Amino acid covariation in a functionally important human immunodeficiency virus type 1 protein region is associated with population subdivision

Genetics

Volumn 182, Issue 1, 2009, Pages 265-275

  Da Silva, Jack ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CHEMOKINE RECEPTOR; VIRUS PROTEIN; GLYCOPROTEIN GP 120; HIV ENVELOPE PROTEIN GP120 (305 321); HIV ENVELOPE PROTEIN GP120 (305-321); PEPTIDE FRAGMENT; VIRUS ENVELOPE PROTEIN;

ARTICLE; EVOLUTION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC DRIFT; GENETIC EPISTASIS; GENETIC SELECTION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PHENOTYPE; POPULATION STRUCTURE; PRIORITY JOURNAL; VIRUS PARTICLE; GENETIC VARIABILITY; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; POPULATION GENETICS; PROTEIN MOTIF; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID MOTIFS; ENV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GENETIC VARIATION; GENETICS, POPULATION; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HUMANS; LINKAGE DISEQUILIBRIUM; PEPTIDE FRAGMENTS;

EID: 67849133316     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.108.099853     Document Type: Article

References (67)

1. AWADALLA, P., A. EYRE-WALKER and J. M. SMITH, 1999 Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 286: 2524-2525. (Pubitemid 30026344)
2. BICKEL, P. J., P. C. COSMAN, R. A. OLSHEN, P. C. SPECTOR, A. G. RODRIGO et al., 1996 Covariability of V3 loop amino acids. AIDS Res. Hum. Retroviruses 12: 1401-1411.
3. BONHOEFFER, S., E. C. HOLMES and M. A. NOWAK, 1995 Causes of HIV diversity. Nature 376: 125.
4. CARDOZO, T., T. KIMURA, S. PHILPOTT, B. WEISER, H. BURGER et al., 2007 Structural basis for coreceptor selectivity by the HIV type 1 V3 loop. AIDS Res. Hum. Retroviruses 23: 415-426.
5. CORMIER, E. G., and T. DRAGIC, 2002 The crown and stem of the V3 loop play distinct roles in human immunodeficiency virus type 1 envelope glycoprotein interactions with the CCR5 coreceptor. J. Virol. 76: 8953-8957.
6. DA SILVA, J., 2006 Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1. Genetics 174: 1689-1694.
7. DE JONG, J. J., A. DE RONDE, W. KEULEN, M. TERSMETTE and J. GOUDSMIT, 1992 Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino acid substitution. J. Virol. 66: 6777-6780.
8. DERDEYN, C. A., J. M. DECKER, F. BIBOLLET-RUCHE, J. L. MOKILI, M. MULDOON et al., 2004 Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303: 2019-2022. (Pubitemid 38393277)
9. DITTMAR, M. T., A. MCKNIGHT, G. SIMMONS, P. R. CLAPHAM, R. A. WEISS et al., 1997 HIV-1 tropism and co-receptor use. Nature 385: 495-496.
10. EDGAR, R. C., 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797. (Pubitemid 38832724)
11. FELSENSTEIN, J., 1965 The effect of linkage on directional selection. Genetics 52: 349-363.
12. FELSENSTEIN, J., 1988 Sex and the evolution of recombination, pp. 74-86 in The Evolution of Sex, edited by R. E. MICHOD and B. R. LEVIN. Sinauer Associates, Sunderland, MA.
13. FOUCHIER, R. A., M. GROENINK, N. A. KOOTSTRA, M. TERSMETTE, H. G. HUISMAN et al., 1992 Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J. Virol. 66: 3183-3187.
14. FROST, S. D. W., M.-J. DUMAURIER, S. WAIN-HOBSON and A. J. L. BROWN, 2001 Genetic drift and within-host metapopulation dynamics of HIV-1 infection. Proc. Natl. Acad. Sci. USA 98: 6975-6980.
15. GAO, F., E. BAILES, D. L. ROBERTSON, Y. CHEN, C. M. RODENBURG et al., 1999 Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397: 436-441. (Pubitemid 29078911)
16. GERRISH, P., 2001 The rhythm of microbial adaptation. Nature 413: 299-302.
17. GILBERT, P. B., V. NOVITSKY and M. ESSEX, 2005 Covariability of selected amino acid positions for HIV type 1 subtypes C and B. AIDS Res. Hum. Retroviruses 21: 1016-1030.
18. GORRY, P. R., R. L. DUNFEE, M. E. MEFFORD, K. KUNSTMAN, T. MORGAN et al., 2007 Changes in the V3 region of gp120 contribute to unusually broad coreceptor usage of an HIV-1 isolate from a CCR5 Δ32 heterozygote. Virology 362: 163-178.
19. HILL, W. G., and A. ROBERTSON, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 226-231.
20. HOFFMAN, N. G., C. A. SCHIFFER and R. SWANSTROM, 2003 Covariation of amino acid positions in HIV-1 protease. Virology 314: 536.
21. HUANG, C.-C., M. TANG, M.-Y. ZHANG, S. MAJEED, E. MONTABANA et al., 2005 Structure of a V3-containing HIV-1 gp120 core. Science 310: 1025-1028.
22. HUANG, C.-C., S. N. LAM, P. ACHARYA, M. TANG, S.-H. XIANG et al., 2007 Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science 317: 1930-1934.
23. HUDSON, R. R., 1985 The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109: 611-631.
24. HUNG, C. S., N. VANDER HEYDEN and L. RATNER, 1999 Analysis of the critical domain in the V3 loop of human immunodeficiency virus type 1 gp120 involved in CCR5 utilization. J. Virol. 73: 8216-8226.
25. HWANG, S. S., T. J. BOYLE, H. K. LYERLY and B. R. CULLEN, 1991 Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 253: 71-74.
26. KARLIN, S., and M. W. FELDMAN, 1970 Linkage and selection: two locus symmetric viability model. Theor. Popul. Biol. 1: 39-71.
27. KIMURA, M., 1956 A model of a genetic system which leads to closer linkage by natural selection. Evolution 10: 278-287.
28. KONDRASHOV, A. S., 1993 Classification of hypotheses on the advantage of amphimixis. J. Hered. 84: 372-387.
29. KORBER, B. T., R. M. FARBER, D. H. WOLPERT and A. S. LAPEDES, 1993 Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. USA 90: 7176-7180.
30. LEMEY, P., A. RAMBAUT and O. G. PYBUS, 2006 HIV evolutionary dynamics within and among hosts. AIDS Rev. 8: 125-140. (Pubitemid 44614030)
31. LEVY, D. N., G. M. ALDROVANDI, O. KUTSCH and G. M. SHAW, 2004 Dynamics of HIV-1 recombination in its natural target cells. Proc. Natl. Acad. Sci. USA 101: 4204-4209.
32. LEWONTIN, R. C., and K.-I. KOJIMA, 1960 The evolutionary dynamics of complex polymorphisms. Evolution 14: 458-472.
33. LI, W.-H., and M. NEI, 1974 Stable linkage disequilibrium without epistasis in subdivided populations. Theor. Popul. Biol. 6: 173-183.
34. LIU, Y., E. EYAL and I. BAHAR, 2008 Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinformatics 24: 1243-1250.
35. MITTON, J. B., and R. K. KOEHN, 1973 Population genetics of marine pelecypods. III. Epistasis between functionally related isoenzymes of Mytilus edulis. Genetics 73: 487-496.
36. MYERS, R. E., and D. PILLAY, 2008 Analysis of natural sequence variation and covariation in human immunodeficiency virus type 1 integrase. J. Virol. 82: 9228-9235.
37. NEI, M., and S. KUMAR, 2000 Molecular Evolution and Phylogenetics. Oxford University Press, London/New York/Oxford.
38. NEI, M., and W.-H. LI, 1973 Linkage disequilibrium in subdivided populations. Genetics 75: 213-219.
39. NIELSEN, R., and Z. YANG, 1998 Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
40. OHTA, T., 1982 Linkage disequilibrium due to random genetic drift in finite subdivided populations. Proc. Natl. Acad. Sci. USA 79: 1940-1944.
41. OHTA, T., and M. KIMURA, 1969 Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics 63: 229-238.
42. PASTORE, C., R. NEDELLEC, A. RAMOS, S. PONTOW, L. RATNER et al., 2006 Human immunodeficiency virus type 1 coreceptor switching: V1/V2 gain-of-fitness mutations compensate for V3 loss-of-fitness mutations. J. Virol. 80: 750-758.
43. PLATT, E. J., J. P. DURNIN and D. KABAT, 2005 Kinetic factors control efficiencies of cell entry, efficacies of entry inhibitors, and mechanisms of adaptation of human immunodeficiency virus. J. Virol. 79: 4347-4356.
44. POON, A. F., F. I. LEWIS, S. L. POND and S. D. FROST, 2007 An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput. Biol. 3: e231.
45. RHEE, S.-Y., T. F. LIU, S. P. HOLMES and R. W. SHAFER, 2007 HIV-1 subtype B protease and reverse transcriptase amino acid covariation. PLoS Comput. Biol. 3: e87.
46. ROSEN, O., M. SHARON, S. R. QUADT-AKABAYOV and J. ANGLISTER, 2006 Molecular switch for alternative conformations of the HIV-1 V3 region: implications for phenotype conversion. Proc. Natl. Acad. Sci. USA 103: 13950-13955.
47. SHANKARAPPA, R., J. B. MARGOLICK, S. J. GANGE, A. G. RODRIGO, D. UPCHURCH et al., 1999 Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73: 10489-10502.
48. SLATKIN, M., 1975 Gene flow and selection in a two-locus system. Genetics 81: 787-802.
49. SLATKIN, M., 1994 Linkage disequilibrium in growing and stable populations. Genetics 137: 331-336.
50. SLATKIN, M., 2008 Linkage disequilibrium - understanding the evolutionary past and mapping the medical future. Nat. Rev. Genet. 9: 477-485.
51. SPECK, R. F., K. WEHRLY, E. J. PLATT, R. E. ATCHISON, I. F. CHARO et al., 1997 Selective employment of chemokine receptors as human immunodeficiency virus type 1 coreceptors determined by individual amino acids within the envelope V3 loop. J. Virol. 71: 7136-7139.
52. TAMURA, K., J. DUDLEY, M. NEI and S. KUMAR, 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596-1599.
53. TEMPLETON, A. R., R. A. REICHERT, A. E. WEISSTEIN, X.-F. YU and R. B. MARKHAM, 2004 Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals. Genetics 167: 1547-1561.
54. TRAVERS, S. A. A., D. C. TULLY, G. P. MCCORMACK and M. A. FARES, 2007 A study of the coevolutionary patterns operating within the env gene of the HIV-1 group M subtypes. Mol. Biol. Evol. 24: 2787-2801.
55. WANG, Q., and C. LEE, 2007 Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase. PLoS ONE 2: e814.
56. WEIR, B. S., 1996 Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates, Sunderland, MA.
57. WEIR, B. S., and W. G. HILL, 1986 Nonuniform recombination within the human beta-globin gene cluster. Am. J. Hum. Genet. 38: 776-781.
58. WHITTAM, T. S., H. OCHMAN and R. K. SELANDER, 1983 Geographic components of linkage disequilibrium in natural populations of Escherichia coli. Mol. Biol. Evol. 1: 67-83.
59. WILLIAMSON, S., 2003 Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol. Biol. Evol. 20: 1318-1325.
60. WOLINSKY, S. M., B. T. KORBER, A. U. NEUMANN, M. DANIELS, K. J. KUNSTMAN et al., 1996 Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272: 537-542. (Pubitemid 26138195)
61. WONG, J. K., C. C. IGNACIO, F. TORRIANI, D. HAVLIR, N. J. FITCH et al., 1997 In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues. J. Virol. 71: 2059-2071.
62. WRIGHT, S., 1940 Breeding structure of populations in relation to speciation. Am. Nat. 74: 232-248.
63. WYATT, R., and J. SODROSKI, 1998 The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science 280: 1884-1888.
64. YAMAGUCHI, Y., and T. GOJOBORI, 1997 Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc. Natl. Acad. Sci. USA 94: 1264-1269.
65. YUSTE, E., C. LOPEZ-GALINDEZ and E. DOMINGO, 2000 Unusual distribution of mutations associated with serial bottleneck passages of human immunodeficiency virus type 1. J. Virol. 74: 9546-9552. (Pubitemid 30746804)
66. ZHANG, L. Q., P. MACKENZIE, A. CLELAND, E. C. HOLMES, A. J. BROWN et al., 1993 Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J. Virol. 67: 3345-3356.
67. ZOLLA-PAZNER, S., 2004 Identifying epitopes of HIV-1 that induce protective antibodies. Nat. Rev. Immunol. 4: 199-210.