Schaller, H., Mackay, P., Leadbetter, G., Murray, K.: Hepatitis B vims genome and their expression in Escherichia coli. Nature (Lond.) 282, 575–579 (1979).

    Article  CAS  Google Scholar 

  59. Perrault, J.: Origin and replication of Defective Interfering Particles. Curr. Topics in Microbiology and Immunology 93, 152–207 (1981).

    Google Scholar 

  60. Perrault, J., Semler, B.L., Leavitt, R.W., Holland, J.J.: Inverted complementary terminal sequences in defective interfering particle RNAs of vesicular somatitis vims and their possible role in autointerference. In: Negative Strand Vimses and the Host Cell (Mahy, B. W.J., Barry, R.D., eds.), 527–538. New York: Academic Press 1978.

    Google Scholar 

  61. Plotch, S. J., Kmg, R. M.: Influenza vims transcriptase: Synthesis in vitro, of large polyadenylic acid containing complementary RNA. J. Virol. 21, 24–34 (1977).

    PubMed  CAS  Google Scholar 

  62. Plotch, S.J., Bouloy, M. Kmg, R.M.: Transfer of 5’ terminal cap of globin mRNA during transcription in vitro. Proc. Nad. Acad. Sci. U.S.A. 76, 1618–1622 (1979)

    Article  CAS  Google Scholar 

  63. Schiffer, M., Edmundson, A. B.: Use of helical wheels to represent the stmctures of proteins and to identify segments with hehcal potential. Biophys. J. 7,121–135 (1967).

    Article  PubMed  CAS  Google Scholar 

  64. Schnitzlein, W. M., Reichmann, M. E.: The size and the cistronic origin of defective vesicular stomatitis vims particle RNAs in relation to homotypic and heterotypic interference. J. Mol. Biol. 101, 307–325 (1976).

    Article  PubMed  CAS  Google Scholar 

  65. Sharp, P. A.: Speculations on RNA splicing. Cell 23, 643–646 (1981).

    Article  PubMed  CAS  Google Scholar 

  66. Sivasuhramanian, N., Nayak, D. P.: Sequence analysis of the polymerase 1 gene and the secondary stmcture prediction of polymerase 1 protein of human influenza vims A/WSN/33. J. Virol. 44, 321–329 (1982).

    Google Scholar 

  67. Sivasuhramanian, N., Nayak, D. P.: Defective interfering influenza RNAs of polymerase 3 gene contain single as well as multiple internal deletions. Virology 124, 232–237 (1983).

    Article  Google Scholar 

  68. Soeda, E., Arrand, J. R., Grififm, B. E.: Polyoma vims DNA: Complete nucleotide sequence of the gene which codes for polyoma vims capsid protein VPl and overlaps the VP2-VP3 genes. J. Virol. 33, 619–630 (1980).

    PubMed  CAS  Google Scholar 

  69. Ueda, M., Nakajima, K., Sugiura, A.: Extra RNAs of von Magnus particles of influenza vims cause reduction of particular polymerase genes. J. Virol. 34, 1–8 (1980).

    PubMed  CAS  Google Scholar 

  70. Van Rompuy, L., Minjou, W, Huylebroeck, D., Devos, R., Fiers, W: Complete nucleotide sequence of the nucleoprotein gene from the human influenza strain /V/PR/8/34 (HON 1). Eur. J. Biochem. 116, 347–353 (1981).

    Article  PubMed  Google Scholar 

  71. Von Heuverswyn, H., Van de Voorde, A., Fiers, W: Nucleotide sequence of the Simian vims 40 Hind II & III restriction fragment J and the total amino acid sequence of the major stmctural protein VPl. Eur. J. Biochem. 91, 415–430 (1978).

    Article  PubMed  Google Scholar 

  72. Von Magnus, P.: Studies on interference in experimental influenza. I. Biological observations. Mineral. Geol. 24 (7), 1 (1947).

    Google Scholar 

  73. Von Magnus, P.: Propagation of the PR-8 strain of influenza A vims in chick embryos. III. Properties of the incomplete vims produced in serial passages of undiluted vims. Acta. Pathol. Microbiol. Scand. 29, 157 (1951).

    Article  Google Scholar 

  74. Von Magnus, P.: Incomplete forms of influenza vims. Adv. Vims Res. 2, 59–68 (1954).

    Article  Google Scholar 

  75. Winter, G., Fields, S.: Cloning of influenza cDNA into M13: The sequence of the RNAsegment encoding the A/PR/8/34 matrix protein. Nucleic Acids Res. 8, 1965–1974 (1980).

    Article  PubMed  CAS  Google Scholar 

  76. Winter, G., Fields, S.: The stmcture of the gene encoding the nucleoprotein of human influenza vims A/PR/8/34. Virology 114, 423–428 (1981).

    Article  PubMed  CAS  Google Scholar 

  77. Winter, G., Fields, S.: Nucleotide sequence of human influenza A/PR/8/34 segment 2. Nucleic Acids Res. 10, 2135–2143 (1982).

    Article  PubMed  CAS  Google Scholar 

  78. Winter, G., Fields, S., Ratti, G.: The stmcture of the two subgenomic RNAs from human influenza vims A/PR/8/34. Nucleic Acid Res. 9, 6907–6915 (1981).

    Article  PubMed  CAS  Google Scholar 

  79. Eisenberg, D., Weiss, R. M., Terwilliger, T. C.: The helical hydrophobic moment: a measure of the amphiphihcity of a helix. Nature 299, 371–374 (1982).

    Article  PubMed  CAS  Google Scholar 

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  1. D. P. Nayak
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  2. N. Sivasubramanian
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  1. Mount Sinai School of Medicine, The Mount Sinai Hospital, New York, N.Y., USA

    Peter Palese

  2. St. Jude Children’s Research Hospital, Memphis, Tenn., USA

    David W. Kingsbury

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Nayak, D.P., Sivasubramanian, N. (1983). The Structure of Influenza Virus Defective Interfering (DI) RNAs and Their Progenitor Genes. In: Palese, P., Kingsbury, D.W. (eds) Genetics of Influenza Viruses. Springer, Vienna. https://doi.org/10.1007/978-3-7091-8706-7_8

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