Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease

Journal of Virology

Volumn 73, Issue 7, 1999, Pages 5497-5508

  Kirchhoff, Frank ^a   Easterbrook, Philippa J ^b   Douglas, Nigel ^c   Troop, Maxine ^b   Greenough, Thomas C ^e   Weber, Jonathan ^d   Carl, Silke ^a   Sullivan, John L ^e   Daniels, Rod S ^c  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^b CHELSEA AND WESTMINSTER HOSPITAL   (United Kingdom)

^c NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^d IMPERIAL COLLEGE SCHOOL OF MEDICINE   (United Kingdom)

^e UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NEF PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CELL COUNT; DISEASE COURSE; DNA SEQUENCE; GENE ACTIVITY; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; HELPER CELL; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; HUMAN TISSUE; IMMUNE SYSTEM; MAJOR CLINICAL STUDY; MOLECULAR CLONING; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; VIRUS LOAD;

EID: 0033052038     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.73.7.5497-5508.1999     Document Type: Article

References (44)

1. Alexander, L., Z. Du, M. Rosenzweig, J. J. Jung, and R. C. Desrosiers. 1997. A role for natural simian immunodeficiency virus and human immunodeficiency virus type 1 nef alleles in lymphocyte activation. J. Virol. 71:6094-6099.
2. Andersen, S., D. C. Shugars, R. Swanstrom, and J. V. Garcia. 1993. Nef from primary isolates of human immunodeficiency virus type 1 suppresses surface CD4 expression in human and mouse T cells. J. Virol. 67:4923-4931.
3. Baur, A. S., E. T. Sawai, P. Dazin, W. J. Fantl, C. Cheng-Mayer, and B. M. Peterlin. 1994. HIV-1 Nef leads to inhibition or activation of T cells depending on its intracellular localization. Immunity 1:373-384.
4. Carl, S., R. Daniels, A. J. Iafrate, M. Troop, P. Easterbrook, J. Skowronski, and F. Kirchhoff. Partial "repair" of defective nef genes in a long-term nonprogressor of HIV-1 infection selectively restores the ability of Nef to enhance infectivity and to down-modulate MHC class I cell surface expression. Submitted for publication.
5. Chowers, M. Y., C. A. Spina, T. J. Kwoh, N. J. Fitch, D. D. Richman, and J. C. Guatelli. 1994. Optimal infectivity in vitro of human immunodeficiency virus type 1 requires an intact nef gene. J. Virol. 68:2906-2914.
6. Craig, H. M., M. W. Pandori, and J. C. Guatelli. 1998. Interaction of HIV-1 Nef with the cellular dileucine-based sorting pathway is required for CD4 down-regulation and optimal viral infectivity. Proc. Natl. Acad. Sci. USA 95: 11229-11234.
7. Deacon, N. J., A. Tsykin, A. Solomon, K. Smith, M. Ludford-Menting, D. J. Hooker, D. A. McPhee, A. L. Greenway, A. Ellett, and C. Chatfield. 1995. Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients. Science 270:988-991.
8. Du, Z., S. M. Lang, V. G. Sasseville, A. A. Lackner, P. O. Ilyinskil, M. D. Daniel, J. U. Jung, and R. C. Desrosiers. 1995. Identification of a nef allele that causes lymphocyte activation and acute disease in macaque monkeys. Cell 82:665-674.
9. Easterbrook, P. J. 1998. Research potentials and pitfalls in the use of an HIV clinical database: Chelsea and Westminster Hospital. J. Acquired Immune Defic. Syndr. Hum. Retrovirol. 17:28-33.
10. Garcia, J. V., and A. D. Miller. 1991. Serine phosphorylation-independent downregulation of cell-surface CD4 by nef. Nature 350:508-511.
11. Goldsmith, M. A., M. T. Warmerdam, R. E. Atchison, M. D. Miller, and W. C. Greene. 1995. Dissociation of the CD4 downregulation and viral infeclivity enhancement functions of human immunodeficiency virus type 1 Nef. J. Virol. 69:4112-4121.
12. Greenough, T. C., M. Somansundaran, D. B. Brettler, R. M. Hesselton, A. Alimenti, F. Kirchhoff, D. Panicali, and J. L. Sullivan. 1994. Normal immune function and inability to isolate virus in culture in an individual with long-term human immunodeficiency type-1 infection. AIDS Res. Hum. Retroviruses 10:395-403.
13. Greenough, T. C., D. B. Brettler, F. Kirchhoff, L. Alexander, R. C. Desrosiers, S. J. O'Brien, M. Somasundaran, K. Luzuriaga, and J. L. Sullivan. Immunological and virological characterization of individuals with long-term non-progressive HIV-1 infection in a hemophilia cohort. Submitted for publication.
14. Grzesiek, S., A. Bax, G. M. Clore, A. M. Gronenborn, J. S. Hu, J. Kaufman, I. Palmer, S. J. Stahl, and P. T. Wingfield. 1996. The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase. Nat. Struct. Biol. 3:340-345.
15. Huang, Y., L. Zhang, and D. D. Ho. 1995. Characterization of nef sequences in long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 69:93-100.
16. Huang, Y., L. Zhang, and D. D. Ho. 1995. Biological characterization of Nef in long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 69:8142-8146.
17. Iafrate, A. J., S. Bronson, and J. Skowronski. 1997. Separable functions of Nef disrupt two aspects of T cell receptor machinery: CD4 expression and CD3 signaling. EMBO J. 16:673-684.
18. International Union of Biochemistry Nomenclature Committee. 1985. Nomenclature for incompletely specified bases in nucleic acid sequences. Eur. J. Biochem. 150:1-5.
19. Kestler, H. W., D. J. Ringler, K. Mori, D. L. Panicali, P. K. Sehgal, M. D. Daniel, and R. C. Desrosiers. 1991. Importance of the nef gene for maintenance of high virus loads and for development of AIDS. Cell 65:651-662.
20. Kirchhoff, F., T. C. Greenough, D. B. Brettler, J. L. Sullivan, and R. C. Desrosiers. 1995. Absence of intact nef sequences in a long-term, non-progressing survivor of HIV-1 infection. N. Engl. J. Med. 332:228-232.
21. Lee, C. H., B. Leung, M. A. Lemmon, J. Zheng, D. Cowburn, J. Kuriyan, and K. Saksela. 1995. A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein. EMBO J. 14: 5906-5015.
22. Lee, C. H., K. Saksela, U. A. Mirza, B. T. Chait, and J. Kuriyan. 1996. Crystal structure of the conserved core of HIV-1 Nef completed with a Src family SH3 domain. Cell 85:931-942.
23. Le Gall, S., M. C. Prevost, J. M. Heard, and O. Schwartz. 1997. Human immunodeficiency virus type I Nef independently affects virion incorporation of major histocompatibility complex class I molecules and virus infectivity. Virology 229:295-301.
24. Mariani, R., and J. Skowronski. 1993. CD4 down-regulation by nef alleles isolated from human immunodeficiency virus type 1-infected individuals. Proc. Natl. Acad. Sci. USA 90:5549-5553.
25. Mariani, R., F. Kirchhoff, T. C. Greenough, J. L. Sullivan, R. C. Desrosiers, and J. Skowronski. 1996. High frequency of defective nef alleles in a long-term survivor with nonprogressive human immunodeficiency virus type 1 infection. J. Virol. 70:7752-7764.
26. McNearney, T., Z. Hornickova, A. Terapleton, A. Birdwell, M. Arens, R. Markham, A. Saah, and L. Ratner. 1995. Nef and LTR sequence variation from sequentially derived human immunodeficiency virus type 1 isolates. Virology 208:388-398.
27. Michael, N. L., G. Chang, L. A. d'Arcy, C. J. Tseng, D. L. Birx, and H. W. Sheppard. 1995. Functional characterization of human immunodeficiency virus type 1 nef genes in patients with divergent rates of disease progression. J. Virol. 69:6758-6769.
28. Miller, M. D., M. T. Warmerdam, I. Gaston, W. C. Greene, and M. B. Feinberg. 1994. The human immunodeficiency virus-1 nef gene product: a positive factor for viral infection and replication in primary lymphocytes and macrophages. J. Exp. Med. 179:101-114.
29. Mills, J. 1997. Effects of 13-17 years of infection with a nef-deleted strain of HIV: the Sydney Blood Bank Cohort, p. 293-299. Report of the Onzieme Colloque Cent Gardes meeting.
30. Myers, G., B. T. Korber, B. Foley, K.-T. Jeang, J. W. Mellors, and S. Wain-Hobson. 1996. Human retroviruses and AIDS 1996: a compilation and analysis of nucleic acid and amino acid sequences. Los Alamos National Laboratory, Los Alamos, N.Mex.
31. Penny, M. A., S. J. Thomas, N. W. Douglas, S. Ranjbar, H. Holmes, and R. S. Daniels. 1996. Env-gene sequences of primary HIV-1 isolates of subtypes B, C, D, E and F obtained from the WHO-Network for HIV: isolation and characterisation. AIDS Res. Hum. Retroviruses 12:741-747.
32. Premkumar, D. R., X. Z. Ma, P. K. Maitra, B. K. Chakrabarti, J. Salkowitz, B. Yen-Lieberman, M. S. Hirsch, and H. W. Kestler. 1996. The nef gene from a long-term HIV type 1 non-progressor. AIDS Res. Hum. Retroviruses 12: 337-345.
33. Ratner, L., T. Joseph, J. Bandres, S. Ghosh, N. Vander Heyden, A Templeton, B. Hahn, W. Powderly, and M. Arens. 1996. Sequence heterogenicity of Nef transcripts in HIV-1-infected subjects at different stages of disease. Virology 223:245-250.
34. Report of an expert group (chairman, N. E. Ray). 1996. The incidence and prevalence of AIDS and prevalence of other severe HIV disease in England and Wales for 1995 to 1999: projection using data to the end of 1994. Commun. Dis. Rep. Rev. 6:R1-R21.
35. Saksela, K., G. Cheng, and D. Baltimore. 1995. Proline-rich (PxxP) motifs in HIV-1 Nef bind to SH3 domains of a subset of Src kinases and are required for the enhanced growth of Nef+ viruses but not for down-regulation of CD4. EMBO J. 14:484-491.
36. Saksela, K. 1997. HIV-1 Nef and host protein kinases. Frontiers Biosci. 2: 606-618.
37. Salvi, R., A. R. Garbuglia, A. Di Caro, S. Pulciani, F. Montella, and A. Benedetto. 1998. Grossly defective nef gene sequences in a a human immu-nodeficiency virus type 1-seropositive long-term nonprogressor. J. Virol. 72: 3646-3657.
38. Schwartz, O., V. Marechal, S. Le Gall, F. Lemonnier, and J. M. Heard. 1996. Endocytosis of major histocompatibility complex class I molecules is induced by the HIV-1 Nef protein. Nat. Med. 2:338-342.
39. Shugars, D. C., M. S. Smith, D. H. Glueck, P. V. Nantermet, F. Seillier-Moiseiwitsch, and R. Swanstrom. 1993. Analysis of human immunodeficiency virus type 1 nef gene sequences present in vivo. J. Virol. 67:4639-4650.
40. Spina, C. A., T. J. Kwoh, M. Y. Chowers, J. C. Guatelli, and D. D. Richman. 1994. The importance of nef in the induction of human immunodeficiency virus type 1 replication from primary quiescent CD4 lymphocytes. J. Exp. Med. 179:115-123.
41. Switzer, W. M., S. Wiktor, V. Soriano, A. Silva-Graca, K. Mansinho, I. M. Coulibaly, E. Ekpini, A E. Greenberg, T. M. Folks, and W. Heneine. 1998. Evidence of Nef truncation in human immunodeficiency virus type 2 infection. J. Infect. Dis. 177:65-71.
42. Weiss, R. A. 1993. How does HIV cause AIDS? Science 260:1273-1279.
43. Wyand, M. S., K. H. Manson, M. Garcia-Moll, D. Monfiori, and R. C. Desrosiers. 1996. Vaccine protection by a triple deletion mutant of simian immunodeficiency virus. J. Virol. 70:3724-3733.
44. Zazopoulos, E., and W. A. Haseltine. 1993. Effect of nef alleles on replication of human immunodeficiency virus type 1. Virology 194:20-27.