Skip to main content

Advertisement

SpringerLink
Log in

Sequence heterogeneity in human immunodeficiency virus type 1 nef in patients presenting with rapid progression and delayed progression to AIDS

  • Original Article
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Genetic heterogeneity in the nef genes from human immunodeficiency virus type 1 (HIV-1)-infected rapid progressors (RPs) and long-term nonprogressors (LTNPs) was analyzed to identify various amino acid substitutions responsible for the discernible difference in disease progression. It was found that the majority of the strains characterized belonged to subtype C, followed by several BC recombinants and subtype A1. Complete nef subtype C sequences from 33 RPs and seven LTNPs were compared, and it was observed that, in the majority of the sequences from both groups, highly conserved functional motifs showed subtle changes. However, drastic changes were observed in two isolates from LTNPs where the arginine cluster was deleted, while in one of them, additionally, acidic residues were replaced by basic residues (EEEEE → RK(R)KKE). The deletion of the arginine cluster and the mutation of acidic residues to basic residues are predicted to delay disease development by abolishing CD4 downmodulation and causing diminution of major histocompatibility complex class I (MHC-I) downregulation, respectively. Nonetheless, this is an exclusive finding in these LTNPs, which necessitates their analysis at the functional level. The synonymous-to-nonsynonymous substitution ratio was greater than one in both of the groups, suggesting amino acid sequence conservation and functional robustness. Interpatient nucleotide distance within the group and between the two groups showed very little variation, confirming genetic relatedness among isolates.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Kirchoff F, Easterbook PJ, Douglas N, Troop M, Greenough TC, Weber J, Carl S, Sullivan TC, Daniels RS (1999) Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease. J Virol 73:5497–5508

    Google Scholar 

  2. Pantaleo G, Fauci AS (1996) Immunopathogenesis of HIV infection. Ann Rev Microbiol 50:825–854

    Article  CAS  Google Scholar 

  3. Flores-Villanueva PO, Hendel H, Caillat-Zucman S, Rappaport J, Burgos-Tiburcio A, Bertin-Maghit S, Ruiz-Morales JA, Teran ME, Rodriguez-Tafur J, Zagury JF (2003) Association of MHC ancestral haplotypes with resistance/susceptibility to AIDS disease development. J Immunol 170:1925–1929

    Article  CAS  PubMed  Google Scholar 

  4. Rodes B, Carlos T, Ellen P, Eva P, Martinez-Padial M, Miguel B, Victoria J, Terri W, Sylvania B, Soriano V (2004) Differences in disease progression in a cohort of long-term nonprogressors after more than 16 years of HIV-1 infection. AIDS 18:1109–1116

    Article  PubMed  Google Scholar 

  5. Saksena N, Wang B, Dyer W (2001) Biological and molecular mechanisms in progression and non-progression of HIV disease. AIDS Rev 3:133–134

    Google Scholar 

  6. Geffin R, Wolf D, Muller R, Hill MD, Stellwag E, Freitag M, Sass G, Scott GB, Baur AS (2000) Functional and structural defects in HIV type 1 nef genes derived from pediatric long-term survivors. AIDS Res Hum Retroviruses 16:1855–1868

    Article  CAS  PubMed  Google Scholar 

  7. Koot M, Keet IPM, Vos AHV, de Goede RE, Ross MT, Cotinho RA, Miedema F, Schellekens PT, Tersmette M (1993) Prognostic value of HIV-1 syncytium-inducing phenotype for rate of CD4 + cell depletion and progression to AIDS. Ann Intern Med 118:681–688

    Article  CAS  PubMed  Google Scholar 

  8. Lum JJ, Cohen OJ, Nie Z, Weaver JG, Gomez TS, Yao XJ, Lynch D, Pilon AA, Hawley N, Kim JE, Chen Z, Montpetit M, Sanchez-Dardon J, Cohen EA, Badley AD (2003) Vpr R77Q is associated with long-term nonprogressive HIV infection and impaired induction of apoptosis. J Clin Invest 111:1547–1554

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  9. Pantaleo G, Graziosi C, Fauci AS (1993) The immunopathogenesis of human immunodeficiency virus infection. N Engl J Med 328:327–335

    Article  CAS  PubMed  Google Scholar 

  10. Rutherford GW (1994) Long-term survival in HIV-1 infection. BMJ 309:283–284

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Boerma JT, Nunn AJ, Whitworth JA (1998) Mortality impact of the AIDS epidemic: evidence from community studies in less developed countries. AIDS 12:S3–S14

    PubMed  Google Scholar 

  12. Morgan D, Maude GH, Malamba SS, Okongo MJ, Wagner HU, Mulder DW, Whitworth JA (1997) HIV-1 disease progression and AIDS-defining disorders in rural Uganda. Lancet 350:245–250

    Article  CAS  PubMed  Google Scholar 

  13. Okongo M, Morgan D, Mayanja B, Ross A, Whitworth J (1998) Causes of death in a rural, population-based human immunodeficiency virus type-1 (HIV-1) natural history cohort in Uganda. Int J Epidemiol 27:698–702

    Article  CAS  PubMed  Google Scholar 

  14. Hogg RS, Strathdee SA, Craib KJP, O’Shaughnessy MV, Montaner JSG, Schecter MT (1994) Lower socioeconomic status and shorter survival following HIV infection. Lancet 344:1120–1124

    Article  CAS  PubMed  Google Scholar 

  15. Jere A, Tripathy S, Agnihotri K, Jadhav S, Paranjape R (2004) Genetic analysis of Indian HIV-1 nef: subtyping, variability and implications. Microbes Infect 6:279–289

    Article  CAS  PubMed  Google Scholar 

  16. Jameel S, Zafrullah M, Ahmad M, Kapoor GS, Sehgal S (1995) Genetic analysis of HIV-1 from Punjab, India reveals the presence of multiple variants. AIDS 9:685–690

    Article  CAS  PubMed  Google Scholar 

  17. Kumar M, Jain SK, Pasha ST, Chattopadhya D, Lal S, Rai A (2006) Genomic diversity in the regulatory nef gene sequences in Indian isolates of HIV type 1: emergence of a distinct subclade and predicted implications. AIDS Res Hum Retroviruses 22:1206–1219

    Article  CAS  PubMed  Google Scholar 

  18. Weiss RA (1993) How does HIV cause AIDS? Science 260:1273–1279

    Article  CAS  PubMed  Google Scholar 

  19. Stoddart CA, Geleziunas R, Ferrell S, Linquist-Stepps V, Moreno ME, Bare C, Xu W, Yonemoto W, Bresnahan PA, McCune JM, Greene WC (2003) Human immunodeficiency virus type 1 nef-mediated downregulation of CD4 correlates with nef enhancement of viral pathogenesis. J Virol 77:2124–2133

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Ariën KK, Verhasselt B (2008) HIV Nef: role in pathogenesis and viral fitness. Current HIV Res 6:200–208

    Article  Google Scholar 

  21. Geyer M, Fackler OT, Peterlin BM (2001) Structure-function relationships in HIV-1 Nef. EMBO Rep 2:580–585

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Frei M. (2011) Histopaque® Troubleshooting Guide. http://www.sigmaaldrich.com/content/dam/sigma-aldrich/articles/biofiles/biofiles-pdf/biofiles_v6_n5.pdf]. Accessed 17 Apr 2010

  23. REGA HIV-1 subtyping tool-version 2.0. http://dbpartners.stanford.edu/RegaSubtyping. Accessed 20 Aug 2012

  24. RIP: Recombinant Identification Program: http://www.hiv.lanl.gov/content/sequence/RIP/RIP.html. Accessed 23 Aug 2012

  25. Felsenstein J (1993) PHYLIP package (v 3.69). http://evolution.genetics.washington.edu/phylip/getme.html. Accessed 07 July 2012

  26. Gaschen B, Taylor J, Yusin K, Foley B, Gao F, Lang D, Novisky V, Haynes B, Hahn BH, Bhattacharya T, Korber B (2002) Diversity consideration in HIV-1 vaccine selection. Science 296:2354–2360

    Article  CAS  PubMed  Google Scholar 

  27. Synonymous Non-synonymous Analysis Program: http://www.hiv.lanl.gov/content/sequence/SNAP/SNAP.html. Accessed 10 Oct 2012

  28. Entropy: Shannon entropy-two: http://www.hiv.lanl.gov/content/sequence/ENTROPY/entropy.html. Accessed 5 Sep 2013

  29. HIV sequence alignments. http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Accessed 11 Sep 2012

  30. Freund J, Kellner R, Konvalinka J, Wolber V, Krausslich HG, Kalbitzer HR (1994) A possible regulation of negative factor (Nef) activity of human immunodeficiency virus type 1 by the viral protease. Eur J Biochem 223:589–593

    Article  CAS  PubMed  Google Scholar 

  31. Fackler OT, Luo W, Geyer M, Alberts AS, Peterlin BM (1999) Activation of Vav by Nef induces cytoskeletal rearrangements and downstream effector functions. Mol Cell 3:729–739

    Article  CAS  PubMed  Google Scholar 

  32. Saksela K, Cheng G, Baltimore D (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

    CAS  PubMed Central  PubMed  Google Scholar 

  33. Arold S, Franken P, Strub MP, Hoh F, Benichou S, Benarous R, Dumas C (1997) The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling. Structure 5:1361–1372

    Article  CAS  PubMed  Google Scholar 

  34. Lee C-H, Saksela K, Mirza UA, Chait BT, Kuriyan J (1996) Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain. Cell 85:931–942

    Article  CAS  PubMed  Google Scholar 

  35. Fackler OT, Lu X, Frost JA, Geyer M, Jiang B, Luo W, Abo A, Alberts AS, Peterlin BM (2000) P21-activated kinase 1 plays a critical role in cellular activation by Nef. Mol Cell Biol 20:2619–2627

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  36. Renkema GH, Manninen A, Manninnen A, Mann DA, Harris M, Saksela K (1999) Identification of the nef-associated kinase as p21-activated kinase 2. Curr Biol 9:1407–1410

    Article  CAS  PubMed  Google Scholar 

  37. Manninen A, Hiipakka M, Vihinen M, Lu W, Mayer BJ, Saksela K (1998) SH3 domain-binding function of HIV-1 Nef is required for association with a PAK-related kinase. Virology 250:273–282

    Article  CAS  PubMed  Google Scholar 

  38. Consensus/Ancestral sequences. http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html#consensus. Accessed 11 Sep 2012

  39. Piguet V, Gu F, Foti M, Demaurex N, Gruenberg J, Carpentier JL, Trono D (1999) Nef-induced CD4 degradation: a diacidic-based motif in Nef functions as a lysosomal targeting signal through the binding of β-COP in endosomes. Cell 97:63–73

    Article  CAS  PubMed  Google Scholar 

  40. Gojobori T, Yamaguchi Y, Ikeo K, Mizokami M (1994) Evolution of pathogenic viruses with special reference to the rates of synonymous and nonsynonymous substitutions. Jpn J Gene 69:481–488

    Article  CAS  Google Scholar 

  41. Dorrell L, Willcox BE, Jones EY, Gillespie GG, Njai H, Sabally S, Jaye A, DeGleria K, Rostron T, Lepin AE, McMichael, Whittle H, Rowland-Jones S (2001) Cytotoxic T lymphocytes recognize structurally diverse, clade-specific and cross-reactive peptides in human immunodeficiency virus type-1 gag through HLA-B53. Eur J Immunol 31:1747–1756

    Article  CAS  PubMed  Google Scholar 

  42. Gordon JI, Duriono RJ, Rudnick DA, Adams SP, Gokel GW (1991) Protein N-myristoylation. J Biol Chem 266:8647–8650

    CAS  PubMed  Google Scholar 

  43. Huang Y, Zhang L, Ho DD (1995) Characterization of nef sequences in long-term survivors of human immunodeficiency virus type 1 infection. J Virol 69:93–100

    CAS  PubMed Central  PubMed  Google Scholar 

  44. Bentham M, Mazaleyrat S, Harris M (2005) Role of myristoylation and N-terminal basic residues in membrane association of the human immunodeficiency virus type 1 Nef protein. J Gen Virol 87:563–571

    Article  Google Scholar 

  45. Piguet V and Trono D (1999) A structure-function Analysis of the Nef Protein of Primate Lentiviruses. HIV Sequence Database. http://www.hiv.lanl.gov/content/sequence/HIV/COMPENDIUM/1999/6/piguet.pdf. Accessed 27 June 2012

  46. Piguet V, Wan L, Borel C, Mangasarian A, Demaurex N, Thomas G, Trono D (2000) HIV -1 Nef protein binds to the cellular protein PACS-I to downregulate class I major histocompatibility complexes. Nature Cell Biol 2:163–167

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  47. Greenberg ME, Iafrate AJ, Skowronski J (1998) The SH3-binding domain binding surface and an acidic motif in HIV-1 Nef regulate trafficking of class-I MHC complexes. Embo J 17:2777–2789

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  48. Mangasarian A, Piguet V, Wang JK, Chen YL, Trono D (1999) Nef-induced CD4 and major histocompatibility complex class I (MHC-I) down-regulation are governed by distinct determinants: N-terminal alpha helix and proline repeat of Nef selectively regulate MHC-I trafficking. J Virol 73:1964–1973

    CAS  PubMed Central  PubMed  Google Scholar 

  49. Blagoveshchenskaya AD, Thomas L, Feliciangeli SF, Hung CH, Thomas G (2002) HIV-1 Nef downregulates MHC-I by a PACS-1 and PI3 K-regulated ARF6 endocytic pathway. Cell 111:853–866

    Article  CAS  PubMed  Google Scholar 

  50. Collins KL, Chen BK, Kalams SA, Walker BD, Baltimore D (1998) HIV-1 Nef protein protects infected primary cells against killing by cytotoxic T lymphocytes. Nature 391:397–401

    Article  CAS  PubMed  Google Scholar 

  51. Agopian K, Wei LB, Garcia VJ, Gabuzda D (2007) CD4 and MHC-I Downregulation are conserved in Primary HIV-1 Nef Alleles from brain and lymphoid tissues, but Pak 2 activation is highly variable. Virology 358:119–135

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  52. O’Neill KE, Kuo LS, Krisko JF, Tomchick DR, Garcia JV, Foster JL (2006) Dynamic evolution of the human immunodeficiency virus type 1 pathogenic factor, Nef. J Virol 80:1311–1320

    Article  PubMed Central  PubMed  Google Scholar 

  53. Baugh LL, Garcia V, Foster LJ (2008) Functional characterization of the human immunodeficiency virus type 1 Nef acidic domain. J Virol 82:9657–9667

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  54. Saksela K, Cheng G, Baltimore D (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

    CAS  PubMed Central  PubMed  Google Scholar 

  55. Saksela K (1997) HIV-1 Nef and host cell kinases. Frontiers in Bioscience 2:d606–d618

    CAS  PubMed  Google Scholar 

Download references

Acknowledgement

The authors are indebted to all of the study participants. Poonam Gupta is the recipient of a Junior Research Fellowship awarded by the Indian Council of Medical Research. The study was funded by the University Grants Commission [F. No. 37-223/2009(SR)].

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Department of Biotechnology, Jamia Millia Islamia, New Delhi, India

    Poonam Gupta, Mohammad Husain & Mohammad Misbah

  2. Division of Biotechnology, National Centre for Disease Control (NCDC), Delhi, India

    Hanu Ram, Supriya Singh Verma, L. S. Chauhan & Arvind Rai

  3. Department of Microbiology, Dr. Ram Manohar Lohia Hospital, New Delhi, India

    Charoo Hans

Authors
  1. Poonam Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mohammad Husain
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Charoo Hans
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hanu Ram
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Supriya Singh Verma
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mohammad Misbah
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. L. S. Chauhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Arvind Rai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mohammad Husain.

Additional information

Nucleotide sequence data reported are available in the GenBank databases under the accession numbers JQ966772 to JQ966797, JX294520 to JX294542, and JX984611.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gupta, P., Husain, M., Hans, C. et al. Sequence heterogeneity in human immunodeficiency virus type 1 nef in patients presenting with rapid progression and delayed progression to AIDS. Arch Virol 159, 2303–2320 (2014). https://doi.org/10.1007/s00705-014-2026-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-014-2026-2

Keywords

Search

Navigation