Intracellular kinetics of a growing virus: A genetically structured simulation for bacteriophage T7

Biotechnology and Bioengineering

Volumn 55, Issue 2, 1997, Pages 375-389

  Endy, Drew ^a   Kong, Deyu ^a   Yin, John ^a  

^a DARTMOUTH COLLEGE   (United States)

Author keywords

Antiviral strategies; Bacteriophage T7; Gene expression; Intracellular growth; Kinetic simulation

Indexed keywords

BIOSYNTHESIS; COLIFORM BACTERIA; COMPUTER SIMULATION; DNA; GENES; GROWTH KINETICS; MOLECULAR STRUCTURE; PHYSIOLOGY;

ANTIVIRAL STRATEGIES; GENE EXPRESSION; INTRACELLULAR KINETICS;

BACTERIOPHAGES;

ARTICLE; BACTERIOPHAGE; DELETION MUTANT; DNA REPLICATION; DOWN REGULATION; GENE STRUCTURE; GENE TARGETING; GENE THERAPY; MOLECULAR RECOGNITION; NONHUMAN; PROTEIN ASSEMBLY; SIMULATION; VIROGENESIS; VIRUS CELL INTERACTION;

EID: 0342506826     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0290(19970720)55:2<375::AID-BIT15>3.0.CO;2-G     Document Type: Article

References (65)

1. Ackermann, H. W., Berthiaume, L. 1995. Atlas of virus diagrams. CRC Press, New York.
2. Adams, M. 1959. Bacteriophages. Interscience, New York.
3. Berlyn, M. K., Low, K. B., Rudd, K. E. 1996. Linkage map of E. coli K-12, edition 9, pp. 1715-1902. In: F. C. Neidhardt, R. Curtiss, III, C. Gross, J. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger, (eds.), E. coli and S. typhimurium: Cellular and molecular biology II. American Society for Microbiology, Washington DC.
4. Bordier, B., Perala-Heape, M., Degols, G., Lebleu, B., Litvak, S., Sarih-Cottin, L., Helene, C. 1995. Sequence-specific inhibition of human immunodeficiency virus (HIV) reverse transcription by antisense oligonucleotides: Comparative study in cell-free assays and in HIV-infected cells. Proc. Nat. Acad. Sci. USA 92: 9383-9387.
5. Bremer, H., Dennis, P. P. 1996. Modulation of chemical composition and other parameters of the cell by growth rate, pp. 1553-1569. In: F. C. Neidhardt, R. Curtiss, III, C. Gross, J. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (eds.), E. coli and S. typhimurium: Cellular and molecular biology II. American Society for Microbiology, Washington DC.
6. Bremer, H., Yuan, D. 1968. RNA chain growth-rate in Escherichia coli. J. Molec. Biol. 38: 163-180.
7. Buchholtz, F., Schneider, F. W. 1987. Computer simulation of T3/T7 phage infection using lag times. Biophys. Chem. 26: 171-179.
8. Burden, R. L., Faires, J. D. 1993. Numerical Analysis. PWS Publishing Co., Boston.
9. Chatterjee, S., Johnson, P. R., Wong, K. K. 1992. Dual-target inhibition of HIV-1 in vitro by means of an adeno-associated virus antisense vector. Science 258: 1485-1488.
10. Dalbow, D. G., Young, R. 1975. Synthesis time of B-galactosidase in Escherichia coli. B/r as a function of growth rate. Biochem. J. 150: 13-20.
11. Dee, K. U., Hammer, D. A., Shuler, M. L. 1995. A model of the binding, entry, uncoating, and RNA synthesis of semliki forest virus in baby hamster kidney (BHK-21) cells. Biotechnol Bioeng. 46: 485-496.
12. Demerec, M., Fano, U. 1944. Bacteriophage-resistant mutants in Escherichia coli. Genetics 30: 119-136.
13. Dennis, P. P., Bremer, H. 1973. Regulation of ribonucleic acid synthesis in Escherichia coli B/r: An analysis of a shift-up 1. Ribosomal RNA chain growth rates. J. Molec. Biol. 75: 145-159.
14. Dennis, P. P., Bremer, H. 1974. Macromolecular composition during steady-state growth of Escherichia coli B/r. J. Bacteriol. 119: 270-281.
15. Donachie, W. D., Robinson, A. C. 1987. Cell division: Parameter values and the process, pp. 1578-1593. In: F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (eds.) E. coli and S. typhimurium: Cellular and molecular biology. American Society for Microbiology, Washington, DC.
16. Donlin, M. J., Johnson, K. A. 1994. Mutants affecting nucleotide recognition by T7 DNA polymerase. Biochemistry 33: 14908-14917.
17. Dunn, J. J., Studier, F. W. 1973. T7 early RNAs and Escherichia coli ribosomal RNAs are cut from large precursor RNAs in vivo by ribonuclease III. Proc. Natl. Acad. Sci. USA 70: 3296-3300.
18. Dunn, J. J., Studier, F. W. 1975. Effect of RNAase III cleavage on translation of bacteriophage T7 messenger RNAs. J. Molec. Biol. 99: 487-499.
19. Dunn, J. J., Studier, F. W. 1983. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Molec. Biol. 166: 477-535. Updated bacteriophage T7 sequence (T7CG) accessed from NCBI GenBank (http://www.ncbi.nlm.nih.gov/).
20. Eigen, M., Biebricher, C. K., Gebinoga, M., Gardiner, W. C. 1991. The hypercycle. Coupling of RNA and protein biosynthesis in the infection cycle of an RNA bacteriophage. Biochemistry 30: 11005-11108.
21. Garcia, R. L., Molineux, I. J. 1995. Rate of translocation of bacteriophage T7 DNA across the membranes of Escherichia Coli. J. Bacteriol. 177: 4066-4076.
22. Gura, T. 1995. Antisense has growing pains. Science 270: 575-577.
23. Hammond, B. 1993. Quantitative study of the control of HIV-1 gene expression. J. Theor. Biol. 163: 199-221.
24. Hausmann, R. 1988. The T7 group, pp. 259-289. In: R. Calendar (ed.), The Bacteriophages, vol. 1. Plenum, New York.
25. Hesselbach, B. A., Nakada, D. 1977a. I protein: Bacteriophage T7-coded inhibitor of Escherichia Coli RNA polymerase. J. Virol. 24: 746-760.
26. Hesselbach, B. A., Nakada, D. 1977b. "Host shutoff" function of bacteriophage. T7: Involvement of T7 gene 2 and gene 0.7 in the inactivation of Escherichia coli RNA polymerase. J. Virol. 24: 736-745.
27. Hillis, D. M., Bull, J. J., White, M. E., Badgett, M. R., Molineux, I. J. 1992. Experimental phylogenetics: Generation of a known phylogeny. Science 255: 589-592.
28. Ikeda, R. A. 1992. The efficiency of promoter clearance distinguishes T7 class II and class III promoters. J. Biol. Chem. 267: 11322-11328.
29. Ikeda, R. A., Bailey P. A. 1992. Inhibition of T7 RNA polymerase by T7 lysozyme in vitro. J. Biol. Chem. 267: 20153-20158.
30. Kong, D., Yin, J. 1995. Whole-virus vaccine development by continuous culture on a complementing host. Bio/Technology 13: 583-586.
31. Lee, S. B., Bailey, J. E. 1984. Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models. Biotechnol. Bioeng. 26: 66-73.
32. Lee, Y., Yin, J. 1996. Detection of evolving viruses. Nature Biotechnol. 14: 491-493.
33. Macdonald, L. E., Zhou, Y., McAllister, W. T. 1993. Termination and slippage by bacteriophage T7 RNA polymerase. J. Molec. Biol. 232: 1030-1047.
34. Maddox, J. 1992. Is molecular biology yet a science? Nature 355: 201.
35. Maslak, M., Jaworski, M. D., Martin, C. T. 1993. Tests of a model for promoter recognition by T7 RNA polymerase: Thymine methyl group contacts. Biochemistry 32: 4270-4274.
36. McAdams, H. H., Shapiro, L. 1995. Circuit simulation of genetic networks. Science 269: 650-656.
37. McAllister, W. T., Wu, H. L. 1978. Regulation of transcription of the late genes of bacteriophage T7. Proc. Nat. Acad. Sci. USA 75: 804-808.
38. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor: Cold Spring Harbor Laboratory.
39. Moffatt, B. A., Studier, F. W. 1988. Entry of bacteriophage T7 DNA into the cell and escape from host restriction. J. Bacteriol. 170: 2095-2105.
40. Murray, J. A. H. 1992. Antisense RNA and DNA. Wiley-Liss, New York.
41. Palsson, B. O., Keasling, J. D., Emerson, S. G. 1990. The regulatory mechanisms of human immunodeficiency virus replication predict multiple expression rates. Proc. Nat. Acad. Sci. USA 87: 772-776.
42. Ponta, H., Reeve, J. N., Pfennig-Yeh, M., Hirsch-Kauffmann, M., Schweiger, M., Herlich, P. 1977. Productive T7 infection of Escherichia coli F+ cells and anucleate minicells. Nature 269: 440-442.
43. Prevelige, P. E., Thomas, D., King., J. 1993. Nucleation and growth phases in the polymerization of coat and scaffolding subunits into icosahedral procapsid shells. Biophys. J. 64: 824-835.
44. Rabkin, S. D., Richardson, C. C. 1990. In vivo analysis of the initiation of bacteriophage T7 DNA replication. Virology 174: 585-592.
45. Robertson, E. S., Nicholson, A. W. 1992. Phosphorylation of Escherichia coli translation initiation factors by the bacteriophage T7 protein kinase. Biochemistry 31: 4822-4827.
46. Roeder, G. S., Sadowski, P. D. 1977. Bacteriophage T7 morphogenesis: Phage-related particles in cells infected with wild-type and mutant T7 phage. Virology 76: 263-285.
47. Rose, J. K., Mosteller, R. D., Yanofsky, C. 1970. Tryptophan messenger ribonucleic acid elongation rates and steady-state levels of tryptophan operon enzymes under various growth conditions. J. Molec. Biol. 51: 541-550.
48. Rothman-Denes L. B., Muthukrishnan, S., Haselkom, R., Studier, F. W. 1973. A T7 gene function required for shut-off of host and early T7 transcription, pp. 227-239. In: C. F. Fox and W. S. Robinson (eds.), Virus research. Academic, New York.
49. Ruggiero, C., Giacomini, M., Varnier, O. E., Gaglio, S. 1994. A qualitative process theory based model of the HIV-1 virus-cell interaction. Comput. Meth. Progr. Biomed. 43: 255-259.
50. Sadowski, P. D., Kerr, C. 1970. Degradation of Escherichia coli B deoxyribonucleic acid after infection with deoxyribonucleic acid-defective amber mutants of bacteriophage T7. J. Virol. 6: 149-155.
51. Shuler, M. L., Leung, S., Dick, C. C. 1979. A mathematical model for the growth of a single bacterial cell. Ann. NY Acad. Sci. 326: 35-55.
52. Son, M., Watson, R. H., Serwer, P. 1993. The direction and rate of bacte-riophage T7 DNA packaging in vitro. Virology 196: 282-289.
53. Steven, A. C., Trus, B. L. 1986. The structure of bacteriophage T7, pp. 1-35. In: J. R. Harris and R. W. Home (eds.), Electron microscopy of proteins, vol. 5: Viral structure. Academic, London.
54. Studier, F. W. 1969. The genetics and physiology of bacteriophage T7. Virology 39: 562-574.
55. Studier, F. W. 1972. Bacteriophage T7. Science 176: 367-376.
56. Studier, F. W., Dunn, J. J. 1983. Organization and expression of bacteriophage T7 DNA. CSH Quant. Biol. 47: 999-1007.
57. Studier, F. W., Moffatt, B. A. 1986. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Molec. Biol. 189: 113-130.
58. Studier, F. W., Rosenberg, A. H., Simon, M. N., Dunn, J. J. 1979. Genetic and physical mapping in the early region of bacteriophage T7 DNA. J. Molec. Biol. 135: 917-937.
59. Summers, W. C. 1970. The process of infection with coliphage T7 IV. Stability of RNA in bacteriophage-infected cells. J. Molec. Biol. 51: 671-678.
60. Wickham, T. J. Shuler, M. L., Hammer, D. A. 1995. A simple model to predict the effectiveness of molecules that block attachment of human rhinoviruses and other viruses. Biotechnol. Prog. 11: 164-170.
61. Yin, J. 1993. Evolution of bacteriophage T7 in a growing plaque. J. Bacteriol. 175: 1272-1277.
62. Young, R. 1992. Bacteriophage lysis: Mechanism and regulation. Microbiol. Rev. 56: 430-481.
63. Zavriev, S. K., Shemyakin, M. F. 1982. RNA polymerase-dependent mechanism for the stepwise T7 phage DNA transport from the virion into E. coli. Nucl Acids Res. 10: 1635-1652.
64. Zhang X., Studier, F. W. 1995. Isolation of transcriptionally active mutants of T7 RNA polymerase that do not support phage growth. J. Molec. Biol. 250: 156-168.
65. Zlotnick, A. 1994. To build a virus capsid: An equilibrium model of the self assembly of polyhedral protein complexes. J. Molec. Biol. 241: 59-67.