Structural defects and variations in the HIV-1 nef gene from rapid, slow and non-progressor children

AIDS

Volumn 17, Issue 9, 2003, Pages 1291-1301

  Casartelli, Nicoletta ^a   Di Matteo, Gigliola ^b   Argentini, Claudio ^c   Cancrini, Caterina ^b   Bernardi, Stefania ^a   Castelli, Guido ^a   Scarlatti, Gabriella ^e   Plebani, Anna ^d   Rossi, Paolo ^a,b   Doria, Margherita ^a  

^a BAMBINO GESÙ CHILDREN S HOSPITAL   (Italy)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

^c ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^d SAN RAFFAELE HOSPITAL   (Italy)

^e UNIVERSITY OF MILAN   (Italy)

Author keywords

Disease progression; HIV; Nef; Pediatrics; Sequence variability

Indexed keywords

ANTIRETROVIRUS AGENT; CD4 ANTIGEN; NEF PROTEIN; VIRUS PROTEIN; VIRUS RNA;

ALLELE; AMINO ACID SEQUENCE; ARTICLE; CHILD; CHILDHOOD DISEASE; CLINICAL ARTICLE; DISEASE COURSE; DNA SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MOLECULAR CLONING; MONONUCLEAR CELL; NEF GENE; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIRUS GENE; VIRUS INFECTION;

ADOLESCENT; ALLELES; AMINO ACID SEQUENCE; CD4 LYMPHOCYTE COUNT; CD4-POSITIVE T-LYMPHOCYTES; CHILD; CHILD, PRESCHOOL; DISEASE PROGRESSION; EPITOPES; EVOLUTION, MOLECULAR; GENE PRODUCTS, NEF; GENES, NEF; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; T-LYMPHOCYTES, CYTOTOXIC; VIRAL CORE PROTEINS;

EID: 0037999096     PISSN: 02699370     EISSN: None     Source Type: Journal    
DOI: 10.1097/00002030-200306130-00003     Document Type: Article

References (50)

1. Kestler HW, Ringlet DJ, Mori K, Panicali DL, Sehgal PK, Daniel MD, et al. Importance of the nef gene for maintenance of high virus loads and for development of AIDS. Cell 1991; 65: 651-662.
2. Du Z, Lang SM, Sasseville VG, Lackner AA, Ilyinskii PO, Daniel MD, et al. Identification of a nef allele that causes lymphocyte activation and acute disease in macaque monkeys. Cell 1995; 82:665-674.
3. Hanna Z, Kay DG, Rebai N, Guimond A, Jothy S, Jolicoeur P. Nef harbors a major determinant of pathogenicity for an AIDS-like disease induced by HIV-1 in transgenic mice. Cell 1998; 95:163-175.
4. Kirchhoff F, Greenough TC, Brettler DB, Sullivan JL, Desrosiers RC. Brief report: absence of intact nef sequences in a long-term survivor with nonprogressive HIV-1 infection. N Engl J Med 1995; 332:228-232.
5. Deacon NJ, Tsykin A, Solomon A, Smith K, Ludford-Menting M, Hooker DJ, et al. Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients. Science 1995; 270:988-991.
6. Salvi R, Garbuglia AR, Di Card A, Pulciani S, Montella F, Benedetto A. Grossly defective nef gene sequences in a human immunodeficiency virus type 1-seropositive long-term nonprogressor. J Virol 1998; 72:3646-3657.
7. Garcia JV, Alfano J, Miller AD. The negative effect of human immunodeficiency virus type 1 Nef on cell surface CD4 expression is not species specific and requires the cytoplasmic domain of CD4. J Virol 1993; 67:1511-1516.
8. Aiken C, Konner J, Landau NR, Lenburg ME, Trono D. Nef induces CD4 endocytosis: requirement for a critical dileucine motif in the membrane-proximal CD4 cytoplasmic domain. Cell 1994; 76:853-864.
9. Schwartz O, Marechat V, Le Gall S, Lemonnier F, Heard JM. Endocytosis of major histocompatibility complex class I molecules is induced by the HIV-1 Nef protein. Nat Med 1996; 2:338-342.
10. Chowers MY, Spina CA, Kwoh TJ, Fitch NJ, Richman DD, Guatelli JC. Optimal infectivity in vitro of human immunodeficiency virus type 1 requires an intact nef gene. J Virol 1994; 68: 2906-2914.
11. Miller MD, Warmerdam MT, Gaston I, Greene WC, Feinberg MB. The human immunodeficiency virus-1 nef gene product: a positive factor for viral infection and replication in primary lymphocytes and macrophages. J Exp Med 1994; 179:101-113.
12. Spina CA, Kwoh TJ, Chowers MY, Guatelli JC, Richman DD. The importance of nef in the induction of human immunodeficiency virus type 1 replication from primary quiescent CD4 lymphocytes. J Exp Med 1994; 179:115-123.
13. Swingler S, Mann A, Jacque J, Brichacek B, Sasseville VG, Williams K, et al. HIV-1 Nef mediates lymphocyte chemotaxis and activation by infected macrophages. Nat Med 1999; 5:997-1003.
14. Wang JK, Kiyokawa E, Verdin E, Trono D. The Nef protein of HIV-1 associates with rafts and primes T cells for activation. Proc Natl Acad Sci USA 2000; 97:394-399.
15. Geleziunas R, Xu W, Takeda K, Ichijo H, Greene WC. HIV-1 Nef inhibits ASK1-dependent death signalling providing a potential mechanism for protecting the infected host cell. Nature 2001; 410:834-838.
16. Wolf D, Witte V, Laffert B, Blume K, Stromer E, Trapp S, et al. HIV-1 Nef associated PAK and P13-kinases stimulate Akt-independent Bad- phosphorylation to induce anti-apoptotic signals. Nat Med 2001; 7:1217-1224.
17. Geyer M, Fackler OT, Peterlin BM. Structure-function relationships in HIV-1 Nef. EMBO Rep 2001; 2:580-585.
18. Skowronski J, Parks D, Mariani R. Altered T cell activation and development in transgenic mice expressing the HIV-1 nef gene. EMBOJ 1993; 12:703-713.
19. Benson RE, Sanfridson A, Ottinger JS, Doyle C, Cullen BR. Downregulation of cell-surface CD4 expression by simian immunodeficiency virus Nef prevents viral super infection. J Exp Med 1993; 177:1561-1566.
20. Ross TM, Oran AE, Cullen BR. Inhibition of HIV-1 progeny virion release by cell-surface CD4 is relieved by expression of the viral Nef protein. Curr Biol 1999; 9:613-621.
21. Lama J, Mangasarian A, Trono D. Cell-surface expression of CD4 reduces HIV-1 infectivity by blocking Env incorporation in a Nef- and Vpu-inhibitable manner. Curr Biol 1999; 9:622-631.
22. Collins KL, Chen BK, Kalams SA, Walker BD, Baltimore D. HIV-1 Nef protein protects infected primary cells against killing by cytotoxic T lymphocytes. Nature 1998; 391:397-401.
23. Mariani R, Kirchhoff F, Greenough TC, Sullivan JL, Desrosiers RC, Skowronski J. High frequency of defective nef alleles in a longterm survivor with nonprogressive human immunodeficiency virus type 1 infection. J Virol 1996; 70:7752-7764.
24. Michael NL, Chang G, d'Arcy LA, Tseng CJ, Birx DL, Sheppard HW. Functional characterization of human immunodeficiency virus type 1 nef genes in patients with divergent rates of disease progression. J Virol 1995; 69:6758-6769.
25. Huang Y, Zhang L, Ho DD. Biological characterization of nef in long-term survivors of human immunodeficiency virus type 1 infection. J Virol 1995; 69:8142-8146.
26. Ratner L, Joseph T, Bandres J, Ghosh S, Vander Heyden N, Templeton A, et al. Sequence heterogeneity of Nef transcripts in HIV-1-infected subjects at different stages of disease. Virology 1996; 223:245-250.
27. Brambilla A, Turchetto L, Gatti A, Bovolenta C, Veglia F, Santagostino E, et al. Defective nef alleles in a cohort of hemophiliacs with progressing and nonprogressing HIV-1 infection. Virology 1999; 259:349-368.
28. Geffin R, Wolf D, Muller R, Hill MD, Stellwag E, Freitag M, et al. Functional and structural defects in HIV type 1 nef genes derived from pediatric long-term survivors. AIDS Res Hum Retroviruses 2000; 16:1855-1868.
29. Kirchhoff F, Easterbrook PJ, Douglas N, Troop M, Greenough TC, Weber J, et al. Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease. J Virol 1999; 73:5497-5508.
30. Tobiume M, Takahoko M, Yamada T, Tatsumi M, Iwamoto A, Matsuda M. Inefficient enhancement of viral infectivity and CD4 downregulation by human immunodeficiency virus type 1 Nef from Japanese long-term nonprogressors. J. Virol 2002; 76: 5959-5965.
31. Center for Disease Control and Prevention. Revised classification system for human immunodeficiency virus infection in children less than 13 years of age. MMWR 1994; 43:1-19.
32. Grignani F, Kinsella T, Mencarelli A, Valtieri M, Riganelli D, Grignani F, et al. High-efficiency gene transfer and selection of human hematopoietic progenitor cells with a hybrid EBV/retroviral vector expressing the green fluorescence protein. Cancer Res. 1998; 58:14-19.
33. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994; 22:4673-4680.
34. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111-120.
35. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986; 3:418-426.
36. Romiti ML, Colognesi C, Cancrini C, Mas A, Berrino M, Salvatori F et al. Prognostic value of a CCR5 defective allele in pediatric HIV-1 infection. Mol Med 2000; 6:28-36.
37. Dean M, Carrington M, Winkler C, Huttley GA, Smith MW, Allikmets R, et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 1996; 273: 1856-1862.
38. Huang Y, Paxton WA, Wolinsky SM, Neumann AU, Zhang L, He T, et al. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat Med 1996; 2:1240-1243.
39. Kuiken C, Foley B, Hahn B, Marx P, McCutchan F, Mellors J et al. Human Retroviruses and AIDS. Los Alamos, New Mexico, USA: Theoretical Biology and Biophysics, Los Alamos National Laboratory; 1999.
40. Saksela K, Cheng G, Baltimore D. 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 1995; 14: 484-491.
41. Greenberg ME, Iafrate AJ, Skowronski J. The SH3 domain-binding surface and an acidic motif in HIV-1 Nef regulate trafficking of class I MHC complexes. EMBO J 1998; 17:2777-2789.
42. Arold ST, Baur AS. Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein. Trends Biochem Sci 2001; 26:356-363.
43. Aldrovandi GM, Gao L, Bristol G, Zack JA. Regions of human immunodeficiency virus type 1 nef required for function in vivo. J Virol 1998; 72:7032-7039.
44. Greenough TC, Sullivan JL, Desrosiers RC. Declining CD4 T-cell counts in a person infected with nef-deleted HIV-1. N Engl J Med 1999; 340:236-237.
45. Learmont JC, Geczy AF, Mills J, Ashton LJ, Raynes-Greenow CH, Garsia RJ, et al. Immunologic and virologic status after 14 to 18 years of infection with an attenuated strain of HIV-1. A report from the Sydney Blood Bank Cohort. N Engl J Med 1999; 340: 1715-1722.
46. Dyer WB, Ogg GS, Demoitie MA, Jin X, Geczy AF, Rowland-Jones SL, et al. Strong human immunodeficiency virus (HIV)-specific cytotoxic T- lymphocyte activity in Sydney Blood Bank Cohort patients infected with nef-defective HIV type 1. J Virol 1999; 73:436-443.
47. Nowak MA, Anderson RM, McLean AR, Wolfs TF, Goudsmit J, May RM. Antigenic diversity thresholds and the development of AIDS. Science 1991; 254:963-969.
48. Nowak MA, Anderson RM, Boerlijst MC, Bonhoeffer S, May RM, McMichael AJ. HIV-1 evolution and disease progression. Science 1996; 274:1008-1011.
49. Korber B, Brander C, Haynes B, Koup R, Kuiken C, Moore J, et al., HIV Molecular Immunology. Los Alamos, New Mexico, USA: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory; 2000.
50. Haas G, Plikat U, Debre P, Lucchiari M, Katlama C, Dudoit Y, et al. Dynamics of viral variants in HIV-1 Nef and specific cytotoxic T lymphocytes in vivo. J Immunol. 1996; 157: 4212-4221.