Natural variation among human adenoviruses: Genome sequence and annotation of human adenovirus serotype 1

Journal of General Virology

Volumn 85, Issue 9, 2004, Pages 2615-2625

  Lauer, Kim P ^a   Llorente, Isabel ^a   Blair, Eric ^a   Seto, Jason ^a   Krasnov, Vladimir ^a   Purkayastha, Anjan ^a,d,e   Ditty, Susan E ^b,e   Hadfield, Ted L ^b,e   Buck, Charles ^c   Tibbetts, Clark ^d,e   Seto, Donald ^a,d,e  

^a GEORGE MASON UNIVERSITY   (United States)

^b ARMED FORCES INSTITUTE OF PATHOLOGY   (United States)

^c American Type Culture Collection ^*  (United States)

^d HQ USAF Surgeon General Office   (United States)

^e EOS Consortium   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; VIRUS DNA;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA SEQUENCE; GENE STRUCTURE; GENETIC CODE; GENETIC CONSERVATION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HUMAN ADENOVIRUS; INVERTED TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SEROTYPE; SPECIES DIFFERENTIATION; VIRUS GENOME;

ADENOVIRUS INFECTIONS, HUMAN; ADENOVIRUSES, HUMAN; AMINO ACID SEQUENCE; CAPSID PROTEINS; DNA PRIMERS; GENOME, VIRAL; HUMANS; MILITARY PERSONNEL; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEROTYPING; SPECIES SPECIFICITY; VARIATION (GENETICS);

ADENOVIRIDAE; EOS; HUMAN ADENOVIRUS;

EID: 4544379400     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/vir.0.80118-0     Document Type: Article

References (63)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
3. Benko, M. & Harrach, B. (2003). Molecular evolution of adenoviruses. In Adenoviruses: Model and Vectors in Virus-Host Interactions, pp. 3-35. Edited by W. Doerfler & P. Bohm. Berlin: Springer.
4. Benko, M., Harrach, B. & Russell, W. C. (2000). The Adenoviridae. In Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses, pp. 227-238. Edited by M. H. V. van Regenmortel, C. M. Fauquet, G. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle & R. B. Wickner. San Diego: Academic Press.
5. Berriman, M. & Rutherford, K. (2003). Viewing and annotating sequence data with Artemis. Brief Bioinform 4, 124-132.
6. Besemer, J. & Borodovsky, M. (1999). Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27, 3911-3920.
7. Binger, M. H. & Flint, S. J. (1984). Accumulation of early and intermediate mRNA species during subgroup C adenovirus productive infections. Virology 136, 387-403.
8. Buescher, E. L (1967). Respiratory disease and the adenoviruses. Med Clin North Am 51, 769-779.
9. Chroboczek, J., Bieber, F. & Jacrot, B. (1992). The sequence of the genome of adenovirus type 5 and its comparison with the genome of adenovirus type 2. Virology 186, 280-285.
10. Concino, M., Goldman, R. A., Caruthers, M. H. & Weinmann, R. (1984). Point mutations of the adenovirus major late promoter with different transcriptional efficiencies in vitro. J Biol Chem 258, 8493-8496.
11. Dan, A., Elo, P., Harrach, B., Zadori, Z. & Benko, M. (2001). Four new inverted terminal repeat sequences from bovine adenoviruses reveal striking differences in the length and content of the ITRs. Virus Genes 22, 175-179.
12. Davison, A. J., Telford, E. A., Watson, M. S., McBride, K. & Mautner, V. (1993). The DNA sequence of adenovirus type 40. J Mol Biol 234, 1308-1316.
13. Davison, A. J., Benko, M. & Harrach, B. (2003). Genetic content and evolution of adenoviruses. J Gen Virol 84, 2895-2908.
14. De Jong, R. N., Van Der Vliet, P. C. & Brenkman, A. B. (2003). Adenovirus DNA replication: protein priming, jumping back and the role for the DNA binding protein DBP. In Adenoviruses: Model and Vectors in Virus-Host Interactions, pp. 187-211. Edited by W. Doerfler & P. Bohm. Berlin: Springer.
15. Dudding, B. A., Wagner, S. C., Zeller, J. A., Gmelich, J. T., French, G. R. & Top, F. H., Jr (1972). Fatal pneumonia associated with adenovirus type 7 in three military trainees. N Engl J Med 286, 1289-1292.
16. Evans, J. D. & Hearing, P. (2002). Adenovirus replication. In Adenoviral Vectors for Gene Therapy, pp. 39-70. Edited by D. T. Curiel & J. T. Douglas. San Diego: Academic Press.
17. Flint, J. & Shenk, T. (1997). Viral transactivating proteins. Annu Rev Genet 31, 177-212.
18. Gao, W., Robbins, P. D. & Gambotto, A. (2003). Human adenovirus type 35: nucleotide sequence and vector development. Gene Ther 10, 1941-1949.
19. Gray, G. C., Goswami, P. R., Malasig, M. D., Hawksworth, A. W., Trump, D. H., Ryan, M. A. & Schnurr, D. P. (2000). Adult adenovirus infections: loss of orphaned vaccines precipitates military respiratory disease epidemics. For the Adenovirus Surveillance Group. Clin Infect Dis 31, 663-670.
20. Hasson, T. B., Soloway, P. D., Ornelles, D. A., Doerfler, W. & Shenk, T. (1989). Adenovirus L1 52- and 55-kilodalton proteins are required for assembly of virions. J Virol 63, 3612-3621.
21. Hatfield, L. & Hearing, P. (1991). Redundant elements in the adenovirus type 5 inverted terminal repeat promote bidirectional transcription in vitro and are important for virus growth in vivo. Virology 184, 265-276.
22. Hatfield, L. & Hearing, P. (1993). The NFIII/OCT-1 binding site stimulates adenovirus DNA replication in vivo and is functionally redundant with adjacent sequences. J Virol 67, 3931-3939.
23. Hayes, B. W., Telling, G. C., Myat, M. M., Williams, J. F. & Flint, S. J. (1990). The adenovirus L4 100-kilodalton protein is necessary for efficient translation of viral late mRNA species. J Virol 64, 2732-2742.
24. Hillemann, M. R. & Werner, J. R. (1954). Recovery of new agent from patients with acute respiratory illness. Proc Soc Exp Biol Med 85, 183-188.
25. Horton, T. M., Tollefson, A. E., Wold, W. S. & Gooding, L. R. (1990). A protein serologically and functionally related to the group C E3 14, 700-kilodalton protein is found in multiple adenovirus serotypes. J Virol 64, 1250-1255.
26. Howitt, J., Anderson, C. W. & Freimuth, P. (2003). Adenovirus interaction with its cellular receptor CAR. In Adenoviruses: Model and Vectors in Virus-Host Interactions, pp. 331-364. Edited by W. Doerfler & P. Bohm. Berlin: Springer.
27. Huang, X. (1994). On global sequence alignment. Comput Appl Biosci 10, 227-235.
28. Lee, R. F., Concino, M. F. & Weinmann, R. (1988). Genetic profile of the transcriptional signals from the adenovirus major late promoter. Virology 165, 51-56.
29. Leegwater, P. A., van Driel, W. & van der Vliet, P. C. (1985). Recognition site of nuclear factor 1, a sequence-specific DNA-binding protein from HeLa cells that stimulates adenovirus DNA replication. EMBO J 4, 1515-1521.
30. Leong, K., Lee, W. & Berk, A. J. (1990). High-level transcription from the adenovirus major late promoter requires downstream binding sites for late phase-specific factors. J Virol 64, 51-60.
31. Leppard, K. N. (1997). E4 gene function in adenovirus, adenovirus vector and adeno-associated virus infections. J Gen Virol 78, 2131-2138.
32. Mathews, M. B. & Shenk, T. (1991). Adenovirus virus-associated RNA and translation control. J Virol 65, 5657-5662.
33. Mei, Y. F., Skog, J., Lindman, K. & Wadell, G. (2003). Comparative analysis of the genome organization of human adenovirus 11, a member of the human adenovirus species B, and the commonly used human adenovirus 5 vector, a member of species C. J Gen Virol 84, 2061-2071.
34. Mul, Y. M., Verrijzer, C. P. & van der Vliet, P. C. (1990). Transcription factors NFI and NFIII/oct-1 function independently, employing different mechanisms to enhance adenovirus DNA replication. J Virol 64, 5510-5518.
35. Oosterom-Dragon, E. A. & Ginsberg, H. S. (1981). Characterization of two temperature-sensitive mutants of type 5 adenovirus with mutations in the 100,000-dalton protein gene. J Virol 40, 491-500.
36. Parks, C. L. & Shenk, T. (1997). Activation of the adenovirus major late promoter by transcription factors MAZ and Spl. J Virol 71, 9600-9607.
37. Pruijn, G. J., van Miltenburg, R. T., Claessens, J. A. & van der Vliet, P. C. (1988). Interaction between the octamer-binding protein nuclear factor III and the adenovirus origin of DNA replication. J Virol 62, 3092-3102.
38. Reach, M., Xu, L.-X. & Young, C. S. H. (1991). Transcription from the adenovirus major late promoter uses redundant activating elements. EMBO J 10, 3439-3446.
39. Roberts, R. J., Akusjarvi, G., Alestrom, P., Gelinas, R. E., Gingeras, T. R., Sciaky, D. & Pettersson, U. (1986). A consensus sequence for the adenovirus-2 genome. In Adenovirus DNA, pp. 1-51. Edited by W. Doerfler. Boston: Martinus Nijhoff.
40. Rowe, W. P., Huebner, R. J., Gilmore, L. K., Parrot, R. H. & Ward, T. G. (1953). Isolation of a cytopathogenic agent from human adenoids undergoing spontaneous degradation in tissue culture. Proc Soc Exp Biol Med 84, 570-573.
41. Russell, W. C. (2000). Update on adenovirus and its vectors. J Gen Virol 81, 2573-2604.
42. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M. A. & Barrell, B. (2000). Artemis: sequence visualization and annotation. Bioinformatics 16, 944-945.
43. Rux, J. J., Kuser, P. R. & Burnett, R. M. (2003). Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution X-ray crystallographic, molecular modeling, and sequence-based methods. J Virol 77, 9553-9566.
44. Ryan, M. A. K., Gray, G. C., Malasig, M. D., Binn, L. N., Asher, L. V., Cute, D., Kehl, S. C., Dunn, B. E. & Yund, A. J. (2001 . Two fatal cases of adenovirus-related illness in previously healthy young adults - Illinois, 2000. Morb Mortal Wkly Rep 50, 553-555.
45. San Martin, C. & Burnett, R. M. (2003). Structural studies on adenoviruses. In Adenoviruses: Model and Vectors in Virus-Host Interactions, pp. 57-94. Edited by W. Doerfler & P. Bohm. Berlin: Springer.
46. Scarpini, C., Arthur, J., Efstathiou, S., McGrath, Y. & Wilkinson, G. (1999). Herpes simplex virus and adenovirus vectors. In DNA Viruses, a Practical Approach, pp. 267-306. Edited by A. J. Cann. New York: Oxford University Press.
47. Schwartz, S., Zhang, Z., Frazer, K. A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R. & Miller, W. (2000). PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 10, 577-586.
48. Seto, D., Koop, B. F., Deshpande, P., Howard, S., Seto, J., Wilk, E., Wang, K. & Hood, L. (1994). Organization, sequence, and function of 34.5 kb of genomic DNA encompassing several murine T-cell receptor α/δ variable gene segments. Genomics 20, 258-266.
49. Sprengel, J., Schmitz, B., Heuss-Neitzel, D., Zock, C. & Doerfler, W. (1994). Nucleotide sequence of human adenovirus type 12 DNA: comparative functional analysis. J Virol 68, 379-389.
50. Stone, D., Furthmann, A., Sandig, V. & Lieber, A. (2003). The complete nucleotide sequence, genome organization, and origin of human adenovirus type 11. Virology 309, 152-165.
51. Sugarman, B. J., Hutchins, B. M., McAllister, D. L., Lu, F. & Thomas, B. K. (2003). The complete nucleotide acid sequence of the adenovirus type 5 reference material (ARM) genome. Bioprocessing J September/October, 27-32.
52. Temperley, S. M. & Hay, R. T. (1992). Recognition of the adenovirus type 2 origin of DNA replication by the virally encoded DNA polymerase and preterminal proteins. EMBO J 11, 761-768.
53. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24, 4876-4882.
54. Vogels, R., Zuijdgeest, D., van Rijnsoever, R. & 20 other authors (2003). Replication-deficient human adenovirus type 35 vectors for gene transfer and vaccination: efficient human cell infection and bypass of preexisting adenovirus immunity. J Virol 77, 8263-8271.
55. Wadell, G. (1984). Molecular epidemiology of human adenoviruses. Curr Top Microbiol Immunol 110, 191-220.
56. Wickham, T. J., Mathias, P., Cheresh, D. A. & Nemerow, G. R. (1993). Integrins αvβ3 and αvβ5 promote adenovirus internalization but not virus attachment. Cell 73, 309-319.
57. Wold, W. S. M. & Gooding, L. R. (1991). Region E3 of adenovirus: a cassette of genes involved in host immunosurveillance and virus-cell interactions. Virology 184, 1-8.
58. Yeh, R. F., Lim, L. P. & Burge, C. B. (2001). Computational inference of homologous gene structures in the human genome. Genome Res 11, 803-816.
59. Yew, P. R., Liu, X. & Berk, A. J. (1994). Adenovirus E1B oncoprotein tethers a transcriptional repression domain to p53. Genes Dev 8, 190-202.
60. Young, C. S. H. (2003). The structure and function of the adenovirus major late promoter. In Adenoviruses: Model and Vectors in Virus-Host Interactions, pp. 213-249. Edited by W. Doerfler & P. Bohm. Berlin: Springer.
61. Zafar, N., Mazumder, R. & Seto, D. (2001). Comparisons of gene colinearity in genomes using GeneOrder2.0. Trends Biochem Sci 26, 514-516.
62. Zhang, W., Low, J. A., Christensen, J. B. & Imperiale, M. J. (2001). Role for the adenovirus IVa2 protein in packaging of viral DNA. J Virol 75, 10446-10454.
63. Zu, Y. L., Takamatsu, Y., Zhao, M. J., Maekawa, T., Handa, H. & Ishii, S. (1992). Transcriptional regulation by a point mutant of adenovirus-2 Ela product lacking DNA-binding activity. J Biol Chem 267, 20181-20187.