Comparative sequence analysis and predictions for the envelope glycoproteins of foamy viruses

Journal of General Virology

Volumn 80, Issue 1, 1999, Pages 245-254

  Wang, George ^a   Mulligan, Mark J ^a,b  

^a University of Alabama at Birmingham   (United States)

^b University of Alabama at Birmingham   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; POL PROTEIN; SIGNAL PEPTIDE; VIRUS ENVELOPE PROTEIN; VIRUS GLYCOPROTEIN;

ARTICLE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SPUMA VIRUS;

HUMAN SPUMARETROVIRUS; RNA VIRUSES; SPUMAVIRUS;

EID: 0032919803     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/0022-1317-80-1-245     Document Type: Article

References (72)

1. 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 Research 25, 3389-3402.
2. Brasseur, R., Cornet, B., Burny, A., Vandenbranden, M. & Ruysschert, J. M. (1988). Mode of insertion into a lipid membrane of the N-terminal HIV gp41 peptide segment. AIDS Research and Human Retroviruses 4, 83-90.
3. Brasseur, R., Vandenbranden, M., Cornet, B., Burny, A. & Ruysschert, J.-M. (1990). Orientation into the lipid bilayer of an asymmetric amphipathic helical peptide located at the N-terminus of viral fusion proteins. Biochimica et Biophysica Acta 1029, 267-273.
4. Bullough, P., Hughson, F., Skehel, J. & Wiley, D. (1994). Structure of influenza haemagglutinin at the pH of membrane fusion. Nature 371, 37-43.
5. Callebaut, I., Labesse, G., Durand, P., Poupon, A., Canard, L., Chomilier, J., Henrissat, B. & Mornon, J. P. (1997). Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Cellular and Molecular Life Sciences 53, 621-645.
6. Chambers, P., Pringle, C. R. & Easton, A. J. (1990). Heptad repeat sequences are located adjacent to hydrophobic regions in several types of virus fusion glycoproteins. Journal of General Virology 71, 3075-3080.
7. Chan, D. C., Fass D., Berger, J. M. & Kim, P. S. (1997). Core structure of gp41 from the HIV envelope glycoprotein. Cell 89, 263-273.
8. Coffin, J. (1986). Genetic variation in AIDS viruses. Cell 46, 1-4.
9. Dias, H. W., Aboud, M. & Flügel, R. M. (1996). Analysis of the phylogenetic placement of different spumaretroviral genes reveals complex pattern of foamy virus evolution. Virus Genes 11, 183-190.
10. Durell, S. R., Martin, S., Ruysschaert, J.-M., Shai, Y. & Blumenthal, R. (1997). What studies of fusion peptides tell us about viral envelope glycoprotein-mediated membrane fusion (Review). Molecular Membrane Biology 14, 97-112.
11. Eisenberg, D. (1984). Three-dimensional structure of membrane and surface proteins. Annual Review of Biochemistry 53, 595-623.
12. Enssle, J., Jordan, I., Maurer, B. & Rethwilm, A. (1996). Foamy virus reverse transcriptase is expressed independently from the Gag protein. Proceedings of the National Academy of Sciences, USA 93, 4137-4141.
13. Fass, D. & Kim, P. S. (1996). Structure of Moloney murine virus envelope domain at 1·7 Å resolution. Nature Structural Biology 3, 365-369.
14. Flügel, R. M., Rethwilm, A., Maurer, B. & Darai, G. (1987). Nucleotide sequence analysis of the env gene and its flanking regions of the human spumaretrovirus reveals two novel genes. EMBO Journal 6, 2077-2084.
15. Gaboriaud, C., Bissery, V., Benchetrit, T. & Mornon, J. P. (1987). Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. FEBS Letters 224, 149-155.
16. Gallaher, W. R. (1987). Detection of a fusion peptide sequence in the transmembrane protein of human immunodeficiency virus. Cell 50, 327-328.
17. Gallaher, W., Ball, J., Garry, R. F., Griffin, M. C. & Montelaro, R. C. (1989). A general model for the transmemebrane protein of HIV and other retroviruses. AIDS Research and Human Retroviruses 5, 431-440.
18. Gatot, J.-S., Callebaut, I., Gaboriaud, C., Mornon, J. P., Portetelle, D., Burny, A., Kerkhofs, P., Kettmann, R. & Willems, L. (1998). Conservative mutations in the immunosuppressive region of the bovine leukemia virus transmembrane protein affect fusion but not infectivity in vivo. Journal of Biological Chemistry 273, 12870-12880.
19. Genetics Computer Group (1997). Program Manual for the Wisconsin Package, Version 9.1. 575 Science Drive, Madison, Wisconsin.
20. Goepfert, P. A., Wang, G. & Mulligan, M. J. (1995). Identification of an ER retrieval signal in a retroviral glycoprotein. Cell 82, 543-544.
21. Goepfert, P. A., Ritter, G. D., Gbkaima, A., Zhang, Y., Hahn, B. H. & Mulligan, M. J. (1996). Analysis of West African hunters for foamy virus infections. AIDS Research and Human Retroviruses 12, 1725-1730.
22. Goepfert, P. A., Shaw, K. L. & Mulligan, M. J. (1997). A sorting motif localizes the foamy virus glycoprotein to the endoplasmic reticulum. Journal of Virology 71, 778-784.
23. Heneine, W., Switzer, W. M., Sandstrom, P., Brown, J., Vedapuri, S., Schable, C. A., Khan, A. S., Lerch, N. W., Schweizer, M., Neumann-Haefelin, D., Chapman, L. E. & Folks, T. M. (1998). Identification of a human population infected with simian foamy viruses. Nature Medicine 4, 403-407.
24. Herchenröder, O., Renne, R., Loncar, D., Cobb, E. K., Murthy, K. K., Schneider, J., Mergia, A. & Luciw, P. A. (1994). Isolation, cloning, and sequencing of simian foamy viruses from chimpanzee (SFVcpz): high homology to human foamy virus (HFV). Virology 201, 187-199.
25. Holzschu, D. L., Delaney, M. A., Renshaw, R. W. & Casey, J. W. (1998). The nucleotide sequence and spliced pol mRNA levels of the non-primate spumavirus bovine foamy virus. Journal of Virology 72, 2177-2182.
26. Huang, Y., Khorchid, A., Wang, J., Parniak, M. A., Darlix, J. L., Wainberg, M. A. & Kleiman, L. (1997). Effect of mutations in the nucleocapsid protein (NCp7) upon PrI60(gag-pol) and tRNA(Lys) incorporation into human immunodeficiency virus type 1. Journal of Virology 71, 4378-4384.
27. Hunter, E. & Swanstrom, R. (1990). Retrovirus envelope glycoproteins. Current Topics in Microbiology and Immunology 157, 187-253.
28. Jackson, M. R., Nilsson, T. & Peterson, P. A. (1990). Identification of a consensus motif for retention of transmembrane proteins in the endoplasmic reticulum. EMBO Journal 9, 3153-3162.
29. Jones, M. K., Anantharamaiah, G. M. & Segrest, J. P. (1992). Computer programs to identify and classify amphipathic α-helical domains. Journal of Lipid Research 33, 287-296.
30. Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
31. Kozak, M. (1989). The scanning model for translation: an update. Journal of Cell Biology 108, 229-241.
32. Kupiec, J.-J., Kay, A., Hayat, M., Ravier, R., Périès, J. & Galibert, F. (1991). Sequence analysis of the simian foamy virus type 1 genome. Gene 101, 185-194.
33. Lemesle-Varloot, L., Henrissat, B., Gaboriaud, C, Bissery, V., Morgat, A. & Mornon, J. P. (1990). Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences. Biochimie 72, 555-574.
34. Lewe, G. & Flügel, R. M. (1990). Comparative analysis of the retroviral Pol and Env protein sequences reveal different evolutionary trees. Virus Genes 3, 195-204.
35. Lim, V. I. (1978), Polypeptide chain folding through a highly helical intermediate as a general principle of globular protein structure formation. FEBS Letters 89, 10-14.
36. Livingstone, C. D. & Barton, G. J. (1996). Identification of functional residues and secondary structure from protein multiple sequence alignment. Methods in Enzymology 266, 497-512.
37. Löchelt, M. & Flügel, R. M. (1995). The molecular biology of human and primate spuma retroviruses. In The Retroviridae, vol. 4, pp. 239-292. Edited by J. A. Levy. New York: Plenum Press.
38. Löchelt, M. & Flügel, R. M. (1996). The human foamy virus pol gene is expressed as a pro-Pol polyprotein and not as a Gag-Pol fusion protein. Journal of Virology 70, 1033-1040.
39. Loh, P. C. (1993). Spumaviruses. In The Retroviridae, 2nd edn. pp. 361-397. Edited by J. A. Levy. New York: Plenum Press.
40. McClure, M. A., Johnson, M. S., Feng, D. F. & Doolittle, R. F. (1988). Sequence comparisons of retroviral proteins: relative rates of change and general phylogeny. Proceedings of the National Academy of Sciences, USA 85, 2469-2473.
41. Matthews, T. J., Wild, C., Chen, C., Bolognesi, D. P. & Greenberg, M. L. (1994). Structural rearrangements in the transmembrane glycoprotein after receptor binding. Immunological Reviews 140, 93-104.
42. Maurer, B., Bannert, H., Darai, G. & Flugel, R. M. (1988). Analysis of the primary structure of the long terminal repeat and the gag and pol genes of the human spumaretrovirus. Journal of Virology 62, 1590-1597.
43. Mergia, A., Shaw, K. E. S., Lackner, J. E. & Luciw, P. A. (1990). Relationship of the env genes and the endonuclease domain of the pol genes of simian foamy virus type 1 and human foamy virus. Journal of Virology 64, 406-410.
44. Moebes, A., Enssle, J., Bieniasz, P. D., Heinkelein, M., Lindemann, D., Bock, M., McClure, M. O. & Rethwilm, A. (1997). Human foamy virus reverse transcription that occurs late in the viral replication cycle. Journal of Virology 71, 7305-7311.
45. Neumann-Haefelin, D. & Schweizer, M. (1997). Nonhuman primate spumavirus infections among persons with occupational exposure. Morbidity and Mortality Weekly Report 46, 129-131.
46. Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. (1997). Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering 10, 1-6.
47. Nothwehr, S. T. & Gordon, J. I. (1990). Targeting of proteins into the eukaryotic secretory pathway: signal peptide structure/function relationships. Bioessays 12, 479-484.
48. Pearson, W. R. (1996). Effective protein sequence comparison. Methods in Enzymology 266, 227-258.
49. Pearson, W. R. & Lipman, D. J. (1990). Improved tools for biological sequence analysis. Proceedings of the National Academy of Sciences, USA 85, 2444-2448.
50. Perlman, D. & Halvorson, H. P. (1983). A putative signal peptidase recognition site and sequence in eukaryotic and prokaryotic signal peptides. Journal of Molecular Biology 167, 391-409.
51. Renne, R., Friedl Schweizer, M., Fleps, U., Turek, R. & Neumann-Haefelin, D. (1992). Genomic organization and expression of simian foam virus type 3 (SFV-3). Virology 186, 597-608.
52. Renshaw, R. W. & Casey, J. W. (1994). Transcriptional mapping of the 3′ end of the bovine syncytial virus genome. Journal of Virology 68, 1021-1028.
53. Rost, B. (1996). PHD: predicting one-dimensional protein structure by profile-based neural network. Methods in Enzymology 266, 525-539.
54. Rost, B. & Sander, C. (1993). Prediction of protein structure at better than 70% accuracy. Journal of Molecular Biology 232, 584-599.
55. Rost, B. & Sander, C. (1994a). Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19, 55-72.
56. Rost, B. & Sander, C. (1994b). Conservation and prediction of solvent accessibility in protein families. Proteins 20, 216-226.
57. Rost, B., Casadio, R., Fariselli, P. & Sander, C. (1995). Transmembrane helices predicted at 95% accuracy. Protein Science 4, 521-533.
58. Russell, R. B. & Sternberg, M. J. E. (1995). How good are we? Current Biology 5, 488-490.
59. Schiffer, M. & Edmundson, A. B. (1967). Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophysical Journal 7, 121-135.
60. Schliephake, A. W. & Rethwilm, A. (1994). Nuclear localization of foamy virus Gag precursor protein. Journal of Virology 68, 4946-4954.
61. Schweizer, M., Turek, R., Hahn, H., Schliephake, A., Netzer, K.-O., Eder, G., Reinhardt, M., Rethwilm, A. & Neumann-Haefelin, D. (1995). Markers of foamy virus infections in monkeys, apes, and accidentally infected humans: appropriate testing fails to confirm suspected foamy virus seroprevalence in humans. AIDS Research and Human Retroviruses 11, 161-170.
62. Schweizer, M., Falcone, V., Gänge, J., Turek, R. & Neumann-Haefelin, D. (1997). Simian foamy virus isolated from an accidentally infected human individual. Journal of Virology 71, 4821-4824.
63. Shin, J., Dunbrack, R. L., Jr, Lee, S. & Strominger, J. L. (1991). Signals for retention of transmembrane proteins in the endoplasmic reticulum studied with CD4 truncation mutants. Proceedings of the National Academy of Sciences, USA 88, 1918-1922.
64. Vonèche, V., Portetelle, D., Kettmann, R., Willems, L., Limbach, K., Paoletti, E., Ruysschaert, J.-M., Burny, A. & Brasseur, R. (1992). Fusiogenic segments of bovine leukemia virus and simian immunodeficiency virus are interchangeable and mediate fusion by means of oblique insertion in the lipid bilayer of their target cells. Proceedings of the National Academy of Sciences, USA 89, 3810-3814.
65. von Heijne, G. (1986). A new method for predicting signal sequence cleavage sites. Nucleic Acids Research 14, 4683-4690.
66. Weiss, R. A. (1998). Retroviral zoonoses. Nature Medicine 4, 391-392.
67. Weissenhorn, W., Dessen, A., Harrison, S. C., Skehel, J. J. & Wiley, D. C. (1997). Atomic structure of the ectodomain from HIV-1 gp41. Nature 387, 426-430.
68. White, J. M. (1990). Viral and cellular membrane fusion proteins. Annual Review of Physiology 52, 675-697.
69. White, J. M. (1992). Membrane fusion. Science 258, 917-924.
70. Wilson, I. A., Skehel, J. J. & Wiley, D. C. (1981). Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution. Nature 289, 366-373.
71. Winkler, I., Bodem, J., Haas, L., Zemba, M., Delius, H., Flower, R., Flugel, R. & Lochelt, M. (1997). Characterization of the genome of feline foamy virus and its proteins shows distinct features different from those of primate spumaviruses. Journal of Virology 71, 6727-6741.
72. Yu, S. F., Baldwin, D. N., Gwynn, S. R., Yendapalli, S. & Linial, M. L. (1996). Human foamy virus replication: a pathway distinct from that of retrovirus and hepadnaviruses. Science 271, 1579-1582.