Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

Virology Journal

Volumn 5, Issue , 2008, Pages

  Ngandu, Nobubelo K ^a   Scheffler, Konrad ^b   Moore, Penny ^c   Woodman, Zenda ^a   Martin, Darren ^a   Seoighe, Cathal ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b STELLENBOSCH UNIVERSITY   (South Africa)

^c NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; VIRUS PROTEIN; VPU PROTEIN; MATRIX PROTEIN; VIRUS DNA;

ARTICLE; BINDING SITE; CHROMOSOME SUBSTITUTION; CONTROLLED STUDY; ENVELOPE GENE; EXON; GENE FUNCTION; GENE MUTATION; GENETIC MODEL; GENETIC SELECTION; GENOME ANALYSIS; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DETERMINATION; PROTEIN DOMAIN; RNA SPLICING; VIRUS PURIFICATION; AMINO ACID SUBSTITUTION; BIOLOGICAL MODEL; CODON; COMPUTER SIMULATION; GENETIC VARIABILITY; GENETICS; REVIEW; SEQUENCE ALIGNMENT; STATISTICAL MODEL; VIRUS GENE; VIRUS GENOME;

HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID SUBSTITUTION; BASE SEQUENCE; CODON; COMPUTER SIMULATION; DNA, VIRAL; GENES, VIRAL; GENETIC VARIATION; GENOME, VIRAL; HIV-1; MODELS, GENETIC; MODELS, STATISTICAL; SELECTION (GENETICS); SEQUENCE ALIGNMENT; VIRAL MATRIX PROTEINS;

EID: 64249107628     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-5-160     Document Type: Article

References (60)

1. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. SV Muse BS Gaut, Mol Biol Evol 1994 11 715 724 7968485
2. A codon-based model of nucleotide substitution for protein-coding DNA sequences. N Goldman Z Yang, Mol Biol Evol 1994 11 725 736 7968486
3. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. R Nielsen Z Yang, Genetics 1998 148 929 936 9539414
4. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Z Yang R Nielsen N Goldman AM Pedersen, Genetics 2000 155 431 449 10790415
5. Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. P Lemey SL Kosakovsky Pond AJ Drummond OG Pybus B Shapiro H Barroso N Taveira A Rambaut, PLoS Comput Biol 2007 3 e29 17305421 10.1371/journal.pcbi.0030029
6. A model of directional selection applied to the evolution of drug resistance in HIV-1. C Seoighe F Ketwaroo V Pillay K Scheffler N Wood R Duffet M Zvelebil N Martinson J McIntyre L Morris W Hide, Mol Biol Evol 2007 24 1025 1031 10.1093/molbev/msm021 17272680
7. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. M Choisy CH Woelk JF Guegan DL Robertson, J Virol 2004 78 1962 1970 14747561 10.1128/JVI.78.4.1962-1970.2004
8. Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design? T de Oliveira M Salemi M Gordon AM Vandamme EJ van Rensburg S Engelbrecht HM Coovadia S Cassol, Genetics 2004 167 1047 1058 15280222 10.1534/genetics.103.018135
9. Genealogical evidence for positive selection in the nef gene of HIV-1. PM Zanotto EG Kallas RF de Souza EC Holmes, Genetics 1999 153 1077 1089 10545443
10. Site-to-site variation of synonymous substitution rates. S Kosakovsky Pond SV Muse, Mol Biol Evol 2005 22 2375 2385 10.1093/molbev/msi232 16107593
11. Evidence for purifying selection acting on silent sites in BRCA1. LD Hurst C Pal, TRENDS in Genetics 2001 17 62 65 10.1016/S0168-9525(00)02173-9 11173101
12. LTR and tat variability of HIV-1 isolates from patients with divergent rates of disease progression. ME Quinones-Mateu A Mas dL Lain V Soriano J Alcami MM Lederman E Domingo, Virus Res 1998 57 11 20 10.1016/S0168-1702(98)00082-3 9833881
13. The 5' and 3' TAR elements of human immunodeficiency virus exert effects at several points in the virus life cycle. AT Das B Klaver B Berkhout, J Virol 1998 72 9217 9223 9765469
14. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. KA Wilkinson RJ Gorelick SM Vasa N Guex A Rein DH Mathews MC Giddings KM Weeks, PLoS Biol 2008 6 e96 10.1371/journal.pbio.0060096 18447581
15. A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter. LA Pereira K Bentley A Peeters MJ Churchill NJ Deacon, Nucleic Acids Res 2000 28 663 668 10637316 10.1093/nar/28.3.663
16. Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity. V Goffin D Demonte C Vanhulle S de Walque Y de Launoit A Burny Y Collette C Van Lint, Nucleic Acids Res 2005 33 4285 4310 16061936 10.1093/nar/gki720
17. A transcriptional regulatory element is associated with a nuclease-hypersensitive site in the pol gene of human immunodeficiency virus type 1. C Van Lint J Ghysdael P Paras Jr A Burny E Verdin, J Virol 1994 68 2632 2648 8139041
18. Identification and characterization of an enhancer in the coding region of the genome of human immunodeficiency virus type 1. E Verdin N Becker F Bex L Droogmans A Burny, Proc Natl Acad Sci 1990 87 4874 4878 2352955 10.1073/pnas.87.12.4874
19. The rev (trs/art) protein of human immunodeficiency virus type 1 affects viral mRNA and protein expression via a cis-acting sequence in the env region. M Hadzopoulou-Cladaras BK Felber C Cladaras A Athanassopoulos A Tse GN Pavlakis, J Virol 1989 63 1265 1274 2783738
20. Probing the details of the HIV-1 Rev-Rev-responsive element interaction: effects of modified nucleotides on protein affinity and conformational changes during complex formation. SB Renwick AD Critchley CJ Adams SM Kelly NC Price PG Stockley, Biochem J 1995 308 Pt 2 447 453 7772026
21. Structural change in Rev responsive element RNA of HIV-1 on binding Rev peptide. RD Peterson J Feigon, J Mol Biol 1996 264 863 877 10.1006/jmbi.1996. 0683 9000617
22. Heterogeneity of HIV-1 Rev response element. A Phuphuakrat P Auewarakul, AIDS Res Hum Retroviruses 2003 19 569 574 10.1089/088922203322230932 12908934
23. Mutational inactivation of an inhibitory sequence in human immunodeficiency virus type 1 results in Rev-independent gag expression. S Schwartz M Campbell G Nasioulas J Harrison BK Felber GN Pavlakis, J Virol 1992 66 7176 7182 1433510
24. Inactivation of the human immunodeficiency virus type 1 inhibitory elements allows Rev-independent expression of Gag and Gag/protease and particle formation. R Schneider M Campbell G Nasioulas BK Felber GN Pavlakis, J Virol 1997 71 4892 4903 9188551
25. Identification and characterization of intragenic sequences which repress human immunodeficiency virus structural gene expression. AW Cochrane KS Jones S Beidas PJ Dillon AM Skalka CA Rosen, J Virol 1991 65 5305 5313 1895385
26. Intergrated functional and bioinformatics approach for the identification and experimental verification of RNA signals: application to HIV-1 INS. H Wolff R Brack-Werner M Neumann T Werner R Schneider, Nucleic Acids Research 2003 31 2839 2851 12771211 10.1093/nar/gkg390
27. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. M Anisimova R Nielsen Z Yang, Genetics 2003 164 1229 1236 12871927
28. Potential impact of recombination on sitewise approaches for detecting positive natural selection. D Shriner DC Nickle MA Jensen JI Mullins, Genet Res 2003 81 115 121 10.1017/S0016672303006128 12872913
29. HIV Sequence Compendium. T Leitner B Foley B Hahn P Marx F McCutchan J Mellors S Wolinsky B Korber, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM, LA-UR 2005 06 0680
30. HyPhy: hypothesis testing using phylogenies. SL Kosakovsky Pond SD Frost SV Muse, Bioinformatics 2005 21 676 679 10.1093/bioinformatics/bti079 15509596
31. Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. SL Kosakovsky Pond D Posada MB Gravenor CH Woelk S Frost, Mol Biol Evol 2006 23 1891 1901 10.1093/molbev/msl051 16818476
32. Robust inference of positive selection from recombining coding sequences. K Scheffler DP Martin C Seoighe, Bioinformatics 2006 22 2493 2499 10.1093/bioinformatics/btl427 16895925
33. CTL response to HIV type 1 subtype C is poorly predicted by known epitope motifs. NG Ngandu H Bredell CM Gray C Williamson C Seoighe, AIDS Res Hum Retroviruses 2007 23 1033 1041 10.1089/aid.2007.0024 17725421
34. Bayes empirical bayes inference of amino acid sites under positive selection. Z Yang WS Wong R Nielsen, Mol Biol Evol 2005 22 1107 1118 10.1093/molbev/msi097 15689528
35. The c3-v4 region is a major target of autologous neutralizing antibodies in human immunodeficiency virus type 1 subtype C infection. PL Moore ES Gray IA Choge N Ranchobe K Mlisana SS Abdool Karim C Williamson L Morris, J Virol 2008 82 1860 1869 18057243 10.1128/JVI.02187-07
36. RNA secondary structure and binding sites for gag gene products in the 5' packaging signal of human immunodeficiency virus type 1. J Clever C Sassetti TG Parslow, J Virol 1995 69 2101 2109 7884856
37. A human immunodeficiency virus type 1-infected individual with low viral load harbors a virus variant that exhibits an in vitro RNA dimerization defect. H Huthoff AT Das M Vink B Klaver F Zorgdrager M Cornelissen B Berkhout, J Virol 2004 78 4907 4913 15078972 10.1128/JVI.78.9.4907-4913.2004
38. Negative and positive mRNA splicing elements act competitively to regulate human immunodeficiency virus type 1 vif gene expression. CM Exline Z Feng CM Stoltzfus, J Virol 2008 82 3921 3931 18272582 10.1128/JVI.01558-07
39. Cloning and functional analysis of multiply spliced mRNA species of human immunodeficiency virus type 1. S Schwartz BK Felber DM Benko EM Fenyo GN Pavlakis, J Virol 1990 64 2519 2529 2335812
40. A suboptimal 5' splice site downstream of HIV-1 splice site A1 is required for unspliced viral mRNA accumulation and efficient virus replication. JM Madsen CM Stoltzfus, Retrovirology 2006 3 10 16457729 10.1186/1742-4690-3-10
41. The strength of the HIV-1 3' splice sites affects Rev function. S Kammler M Otte I Hauber J Kjems J Hauber H Schaal, Retrovirology 2006 3 89 17144911 10.1186/1742-4690-3-89
42. Influence of the small leader exons 2 and 3 on human immunodeficiency virus type 1 gene expression. J Krummheuer C Lenz S Kammler A Scheid H Schaal, Virology 2001 286 276 289 10.1006/viro.2001.0974 11485396
43. A second exon splicing silencer within human immunodeficiency virus type 1 tat exon 2 represses splicing of Tat mRNA and binds protein hnRNP H. S Jacquenet A Mereau PS Bilodeau L Damier CM Stoltzfus C Branlant, J Biol Chem 2001 276 40464 40475 10.1074/jbc.M104070200 11526107
44. Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing. S Jacquenet D Ropers PS Bilodeau L Damier A Mougin CM Stoltzfus C Branlant, Nucleic Acids Res 2001 29 464 478 11139617 10.1093/nar/29.2.464
45. The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability. LW Hung EL Holbrook SR Holbrook, Proc Natl Acad Sci USA 2000 97 5107 5112 10792052 10.1073/pnas.090588197
46. Env and Vpu proteins of human immunodeficiency virus type 1 are produced from multiple bicistronic mRNAs. S Schwartz BK Felber EM Fenyo GN Pavlakis, J Virol 1990 64 5448 5456 2214021
47. Overlapping cis sites used for splicing of HIV-1 env/nef and rev mRNAs. AK Swanson CM Stoltzfus, J Biol Chem 1998 273 34551 34557 10.1074/jbc.273.51. 34551 9852125
48. Effect of polypurine tract (PPT) mutations on human immunodeficiency virus type 1 replication: a virus with a completely randomized PPT retains low infectivity. LR Miles BE Agresta MB Khan S Tang JG Levin MD Powell, J Virol 2005 79 6859 6867 15890925 10.1128/JVI.79.11.6859-6867.2005
49. Specificities involved in the initiation of retroviral plus-strand DNA. GX Luo L Sharmeen J Taylor, J Virol 1990 64 592 597 1688626
50. Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis. JW Rausch SF Le Grice, Nucleic Acids Res 2007 35 256 268 17164285 10.1093/nar/gkl909
51. Sequence and structural determinants required for priming of plus-strand DNA synthesis by the human immunodeficiency virus type 1 polypurine tract. MD Powell JG Levin, J Virol 1996 70 5288 5296 8764039
52. The sequence features important for plus strand priming by human immunodeficiency virus type 1 reverse transcriptase. KA Pullen AJ Rattray JJ Champoux, J Biol Chem 1993 268 6221 6227 7681062
53. 'Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. JW Rausch SF Le Grice, Int J Biochem Cell Biol 2004 36 1752 1766 10.1016/j.biocel.2004.02.016 15183342
54. Specific and independent recognition of U3 and U5 att sites by human immunodeficiency virus type 1 integrase in vivo. T Masuda MJ Kuroda S Harada, J Virol 1998 72 8396 8402 9733892
55. Structure-based mutagenesis of the human immunodeficiency virus type 1 DNA attachment site: effects on integration and cDNA synthesis. HE Brown H Chen A Engelman, J Virol 1999 73 9011 9020 10516007
56. Detecting hypermutations in viral sequences with an emphasis on G - > A hypermutation. PP Rose BT Korber, Bioinformatics 2000 16 400 401 10.1093/bioinformatics/16.4.400 10869039
57. A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. K Hanada Y Suzuki T Gojobori, Mol Biol Evol 2004 21 1074 1080 10.1093/molbev/msh109 15014142
58. In vitro evidence for a long range pseudoknot in the 5'-untranslated and matrix coding regions of HIV-1 genomic RNA. JC Paillart E Skripkin B Ehresmann C Ehresmann R Marquet, J Biol Chem 2002 277 5995 6004 10.1074/jbc.M108972200 11744696
59. MATCH: A tool for searching transcription factor binding sites in DNA sequences. AE Kel E Gossling I Reuter E Cheremushkin OV Kel-Margoulis E Wingender, Nucleic Acids Res 2003 31 3576 3579 12824369 10.1093/nar/gkg585
60. TRANSFAC: transcriptional regulation, from patterns to profiles. V Matys E Fricke R Geffers E Gossling M Haubrock R Hehl K Hornischer D Karas AE Kel OV Kel-Margoulis DU Kloos S Land B Lewicki-Potapov H Michael R Munch I Reuter S Rotert H Saxel M Scheer S Thiele E Wingender, Nucleic Acids Res 2003 31 374 378 12520026 10.1093/nar/gkg108