Conservation of functional domains and limited heterogeneity of HIV-I reverse transcriptase gene following vertical transmission

Retrovirology

Volumn 2, Issue , 2005, Pages

  Sundaravaradan, Vasudha ^a   Hahn, Tobias ^a   Ahmad, Nafees ^a  

^a UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE; ZALCITABINE; ZIDOVUDINE;

ADULT; ARTICLE; CLINICAL ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; ENZYME ACTIVITY; FEMALE; GENE FUNCTION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC HETEROGENEITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INFANT; MALE; NEWBORN; OPEN READING FRAME; PHYLOGENY; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN POLYMERIZATION; REVERSE TRANSCRIPTION; SEQUENCE ANALYSIS; VERTICAL TRANSMISSION; VIRUS REPLICATION;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 27444438897     PISSN: 17424690     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-2-36     Document Type: Article

References (72)

1. Lepage P, Van de Perre P, Carael M, Nsengumuremyi F, Nkurunziza J, Butzler JP, Sprecher S: Postnatal transmission of HIV from mother to child. Lancet 1987, 2:400.
2. Lowe DM, Parmar V, Kemp SD, Larder BA: Mutational analysis of two conserved sequence motifs in HIV-1 reverse transcriptase. FEBS Lett 1991, 282:231-234.
3. Weinbreck PLV, Denis F, Vidal B, Muvnier M, DeLumley I: Postnatal transmission of HIV infection. Lancet 1988, 1:482.
4. Ziegler JB, Cooper DA, Johnson RO, Gold J: Postnatal transmission of AIDS-associated retrovirus from mother to infant. Lancet 1985, 1:896-898.
5. Ahmad N: Molecular mechanisms of human immunodeficiency virus type 1 mother-infant transmission. Adv Pharmacol 2000, 49:387-416.
6. Blanche S, Rouzioux C, Moscato ML, Veber F, Mayaux MJ, Jacomet C, Tricoire J, Deville A, Vial M, Firtion G: A prospective study of infants born to women seropositive for human immunodeficiency virus type 1. HIV Infection in Newborns French Collaborative Study Group. N Engl J Med 1989, 320:1643-1648.
7. Mok JQ, Giaquinto C, De Rossi A, Grosch-Worner I, Ades AE, Peckham CS: Infants born to mothers seropositive for human immunodeficiency virus. Preliminary findings from a multi-centre European study, Lancet 1987, 1:1164-1168.
8. Ryder RW, Nsa W, Hassig SE, Behets F, Rayfield M, Ekungola B, Nelson AM, Mulenda U, Francis H, Mwandagalirwa K: Perinatal transmission of the human immunodeficiency virus type 1 to infants of seropositive women in Zaire. N Engl J Med 1989, 320:1637-1642.
9. Gotte M, Li X, Wainberg MA: HIV-1 reverse transcription: a brief overview focused on structure-function relationships among molecules involved in initiation of the reaction. Arch Biochem Biophys 1999, 365:199-210.
10. Matala E, Crandall KA, Baker RC, Ahmad N: Limited heterogeneity of HIV type 1 in infected mothers correlates with lack of vertical transmission. AIDS Res Hum Retroviruses 2000, 16:1481-1489.
11. Larder BA, Kemp SD, Darby G: Related functional domains in virus DNA polymerases. Embo J 1987, 6:169-175.
12. Kamer G, Argos P: Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 1984, 12:7269-7282.
13. Toh H, Hayashida H, Miyata T: Sequence homology between retroviral reverse transcriptase and putative polymerases of hepatitis B virus and cauliflower mosaic virus. Nature 1983, 305:827-829.
14. Ding J, Hughes SH, Arnold E: Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse transcriptase with a double-stranded DNA template-primer. Biopolymers 1997, 44:125-138.
15. di Marzo Veronese F, Copeland TD, DeVico AL, Rahman R, Oroszlan S, Gallo RC, Sarngadharan MG: Characterization of highly immunogenic p66/p51 as the reverse transcriptase of HTLV-III/LAV. Science 1986, 231:1289-1291.
16. Gotte M, Maier G, Gross HJ, Heumann H: Localization of the active site of HIV-1 reverse transcriptase-associated RNase H domain on a DNA template using site-specific generated hydroxyl radicals. J Biol Chem 1998, 273:10139-10146.
17. Hizi A, McGill C, Hughes SH: Expression of soluble, enzymatically active, human immunodeficiency virus reverse transcriptase in Escherichia Coli and analysis of mutants. Proc Natl Acad Sci U S A 1988, 85:1218-1222.
18. Prasad VR, Goff SP: Linker insertion mutagenesis of the human immunodeficiency virus reverse transcriptase expressed in bacteria: definition of the minimal polymerase domain. Proc Natl Acad Sci U S A 1989, 86:3104-3108.
19. Larder BA, Purifoy DJ, Powell KL, Darby G: Site-specific mutagenesis of AIDS virus reverse transcriptase. Nature 1987, 327:716-717.
20. Le Grice SF, Naas T, Wohlgensinger B, Schatz O: Subunit-selective mutagenesis indicates minimal polymerase activity in heterodimer-associated p51 HIV-1 reverse transcriptase. Embo J 1991, 10:3905-3911.
21. Boyer PL, Ferris AL, Clark P, Whitmer J, Frank P, Tantillo C, Arnold E, Hughes SH: Mutational analysis of the fingers and palm sub-domains of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase. J Mol Biol 1994, 243:472-483.
22. Jacobo-Molina A, Ding J, Nanni RG, Clark AD Jr, Lu X, Tantillo C, Williams RL, Kamer G, Ferris AL, Clark P: Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. Proc Natl Acad Sci U S A 1993, 90:6320-6324.
23. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA: Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 1992, 256:1783-1790.
24. Julias JG, McWilliams MJ, Sarafianos SG, Alvord WG, Arnold E, Hughes SH: Mutation of amino acids in the connection domain of human immunodeficiency virus type 1 reverse transcriptase that contact the template-primer affects RNase H activity. J Virol 2003, 77:8548-8554.
25. Julias JG, McWilliams MJ, Sarafianos SG, Arnold I, Hughes SH: Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo. Proc Natl Acad Sci U S A 2002, 99:9515-9520.
26. Ding J, Jacobo-Molina A, Tantillo C, Lu X, Nanni RG, Arnold E: Buried surface analysis of HIV-1 reverse transcriptase p66/p51 heterodimer and its interaction with dsDNA template/primer. J Mol Recognit 1994, 7:157-161.
27. Gao G, Orlova M, Georgiadis MM, Hendrickson WA, Goff SP: Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection. Proc Natl Acad Sci U S A 1997, 94:407-411.
28. Harris D, Kaushik N, Pandey PK, Yadav PN, Pandey VN: Functional analysis of amino acid residues constituting the dNTP binding pocket of HIV-1 reverse transcriptase. J Biol Chem 1998, 273:33624-33634.
29. Harris D, Yadav PN, Pandey VN: Loss of polymerase activity due to Tyr to Phe substitution in the YMDD motif of human immunodeficiency virus type-1 reverse transcriptase is compensated by Met to Val substitution within the same motif. Biochemistry 1998, 37:9630-9640.
30. Boyer PL, Ferris AL, Hughes SH: Cassette mutagenesis of the reverse transcriptase of human immunodeficiency virus type I. J Virol 1992, 66:1031-1039.
31. Chao SF, Chan VL, Juranka P, Kaplan AH, Swanstrom R, Hutchison CA 3rd: Mutational sensitivity patterns define critical residues in the palm subdomain of the reverse transcriptase of human immunodeficiency virus type 1. Nucleic Acids Res 1995, 23:803-810.
32. Mulky A, Sarafianos SG, Arnold E, Wu X, Kappes JC: Subunit-specific analysis of the human immunodeficiency virus type 1 reverse transcriptase in vivo. J Virol 2004, 78:7089-7096.
33. Huelsenbeck JP, Crandall KA: Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Sys 1997:437-466.
34. Swofford DI: PAUP* Phylogenetic analysis using parsimony and other methods 4.0.0b2. Sinauer associated, Sunderland, MA; 1999.
35. Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
36. Nielsen R, Yang Z: Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 1998, 148:929-936.
37. Yang Z: Phylogenetic Analysis of Maximum Likelihood (PAML). 3.0th edition. University College of London: London; 2000.
38. Nei M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3:418-426.
39. Zanotto, PM, Kallas EG, de Souza RF, Holmes EC: Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 1999, 153:1077-1089.
40. Hahn T, Ramakrishnan R, Ahmad N: Evaluation of genetic diversity of human immunodeficiency virus type 1 NEF gene associated with vertical transmission. J Biomed Sci 2003, 10:436-450.
41. Jacobo-Molina A, Arnold E: HIV reverse transcriptase structure-function relationships. Biochemistry 1991, 30:6351-6356.
42. Sarafianos SG, Das K, Tantillo C, Clark AD Jr, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E: Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. Embo J 2001, 20:1449-1461.
43. Huang H, Chopra R, Verdine GL, Harrison SC: Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 1998, 282:1669-1675.
44. Boyer PL, Ding J, Arnold E, Hughes SH: Subunit specificity of mutations that confer resistance to nonnucleoside inhibitors in human immunodeficiency virus type 1 reverse transcriptase. Antimicrob Agents Chemother 1994, 38:1909-1914.
45. Cornelissen M, van den Burg R. Zorgdrager F, Lukashov V, Goudsmit J: pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D. J Virol 1997, 71:6348-6358.
46. Vergne L, Peeters M, Mpoudi-Ngole E, Bourgeois A, Liegeois F, Toure-Kane C, Mboup S, Mulanga-Kabeya C, Saman E, Jourdan J, et al.: Genetic diversity of protease and reverse transcriptase sequences in non-subtype-B human immunodeficiency virus type 1 strains: evidence of many minor drug resistance mutations in treatment-naive patients. J Clin Microbiol 2000, 38:3919-3925.
47. Tantillo C, Ding J, Jacobo-Molina A, Nanni RG, Boyer PL, Hughes SH, Pauwels R, Andries K, Janssen PA, Arnold E: Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. Implications for mechanisms of drug inhibition and resistance. J Mol Biol 1994, 243:369-387.
48. Turner D, Brenner B, Wainberg MA: Relationships among various nucleoside resistance-conferring mutations in the reverse transcriptase of HIV-1. J Antimicrob Chemother 2004, 53:53-57.
49. Turner D, Roldan A, Brenner B, Moisi D, Routy JP, Wainberg MA: Variability in the PR and RT genes of HIV-1 isolated from recently infected subjects. Antivir Chem Chemother 2004, 15:255-259.
50. Shafer RW, Hsu P, Patick AK, Craig C, Brendel V: Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors. J Virol 1999, 73:6197-6202.
51. Borrow P, Lewicki H, Wei X, Horwitz MS, Peffer N, Meyers H, Nelson JA, Gairin JE, Hahn BH, Oldstone MB, Shaw GM: Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat Med 1997, 3:205-211.
52. Harrer T, Harrer E, Kalams SA, Barbosa P, Trocha A, Johnson RP, Elbeik T, Feinberg MB, Buchbinder SP, Walker BD: Cytotoxic T lymphocytes in asymptomatic long-term nonprogressing HIV-1 infection. Breadth and specificity of the response and relation to in vivo viral quasispecies in a person with prolonged infection and low viral load. J Immunol 1996, 156:2616-2623.
53. Harrer T, Harrer E, Kalams SA, Elbeik T, Staprans SI, Feinberg MB, Cao Y, Ho DD, Yilma T, Caliendo AM, et al.: Strong cytotoxic T cell and weak neutralizing antibody responses in a subset of persons with stable nonprogressing HIV type 1 infection. AIDS Res Hum Retroviruses 1996, 12:585-592.
54. Klein MR, van Baalen CA, Holwerda AM, Kerkhof Garde SR, Bende RJ, Keet IP, Eeftinck-Schattenkerk JK, Osterhaus AD, Schuitemaker H, Miedema F: Kinetics of Gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: a longitudinal analysis of rapid progressors and long-term asymptomatics. J Exp Med 1995, 181:1365-1372.
55. Rinaldo CR Jr, Beltz LA, Huang XL, Gupta P, Fan Z, Torpey DJ 3rd: Anti-HIV type 1 cytotoxic T lymphocyte effector activity and disease progression in the first 8 years of HIV type 1 infection of homosexual men. AIDS Res Hum Retroviruses 1995, 11:481-489.
56. Wilson CC, Brown RC, Korber BT, Wilkes BM, Ruhl DJ, Sakamoto D, Kunstman K, Luzuriaga K, Hanson IC, Widmayer SM. Wiznia A, Clapp S, Aman AJ, Koup RA, Wolinsky SM, Walker BD: Frequent detection of escape from cytotoxic T-lymphocyte recognition in perinatal human immunodeficiency virus (HIV) type 1 transmission: the ariel project for the prevention of transmission of HIV from mother to infant. J Virol 1999, 73:3975-3985.
57. Menendez-Arias L, Mas A, Domingo E: Cytotoxic T-lymphocyte responses to HIV-1 reverse transcriptase (review). Virol Immunol 1998, 11:167-181.
58. Hahn T, Ahmad N: Genetic characterization of HIV type 1 gag p17 matrix genes in isolates from infected mothers lacking perinatal transmission. AIDS Res Hum Retroviruses 2001, 17:1673-1680.
59. Husain M, Hahn T, Yedavalli VR, Ahmad N: Characterization of HIV type 1 tat sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 2001, 17:765-773.
60. Yedavalli VR, Chappey C, Ahmad N: Maintenance of an intact human immunodeficiency virus type 1 vpr gene following mother-to-infant transmission. J Virol 1998, 72:6937-6943.
61. Yedavalli VR, Chappey C, Matala E, Ahmad N: Conservation of an intact vif gene of human immunodeficiency virus type 1 during maternal-fetal transmission. J Virol 1998, 72:1092-1102.
62. Yedavalli VR, Husain M, Horodner A, Ahmad N: Molecular characterization of HIV type 1 vpu genes from mothers and infants after perinatal transmission. AIDS Res Hum Retroviruses 2001, 17:1089-1098.
63. Albert J, Wahlberg J, Leitner T, Escanilla D, Uhlen M: Analysis of a rape case by direct sequencing of the human immunodeficiency virus type 1 pol and gag genes. J Virol 1994, 68:5918-5924.
64. Holmes EC, Zhang LQ, Simmonds P, Rogers AS, Brown AJ: Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon. J Infect Dis 1993, 167:1411-1414.
65. Huang Y, Zhang L, Ho DD: Characterization of gag and pol sequences from long-term survivors of human immunodeficiency virus type 1 infection. Virology 1998, 240:36-49.
66. Korber BT, Learn G, Mullins JI, Hahn BH, Wolinsky S: Protecting HIV databases. Nature 1995, 378:242-244.
67. Wolinsky SM, Korber BT, Neumann AU, Daniels M, Kunstman KJ, Whetsell AJ, Furtado MR, Cao Y, Ho DD, Safrit JT: Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 1996, 272:537-542.
68. Ahmad N, Baroudy BM, Baker RC, Chappey C: Genetic analysis of human immunodeficiency virus type 1 envelope V3 region isolates from mothers and infants after perinatal transmission. J Virol 1995, 69:1001-1012.
69. Hahn T, Matala E, Chappey C, Ahmad N: Characterization of mother-infant HIV type 1 gag p17 sequences associated with perinatal transmission. AIDS Res Hum Retroviruses 1999, 15:875-888.
70. Sabbaj S, Edwards BH, Ghosh MK, Semrau K, Cheelo S, Thea DM, Kuhn L, Ritter GD, Mulligan MJ, Goepfert PA, et al.: Human immunodeficiency virus-specific CD8(+) T cells in human breast milk. J Virol 2002, 76:7365-7373.
71. Matala E, Hahn T, Yedavalli VR, Ahmad N: Biological characterization of HIV type 1 envelope V3 regions from mothers and infants associated with perinatal transmission. AIDS Res Hum Retroviruses 2001, 17:1725-1735.
72. Akaike H: A new look at the statistical model identification. IEEE Trans Autom Contr 1974, 19:716-723.