title: Positive selection of primate genes that promote HIV-1 replication.
abstract: Evolutionary analyses have revealed that most host-encoded restriction factors against HIV have experienced virus-driven selection during primate evolution. However, HIV also depends on the function of many human proteins, called host factors, for its replication. It is not clear whether virus-driven selection shapes the evolution of host factor genes to the extent that it is known to shape restriction factor genes. We show that five out of 40 HIV host factor genes (13%) analyzed do bear strong signatures of positive selection. Some of these genes (CD4, NUP153, RANBP2/NUP358) have been characterized with respect to the HIV lifecycle, while others (ANKRD30A/NY-BR-1 and MAP4) remain relatively uncharacterized. One of these, ANKRD30A, shows the most rapid evolution within this set of genes and is induced by interferon stimulation. We discuss how evolutionary analysis can aid the study of host factors for viral replication, just as it has the study of host immunity systems.
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Meyerson
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Rowley
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA; Regents School of Austin, 3230 Travis Country Circle, Austin, TX, USA.
authors.forename: Christina H
authors.initials: CH
authors.lastname: Swan
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA.
authors.forename: Dona T
authors.initials: DT
authors.lastname: Le
authors.affiliation: Department of Veterinary Sciences, Michale E Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, Bastrop, TX, USA.
authors.forename: Gregory K
authors.initials: GK
authors.lastname: Wilkerson
authors.affiliation: Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712-1191, USA. Electronic address: saras@austin.utexas.edu.
authors.forename: Sara L
authors.initials: SL
authors.lastname: Sawyer
mesh_terms: D000818:Animals; D015497:HIV-1 / Q000502:physiology*; D054884:Host-Pathogen Interactions; D006801:Humans; D011323:Primates; D012641:Selection, Genetic; D014779:Virus Replication
keywords: Arms race; Co-factors; Genetic conflict; Host factors; Paleovirology
references.citation: PLoS Pathog. 2009 May;5(5):e1000437
references.pmid: 19478882
references.citation: PLoS Genet. 2010 Oct 21;6(10):e1001169
references.pmid: 20975951
references.citation: Virology. 2013 Sep 1;443(2):329-37
references.pmid: 23755966
references.citation: PLoS One. 2012;7(9):e46037
references.pmid: 23049930
references.citation: Science. 2008 Feb 15;319(5865):921-6
references.pmid: 18187620
references.citation: Science. 2007 Apr 13;316(5822):222-34
references.pmid: 17431167
references.citation: J Virol. 2013 Sep;87(18):10094-104
references.pmid: 23843647
references.citation: Mol Biol Evol. 1994 Sep;11(5):725-36
references.pmid: 7968486
references.citation: Nat Genet. 2004 Jun;36(6):565-74
references.pmid: 15167933
references.citation: Future Microbiol. 2010 Feb;5(2):303-11
references.pmid: 20143951
references.citation: PLoS Pathog. 2013;9(10):e1003693
references.pmid: 24130490
references.citation: Cell Host Microbe. 2009 Apr 23;5(4):318-28
references.pmid: 19380111
references.citation: Cell Host Microbe. 2008 Jun 12;3(6):388-98
references.pmid: 18541215
references.citation: PLoS Pathog. 2009 Feb;5(2):e1000300
references.pmid: 19214216
references.citation: PLoS Pathog. 2012;8(7):e1002772
references.pmid: 22807672
references.citation: PLoS Biol. 2010 Aug 24;8(8):
references.pmid: 20808775
references.citation: J Virol. 2010 Jul;84(14):7124-34
references.pmid: 20444900
references.citation: Nature. 2011 Dec 21;481(7381):365-70
references.pmid: 22190034
references.citation: Nat Genet. 2010 May;42(5):400-5
references.pmid: 20364138
references.citation: Cell Host Microbe. 2010 Jun 25;7(6):427-39
references.pmid: 20542247
references.citation: Cell Host Microbe. 2008 Nov 13;4(5):495-504
references.pmid: 18976975
references.citation: Nat Rev Microbiol. 2007 Apr;5(4):253-63
references.pmid: 17325726
references.citation: Mol Biol Evol. 2009 Dec;26(12):2865-75
references.pmid: 19726537
references.citation: J Mol Evol. 2008 May;66(5):446-56
references.pmid: 18414925
references.citation: Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2832-7
references.pmid: 15689398
references.citation: PLoS Pathog. 2012;8(5):e1002666
references.pmid: 22570610
references.citation: J Virol. 2012 Apr;86(7):3851-60
references.pmid: 22301135
references.citation: Nature. 1998 Jun 18;393(6686):648-59
references.pmid: 9641677
references.citation: Virus Res. 2011 Nov;161(2):101-14
references.pmid: 21871504
references.citation: J Biol Chem. 2004 Nov 19;279(47):48883-92
references.pmid: 15371438
references.citation: J Virol. 2006 Apr;80(8):3853-62
references.pmid: 16571802
references.citation: Nat Rev Microbiol. 2012 May 08;10(6):395-406
references.pmid: 22565131
references.citation: PLoS Biol. 2013;11(5):e1001571
references.pmid: 23723737
references.citation: J Biol Chem. 2009 Jul 17;284(29):19463-73
references.pmid: 19460752
references.citation: Annu Rev Genet. 2012;46:677-700
references.pmid: 23145935
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17614-9
references.pmid: 17101967
references.citation: Genome Res. 2005 Mar;15(3):343-51
references.pmid: 15710750
references.citation: J Virol. 2011 Aug;85(15):7818-27
references.pmid: 21593146
references.citation: Immunity. 2012 Sep 21;37(3):399-411
references.pmid: 22999946
references.citation: Cell Host Microbe. 2012 Feb 16;11(2):205-17
references.pmid: 22305291
references.citation: PLoS Pathog. 2013 Jan;9(1):e1003135
references.pmid: 23359341
references.citation: Comput Appl Biosci. 1997 Oct;13(5):555-6
references.pmid: 9367129
references.citation: Mol Biosyst. 2012 Apr;8(4):1297-303
references.pmid: 22307679
references.citation: J Virol. 2009 Jul;83(13):6522-33
references.pmid: 19369352
references.citation: J Mol Evol. 2007 Jun;64(6):646-55
references.pmid: 17557167
references.citation: PLoS Biol. 2004 Sep;2(9):E275
references.pmid: 15269786
references.citation: Exp Biol Med (Maywood). 2011 Aug;236(8):962-7
references.pmid: 21727185
references.citation: Nature. 2010 Feb 11;463(7282):813-7
references.pmid: 20027183
references.citation: J Virol. 2012 Dec;86(23):12472-83
references.pmid: 22973036
references.citation: Trends Genet. 2012 Feb;28(2):89-100
references.pmid: 22197521
references.citation: Nat Rev Drug Discov. 2002 Sep;1(9):727-30
references.pmid: 12209152
references.citation: Trends Microbiol. 2011 Oct;19(10):501-8
references.pmid: 21855347
references.citation: Cell Microbiol. 2006 Mar;8(3):387-400
references.pmid: 16469052
references.citation: Cell. 2008 Oct 31;135(3):417-20
references.pmid: 18984154
references.citation: Cell Host Microbe. 2012 Jan 19;11(1):91-8
references.pmid: 22264516
references.citation: PLoS Pathog. 2011 Dec;7(12):e1002439
references.pmid: 22174692
references.citation: Rev Med Virol. 2011 Nov;21(6):358-69
references.pmid: 21823192
references.citation: Cell. 2008 Oct 3;135(1):49-60
references.pmid: 18854154
references.citation: Trends Microbiol. 2011 Jun;19(6):286-94
references.pmid: 21531564
references.citation: PLoS Pathog. 2009 May;5(5):e1000443
references.pmid: 19461879
references.citation: Cold Spring Harb Perspect Med. 2012 May;2(5):a006940
references.pmid: 22553496
references.citation: Bioinformatics. 1999 Sep;15(9):763-4
references.pmid: 10498777
references.citation: PLoS One. 2008;3(11):e3746
references.pmid: 19015730
references.citation: Cold Spring Harb Perspect Med. 2012 Apr;2(4):a007203
references.pmid: 22474614
references.citation: Annu Rev Chem Biomol Eng. 2011;2:77-96
references.pmid: 22432611
references.citation: Cell Host Microbe. 2012 Feb 16;11(2):194-204
references.pmid: 22284954
references.citation: Virology. 2012 Jan 5;422(1):13-21
references.pmid: 22018492
references.citation: PLoS Pathog. 2013 May;9(5):e1003352
references.pmid: 23675300
references.citation: Biochim Biophys Acta. 2011 Sep;1813(9):1634-45
references.pmid: 21167871