메뉴 건너뛰기




Volumn 31, Issue 9, 2014, Pages 2402-2414

Evolutionary analysis identifies an MX2 haplotype associated with natural resistance to HIV-1 infection

Author keywords

Adaptive evolution; HIV 1 infection; MX2; Positive selection

Indexed keywords

ALPHA INTERFERON; MX2 PROTEIN, HUMAN; MYXOVIRUS RESISTANCE PROTEIN;

EID: 84906748712     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu193     Document Type: Article
Times cited : (23)

References (61)
  • 2
    • 0036272936 scopus 로고    scopus 로고
    • Accuracy and power of Bayes prediction of amino acid sites under positive selection
    • Anisimova M, Bielawski JP, Yang Z. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection.Mol Biol Evol. 19:950-958.
    • (2002) Mol Biol Evol. , vol.19 , pp. 950-958
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 3
    • 34547793042 scopus 로고    scopus 로고
    • Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites
    • Anisimova M, Yang Z. 2007. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol. 24:1219-1228.
    • (2007) Mol Biol Evol. , vol.24 , pp. 1219-1228
    • Anisimova, M.1    Yang, Z.2
  • 4
    • 34248531947 scopus 로고    scopus 로고
    • Polymorphisms in IRF-1 associated with resistance to HIV-1 infection in highly exposed uninfected Kenyan sex workers
    • Ball TB, Ji H, Kimani J, McLaren P, Marlin C, Hill AV, Plummer FA. 2007. Polymorphisms in IRF-1 associated with resistance to HIV-1 infection in highly exposed uninfected Kenyan sex workers. AIDS 21: 1091-1101.
    • (2007) AIDS , vol.21 , pp. 1091-1101
    • Ball, T.B.1    Ji, H.2    Kimani, J.3    McLaren, P.4    Marlin, C.5    Hill, A.V.6    Plummer, F.A.7
  • 7
    • 79954554384 scopus 로고    scopus 로고
    • GeCo++: A C++ library for genomic features computation and annotation in the presence of variants
    • Cereda M, Sironi M, Cavalleri M, Pozzoli U. 2011. GeCo++: a C++ library for genomic features computation and annotation in the presence of variants. Bioinformatics 27:1313-1315.
    • (2011) Bioinformatics , vol.27 , pp. 1313-1315
    • Cereda, M.1    Sironi, M.2    Cavalleri, M.3    Pozzoli, U.4
  • 8
    • 84867647908 scopus 로고    scopus 로고
    • Rules of engagement: Molecular insights from host-virus arms races
    • DaughertyMD, Malik HS. 2012. Rules of engagement: molecular insights from host-virus arms races. Annu Rev Genet. 46:677-700.
    • (2012) Annu Rev Genet. , vol.46 , pp. 677-700
    • Daugherty, M.D.1    Malik, H.S.2
  • 9
    • 77957233168 scopus 로고    scopus 로고
    • Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology
    • Delport W, Poon AF, Frost SD, Kosakovsky Pond SL. 2010. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26:2455-2457.
    • (2010) Bioinformatics , vol.26 , pp. 2455-2457
    • Delport, W.1    Poon, A.F.2    Frost, S.D.3    Kosakovsky Pond, S.L.4
  • 10
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium
    • ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2    Dunham, I.3    Green, E.D.4    Gunter, C.5    Snyder, M.6
  • 12
    • 84901459944 scopus 로고    scopus 로고
    • Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing datasets
    • Fagny M, Patin E, Enard D, Barreiro LB, Quintana-Murci L, Laval G. 2014. Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing datasets. Mol Biol Evol. 31(7):1850-1868.
    • (2014) Mol Biol Evol. , vol.31 , Issue.7 , pp. 1850-1868
    • Fagny, M.1    Patin, E.2    Enard, D.3    Barreiro, L.B.4    Quintana-Murci, L.5    Laval, G.6
  • 13
    • 84879593719 scopus 로고    scopus 로고
    • A 175 million year history of T cell regulatory molecules reveals widespread selection, with adaptive evolution of disease alleles
    • Forni D, Cagliani R, Pozzoli U, Colleoni M, Riva S, Biasin M, Filippi G, De Gioia L, Gnudi F, Comi GP, et al. 2013. A 175 million year history of T cell regulatory molecules reveals widespread selection, with adaptive evolution of disease alleles. Immunity 38:1129-1141.
    • (2013) Immunity , vol.38 , pp. 1129-1141
    • Forni, D.1    Cagliani, R.2    Pozzoli, U.3    Colleoni, M.4    Riva, S.5    Biasin, M.6    Filippi, G.7    De Gioia, L.8    Gnudi, F.9    Comi, G.P.10
  • 15
    • 67449110978 scopus 로고    scopus 로고
    • Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions
    • Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Riva S, Clerici M, Bresolin N, Sironi M. 2009. Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. J Exp Med. 206:1395-1408.
    • (2009) J Exp Med. , vol.206 , pp. 1395-1408
    • Fumagalli, M.1    Pozzoli, U.2    Cagliani, R.3    Comi, G.P.4    Riva, S.5    Clerici, M.6    Bresolin, N.7    Sironi, M.8
  • 16
    • 80755153638 scopus 로고    scopus 로고
    • Structure ofmyxovirus resistance protein a reveals intra- and intermolecular domain interactions required for the antiviral function
    • Gao S, von der Malsburg A, Dick A, Faelber K, Schroder GF, Haller O, Kochs G, Daumke O. 2011. Structure ofmyxovirus resistance protein a reveals intra- and intermolecular domain interactions required for the antiviral function. Immunity 35:514-525.
    • (2011) Immunity , vol.35 , pp. 514-525
    • Gao, S.1    Von Der Malsburg, A.2    Dick, A.3    Faelber, K.4    Schroder, G.F.5    Haller, O.6    Kochs, G.7    Daumke, O.8
  • 20
    • 78651515640 scopus 로고    scopus 로고
    • Human MxA protein: An interferon-induced dynamin-like GTPase with broad antiviral activity
    • Haller O, Kochs G. 2011. Human MxA protein: an interferon-induced dynamin-like GTPase with broad antiviral activity. J Interferon Cytokine Res. 31:79-87.
    • (2011) J Interferon Cytokine Res. , vol.31 , pp. 79-87
    • Haller, O.1    Kochs, G.2
  • 23
    • 2942676463 scopus 로고    scopus 로고
    • Inhibition of nuclear import and cell-cycle progression by mutated forms of the dynamin-like GTPase MxB
    • King MC, Raposo G, Lemmon MA. 2004. Inhibition of nuclear import and cell-cycle progression by mutated forms of the dynamin-like GTPase MxB. Proc Natl Acad Sci U S A. 101:8957-8962.
    • (2004) Proc Natl Acad Sci U S A. , vol.101 , pp. 8957-8962
    • King, M.C.1    Raposo, G.2    Lemmon, M.A.3
  • 25
    • 17744396121 scopus 로고    scopus 로고
    • Not so different after all: A comparison of methods for detecting amino acid sites under selection
    • Kosakovsky Pond SL, Frost SD. 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 22:1208-1222.
    • (2005) Mol Biol Evol. , vol.22 , pp. 1208-1222
    • Kosakovsky Pond, S.L.1    Frost, S.D.2
  • 32
    • 84863285086 scopus 로고    scopus 로고
    • Systematic identification of type i and type II interferon-induced antiviral factors
    • Liu SY, Sanchez DJ, Aliyari R, Lu S, Cheng G. 2012. Systematic identification of type I and type II interferon-induced antiviral factors. Proc Natl Acad Sci U S A. 109:4239-4244.
    • (2012) Proc Natl Acad Sci U S A. , vol.109 , pp. 4239-4244
    • Liu, S.Y.1    Sanchez, D.J.2    Aliyari, R.3    Lu, S.4    Cheng, G.5
  • 35
    • 0034044314 scopus 로고    scopus 로고
    • The PSIPRED protein structure prediction server
    • McGuffin LJ, Bryson K, Jones DT. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16:404-405.
    • (2000) Bioinformatics , vol.16 , pp. 404-405
    • McGuffin, L.J.1    Bryson, K.2    Jones, D.T.3
  • 37
    • 84867659115 scopus 로고    scopus 로고
    • Evolution-guided identification of antiviral specificity determinants in the broadly acting interferon-induced innate immunity factor MxA
    • Mitchell PS, Patzina C, Emerman M, Haller O, Malik HS, Kochs G. 2012. Evolution-guided identification of antiviral specificity determinants in the broadly acting interferon-induced innate immunity factor MxA. Cell Host Microbe 12:598-604.
    • (2012) Cell Host Microbe , vol.12 , pp. 598-604
    • Mitchell, P.S.1    Patzina, C.2    Emerman, M.3    Haller, O.4    Malik, H.S.5    Kochs, G.6
  • 38
    • 58949097921 scopus 로고    scopus 로고
    • The "immunologic advantage" of HIVexposed seronegative individuals
    • ESN Study Group.
    • Miyazawa M, Lopalco L, Mazzotta F, Lo Caputo S, Veas F, Clerici M, ESN Study Group. 2009. The "immunologic advantage" of HIVexposed seronegative individuals. AIDS 23:161-175.
    • (2009) AIDS , vol.23 , pp. 161-175
    • Miyazawa, M.1    Lopalco, L.2    Mazzotta, F.3    Lo Caputo, S.4    Veas, F.5    Clerici, M.6
  • 40
    • 27844602105 scopus 로고    scopus 로고
    • The geographic spread of the CCR5 Delta32 HIV-resistance allele
    • Novembre J, Galvani AP, Slatkin M. 2005. The geographic spread of the CCR5 Delta32 HIV-resistance allele. PLoS Biol. 3:e339.
    • (2005) PLoS Biol. , vol.3
    • Novembre, J.1    Galvani, A.P.2    Slatkin, M.3
  • 41
    • 50849100134 scopus 로고    scopus 로고
    • Antiretroelement activity of APOBEC3H was lost twice in recent human evolution
    • OhAinle M, Kerns JA, Li MM, Malik HS, Emerman M. 2008. Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. Cell Host Microbe 4:249-259.
    • (2008) Cell Host Microbe , vol.4 , pp. 249-259
    • Ohainle, M.1    Kerns, J.A.2    Li, M.M.3    Malik, H.S.4    Emerman, M.5
  • 44
    • 4744357399 scopus 로고    scopus 로고
    • Missorting of LaCrosse virus nucleocapsid protein by the interferon- induced MxA GTPase involves smooth ER membranes
    • Reichelt M, Stertz S, Krijnse-Locker J, Haller O, Kochs G. 2004. Missorting of LaCrosse virus nucleocapsid protein by the interferon- induced MxA GTPase involves smooth ER membranes. Traffic 5:772-784.
    • (2004) Traffic , vol.5 , pp. 772-784
    • Reichelt, M.1    Stertz, S.2    Krijnse-Locker, J.3    Haller, O.4    Kochs, G.5
  • 45
    • 33749575795 scopus 로고    scopus 로고
    • Standardized subsets of the HGDP-CEPH human genome diversity cell line panel, accounting for atypical and duplicated samples and pairs of close relatives
    • Rosenberg NA. 2006. Standardized subsets of the HGDP-CEPH human genome diversity cell line panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet. 70:841-847.
    • (2006) Ann Hum Genet. , vol.70 , pp. 841-847
    • Rosenberg, N.A.1
  • 46
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unified platform for automated protein structure and function prediction
    • Roy A, Kucukural A, Zhang Y. 2010. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 5: 725-738.
    • (2010) Nat Protoc. , vol.5 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 47
    • 84891831760 scopus 로고    scopus 로고
    • A single nucleotide polymorphism of porcine MX2 gene provides antiviral activity against vesicular stomatitis virus
    • Sasaki K, Tungtrakoolsub P, Morozumi T, Uenishi H, Kawahara M, Watanabe T. 2014. A single nucleotide polymorphism of porcine MX2 gene provides antiviral activity against vesicular stomatitis virus. Immunogenetics 66:25-32.
    • (2014) Immunogenetics , vol.66 , pp. 25-32
    • Sasaki, K.1    Tungtrakoolsub, P.2    Morozumi, T.3    Uenishi, H.4    Kawahara, M.5    Watanabe, T.6
  • 49
    • 0344464730 scopus 로고    scopus 로고
    • Libsequence: A C++ class library for evolutionary genetic analysis
    • Thornton K. 2003. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19:2325-2327.
    • (2003) Bioinformatics , vol.19 , pp. 2325-2327
    • Thornton, K.1
  • 50
    • 84890476408 scopus 로고    scopus 로고
    • Mx proteins: Antiviral gatekeepers that restrain the uninvited
    • Verhelst J, Hulpiau P, Saelens X. 2013. Mx proteins: antiviral gatekeepers that restrain the uninvited. Microbiol Mol Biol Rev. 77: 551-566.
    • (2013) Microbiol Mol Biol Rev. , vol.77 , pp. 551-566
    • Verhelst, J.1    Hulpiau, P.2    Saelens, X.3
  • 51
    • 0043123111 scopus 로고    scopus 로고
    • RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences
    • Wernersson R, Pedersen AG. 2003. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 31:3537-3539.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3537-3539
    • Wernersson, R.1    Pedersen, A.G.2
  • 53
    • 84855266301 scopus 로고    scopus 로고
    • A population genetics-phylogenetics approach to inferring natural selection in coding sequences
    • Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M. 2011. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet. 7:e1002395.
    • (2011) PLoS Genet. , vol.7
    • Wilson, D.J.1    Hernandez, R.D.2    Andolfatto, P.3    Przeworski, M.4
  • 54
    • 20944448714 scopus 로고
    • Genetical structure of populations
    • Wright S. 1950. Genetical structure of populations. Nature 166: 247-249.
    • (1950) Nature , vol.166 , pp. 247-249
    • Wright, S.1
  • 55
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
    • (1997) Comput Appl Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 56
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
    • (2007) Mol Biol Evol. , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 57
    • 0031960185 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous rate variation in nuclear genes of mammals
    • Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 46:409-418.
    • (1998) J Mol Evol. , vol.46 , pp. 409-418
    • Yang, Z.1    Nielsen, R.2
  • 58
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical Bayes inference of amino acid sites under positive selection
    • Yang Z, Wong WS, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22: 1107-1118.
    • (2005) Mol Biol Evol. , vol.22 , pp. 1107-1118
    • Yang, Z.1    Wong, W.S.2    Nielsen, R.3
  • 59
    • 27844439855 scopus 로고    scopus 로고
    • Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    • Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22:2472-2479.
    • (2005) Mol Biol Evol. , vol.22 , pp. 2472-2479
    • Zhang, J.1    Nielsen, R.2    Yang, Z.3
  • 60
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Zhang Y. 2008. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40.
    • (2008) BMC Bioinformatics , vol.9 , pp. 40
    • Zhang, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.