Journal of Biomedical Science

, Volume 12, Issue 5, pp 701–710 | Cite as

Structural analysis of reverse transcriptase mutations at codon 215 explains the predominance of T215Y over T215F in HIV-1 variants selected under antiretroviral therapy

  • Nouara Yahi
  • Jacques Fantini
  • Mireille Henry
  • Christian Tourrès
  • Catherine Tamalet
Article

Summary

Mutations at codon 215 of HIV-1 reverse transcriptase (RT) confer resistance to nucleoside analogs through RT-catalyzed ATP-dependent phosphorolysis. We showed that mutation T215Y is predominant over T215F (respectively 38.8 vs. 7.04% of 7312 sequences from a cohort of patients receiving antiretroviral therapy in France). Ambiguous mixtures at codon 215 (e.g. TNYS and TFSI) were resolved by cloning and sequencing representative clinical samples. Mutation T215F was preferentially associated with K70R (>71%), D67N (>73%) and K219Q/E/N (>76%), whereas T215Y was associated with M41L (>84%) and L210W (>58%). A similar distribution was observed with RT sequences stored in the Stanford HIV Drug Resistance Database. The structural background of these two distinct mutational patterns was investigated by molecular modeling of ATP-mutant RT complexes, on the basis of known ATP–protein interactions. We found that the aromatic side chain of tyrosine (Y) – but not phenylalanine (F) – optimally stacked with the adenine ring of ATP. Mutation L210W further stabilized this aromatic π–π stacking interaction, increasing the affinity of the T215Y/L210W double mutant for ATP. Overall, this study provides a biochemical basis accounting for the evolutionary pathway of T215 mutations in HIV-1 RT, leading to the preferential selection of T215Y vs. T215F.

Keywords

aromatic antiretroviral CH–π interaction fitness HIV-1 π–π interaction mutation resistance therapy 

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References

  1. 1.
    Susman E. (2002). Many HIV patients carry mutated drug-resistant strains. Lancet 359 : 49CrossRefPubMedGoogle Scholar
  2. 2.
    Larder B.A., Kellam P., Kemp S.D. (1991). Zidovudine resistance predicted by direct detection of mutations in DNA from HIV-infected lymphocytes. AIDS 5: 137–144PubMedCrossRefGoogle Scholar
  3. 3.
    Yahi N., Tamalet C., Tourrès C., Tivoli N., Ariasi F., Volot F., Gastaut J.A., Gallais H., Moreau J., and Fantini J. (1999). Mutation patterns of the reverse transcriptase and protease genes in human immunodeficiency virus type 1-infected patients undergoing combination therapy: survey of 787 sequences. J. Clin. Microbiol. 37: 4099–4106PubMedGoogle Scholar
  4. 4.
    Violin M., Cozzi-Lepri A., Velleca R., Vincenti A., D’Elia S., Cjiodo F., Ghinelli F., Bertoli A., d’Arminio Monforte A., Perno C.F., Moroni M., and Balotta C. (2004). Risk of failure in patients with 215 HIV-1 revertants starting their first thymidine analog-containing highly active antiretroviral therapy. AIDS 18: 227–235CrossRefPubMedGoogle Scholar
  5. 5.
    Yerly S., Rakik A., De Loes S.K., Hirschel B., Descamps D., Brun-Vézinet F., and Perrin L. (1998). Switch to unusual amino acids at codon 215 the human immunodeficiency virus type 1 reverse transcriptase gene in seroconvertors infected with zidovudine-resistant variants. J. Virol. 72: 3520–3523PubMedGoogle Scholar
  6. 6.
    Lacey S.F., and Larder B. (1994). Mutagenic studies of codons 74 and 215 of the in human immunodeficiency virus type 1 reverse transcriptase which are significant in nucleoside analog resistance. J. Virol. 68: 3421–3424PubMedGoogle Scholar
  7. 7.
    Larder B. (1994). Interactions between drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase. J. Gen. Virol. 75: 951–957PubMedCrossRefGoogle Scholar
  8. 8.
    Gao H.Q., Boyer P.L., Sarafianos S.G., Arnold E., and Hughes S.H. (2000). The role of steric hindrance in 3TC resistance of human immunodeficiency virus type-1 reverse transcriptase. J. Mol. Biol. 300: 403–418CrossRefPubMedGoogle Scholar
  9. 9.
    Lacey S.F., Reardon J.E., Furfine E.S., Kunkel T.A., Bebeneck K., Eckert K.A., Kemp S.D., and Larder B.A. (1992). Biochemical studies on the reverse transcriptase and RNase H activities from human immunodeficiency virus strains resistant to 3′-azido-3′deoxythymidine. J. Biol. Chem. 267: 15789–15794PubMedGoogle Scholar
  10. 10.
    Sluis-Cremer N., Arion D. and Parniak M.A., Molecular mechanisms of HIV-1 resistance to nucleoside reverse transcriptase inhibitors (NRTIs). 57: 1408–1422, 2000Google Scholar
  11. 11.
    Boyer P.L., Sarafianos S.G., Arnold E., and Hugues S.H. (2001). Selective excision of AZTMP by drug-resistant human immunodeficiency virus reverse transcriptase. J. Virol. 75: 4832–4842CrossRefPubMedGoogle Scholar
  12. 12.
    Meyer, P.R., Matsuura S.E., Tolun A.A., Pfeifer I., So A.G., Mellors J.W., and Scott W.A. (2002). Effects of specific zidovudine resistance mutations and substrate structure on nucleotide-dependent primer unblocking by human immunodeficiency virus type 1 reverse transcriptase. Antimicrob. Agents Chemother. 46: 1540–1545CrossRefPubMedGoogle Scholar
  13. 13.
    Yahi N., Tamalet C., Tourrès C., Tivoli N., and Fantini J. (2000). Mutation L210W of HIV-1 reverse transcriptase in patients receiving combination therapy. Incidence, association with other mutations and effects of the structure of mutated reverse transcriptase. J. Biomed. Sci. 7: 507–513CrossRefPubMedGoogle Scholar
  14. 14.
    Chappey C., Wrin T., Deeks S. and Petropoulos C.J., Evolution of amino acid 215 in HIV-1 reverse transcriptase in response to intermittent drug selection. XII International HIV Drug Resistance Workshop, Los Cabos, Mexico, Abstract 32, June 10–14, 2003Google Scholar
  15. 15.
    Hu Z.X., Reid P., Lu J., and Kuritzkes D.R. (2004). Fitness of T215Y vs T215F mutants in HIV-1 RT: comparison of specific thymidine analogue-resistance mutation patterns. Antiviral Therapy 59: S68Google Scholar
  16. 16.
    Tamalet C., Fantini J., Tourrès C., and Yahi N. (2003). Resistance of HIV-1 to multiple antiretroviral drugs in France: a 6-year survey (1997–2002) based on an analysis of over 7000 genotypes. AIDS 17: 2383–2388CrossRefPubMedGoogle Scholar
  17. 17.
    Yahi N., Fantini J., Tourrès C., Tivoli N., Koch N., and Tamalet C. (2001). Use of drug resistance sequence data for the systematic detection of non-B human immunodeficiency virus type 1 (HIV-1) subtypes: how to create a sentinel site for monitoring the genetic diversity of HIV-1 at a country scale. J. Infect. Dis. 183 : 1311–1317CrossRefPubMedGoogle Scholar
  18. 18.
    Shafer R.W., Dupnik K.M., Winters M.A. and Eshleman S.H., A guide to HIV-1 reverse transcriptase and protease sequencing for drug resistance studies. Human Retroviruses and AIDS, Theoretical Biology and Biophysics. Los Alamos National Laboratories, 2001Google Scholar
  19. 19.
    Shafer R.W. (2002). Genotypic testing for human immunodeficiency virus type 1 drug Resistance. Clin. Microbiol. Rev. 15: 247–277CrossRefPubMedGoogle Scholar
  20. 20.
    Huang H., Chopra R., Verdine G.L., and Harrison S.C. (1998). Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase. Implications for drug resistance. Science 282: 1669–1675PubMedCrossRefGoogle Scholar
  21. 21.
    Schwede T., Kopp J., Guex N., and Peitsch M.C. (2003). SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31: 3381–3385CrossRefPubMedGoogle Scholar
  22. 22.
    Ren J., Esnouf R.M., Hopkins A.L., Jones E.Y., Kirby I., Keeling J., Ross C.K., Larder B.A., Stuart D.I., and Stammers D.K. (1998). 3′Azido-3′deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes. Proc. Natl. Acad. Sci. USA 95: 9518–9523CrossRefPubMedGoogle Scholar
  23. 23.
    Guex N., and Peitsch M.C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714–2723CrossRefPubMedGoogle Scholar
  24. 24.
    Nishio M., Umezawa Y., Hirota M., and Takeuchi Y. (1995). The CH/π interaction: significance in molecular recognition. Tetrahedron 51: 8665–8701CrossRefGoogle Scholar
  25. 25.
    25. Tamalet C., Yahi N., Tourrès C., Colson P., Quinson A.M., Poizot-Martin I., Dhiver C., and Fantini J. (2000). Multidrug resistance genotypes (insertions in the beta3-beta4 finger subdomain and MDR mutations) of HIV-1 reverse transcriptase from extensively treated patients: incidence and association with other resistance mutations. Virology 270: 310–316CrossRefPubMedGoogle Scholar
  26. 26.
    Boucher C.A., Sullivan E.O., Mulder J.W., Ramautarsing C., Kellam P., Darby G., Lange J.M., Goudsmit J., and Larder B.A. (1992). Ordered appearance of zidovudine resistance mutations furing treatment of 18 human immunodeficiency virus-positive subjects. J. Infect. Dis. 165: 105–110PubMedGoogle Scholar
  27. 27.
    Arion D., Kaushik N., McCormick S., Borkow G., and Parniak M.A. (1998). Phenotypic mechanism of HIV-1 resistance to 3′-azido-3′-deoxythymidine (AZT): increased polymerization processivity and enhanced sensitivity to pyrophosphate of the mutant viral reverse transcriptase. Biochemistry 37: 15908–15917PubMedCrossRefGoogle Scholar
  28. 28.
    Babor M., Sobolev V., and Edelman M. (2002). Conserved positions for ribose recognition: importance of water bridging interactions among ATP, ADP and FAD-protein complexes J. Mol. Biol. 323: 523–532CrossRefPubMedGoogle Scholar
  29. 29.
    Mao L., Wang Y., Liu Y., and Hu X. (2004). Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis. J. Mol. Biol. 336 : 787–807CrossRefPubMedGoogle Scholar
  30. 30.
    Moodie S.L., Mitchell J.B.O., and Thornton J.M. (1996). Protein recognition of adenylate: an example of a fuzzy recognition template J. Mol. Biol. 263: 486–500CrossRefPubMedGoogle Scholar
  31. 31.
    Ramon-Maiques S., Marina A., Uriarte M., Fita I., and Rubio V. (2000). The 1.5 Å resolution crystal structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus, bound to ADP, confirms that this thermostable enzyme is a carbamate kinase, and provides insight into substrate binding and stability in carbamate kinases. J. Mol. Biol. 299: 463–476CrossRefPubMedGoogle Scholar
  32. 32.
    Kaushik N., Singh K., Alluru K.I., and Modak M.J. (1999). Tyrosine 222, a member of the YXDD motif of MuLV RT, is catalytically essential and is a major component of the fidelity center. Biochemistry 38: 2617–2627CrossRefPubMedGoogle Scholar
  33. 33.
    Chamberlain P.P., Ren J., Nichols C.E., Douglas L., Lennerstrand J., Larder B.A., Stuart D.L., and Stammers D.K. (2002). Structures of zidovudine- or lamivudine-resistant human immunodeficiency virus type 1 reverse transcriptases containing mutations at codons 41, 184, and 215. J. Virol. 76: 10015–10019CrossRefPubMedGoogle Scholar

Copyright information

© National Science Council, Taipei 2005

Authors and Affiliations

  • Nouara Yahi
    • 1
  • Jacques Fantini
    • 1
  • Mireille Henry
    • 2
  • Christian Tourrès
    • 2
  • Catherine Tamalet
    • 2
  1. 1.Laboratoire de Biochimie et Physicochimie des Membranes Biologiques, Faculté des Sciences et Techniques St-JérômeUniversité Paul CézanneMarseilleFrance
  2. 2.Laboratoire de VirologieUF SIDA, Hôpital de la TimoneMarseilleFrance

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