Positive selection of primate genes that promote HIV-1 replication

Virology

Volumn 454-455, Issue 1, 2014, Pages 291-298

  Meyerson, Nicholas R ^a   Rowley, Paul A ^a   Swan, Christina H ^a,b   Le, Dona T ^a   Wilkerson, Gregory K ^c   Sawyer, Sara L ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b Regents School of Austin   (United States)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

Arms race; Co factors; Genetic conflict; Host factors; Paleovirology

Indexed keywords

CD4 ANTIGEN; CHEMOKINE RECEPTOR CXCR4; INTERFERON;

ANIMAL CELL; ANKRD30A GENE; ARTICLE; CD4 GENE; CELL STRAIN HEK293; CODON; COMPARATIVE STUDY; CONTROLLED STUDY; CXCR4 GENE; GENE; GENE DOSAGE; GENE SILENCING; GENETIC ANALYSIS; GENETIC SELECTION; GENETIC SUSCEPTIBILITY; HELA CELL; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN TISSUE; INFECTION SENSITIVITY; INNATE IMMUNITY; LEUKEMIA CELL LINE; MAP4 GENE; MOLECULAR EVOLUTION; NONHUMAN; NUP153 GENE; PRIMATE; PRIORITY JOURNAL; RANBP2 GENE; RNA INTERFERENCE; SEQUENCE ALIGNMENT; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS REPLICATION;

ARMS RACE; CO-FACTORS; GENETIC CONFLICT; HOST FACTORS; PALEOVIROLOGY;

ANIMALS; HIV-1; HOST-PATHOGEN INTERACTIONS; HUMANS; PRIMATES; SELECTION, GENETIC; VIRUS REPLICATION;

EID: 84896499483     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2014.02.029     Document Type: Article

References (69)

1. Blanco-Melo D., Venkatesh S., Bieniasz P.D. Intrinsic cellular defenses against human immunodeficiency viruses. Immunity 2012, 37:399-411.
2. Brass A.L., Dykxhoorn D.M., Benita Y., Yan N., Engelman A., Xavier R.J., Lieberman J., Elledge S.J. Identification of host proteins required for HIV infection through a functional genomic screen. Science 2008, 319:921-926.
3. Bushman F.D., Malani N., Fernandes J., D'Orso I., Cagney G., Diamond T.L., Zhou H., Hazuda D.J., Espeseth A.S., et al. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathol. 2009, 5:e1000437.
4. Cherepanov P. Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase. J. Biol. Chem. 2004, 279:48883-48892.
5. Ciccarelli F.D. Complex genomic rearrangements lead to novel primate gene function. Genome Res. 2005, 15:343-351.
6. Cohen S., Au S., Panté N. How viruses access the nucleus. BBA - Mol. Cell Res. 2011, 1813:1634-1645. (Elsevier B.V).
7. Comeron J.M. K-estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinform. (Oxf., Engl.) 1999, 15:763-764.
8. Compton A.A., Emerman M. Convergence and divergence in the evolution of the APOBEC3G-Vif interaction reveal ancient origins of simian immunodeficiency viruses. PLoS Pathol. 2013, 9:e1003135.
9. Compton A.A., Hirsch V.M., Emerman M. The host restriction factor APOBEC3G and retroviral Vif protein coevolve due to ongoing genetic conflict. Cell Host Microbe 2012, 11:91-98.
10. Daugherty M.D., Malik H.S. Rules of engagement: molecular insights from host-virus arms races. Annu. Rev. Genet. 2012, 46:677-700.
11. Demogines A., East A.M., Lee J.-H., Grossman S.R., Sabeti P.C., Paull T.T., Sawyer S.L. Ancient and recent adaptive evolution of primate non-homologous end joining genes. PLoS Genet. 2010, 6:e1001169.
12. Demogines A., Abraham J., Choe H., Farzan M., Sawyer S.L. Dual host-virus arms races shape an essential housekeeping protein. PLoS Biol. 2013, 11:e1001571.
13. Di Nunzio F., Danckaert A., Fricke T., Perez P., Fernandez J., Perret E., Roux P., Shorte S., Charneau P., et al. Human nucleoporins promote HIV-1 docking at the nuclear pore, nuclear import and integration. PLoS One 2012, 7:e46037.
14. Duggal N.K., Fu W., Akey J.M., Emerman M. Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations. Virology 2013, 443:329-337. (Elsevier).
15. de Chassey B., Meyniel-Schicklin L., Aublin-Gex A., André P., Lotteau V. Genetic screens for the control of influenza virus replication: from meta-analysis to drug discovery. Mol. BioSyst. 2012, 8:1297.
16. Fernandez-Garcia M.-D., Mazzon M., Jacobs M., Amara A. Pathogenesis of flavivirus infections: using and abusing the host cell. Cell Host Microbe 2009, 5:318-328.
17. Friedel C.C., Haas J. Virus-host interactomes and global models of virus-infected cells. Trends Microbiol. 2011, 19:501-508. (Elsevier Ltd.).
18. Friedrich B.M., Dziuba N., Li G., Endsley M.A., Murray J.L., Ferguson M.R. Host factors mediating HIV-1 replication. Virus Res. 2011, 161:101-114. (Elsevier B.V).
19. Gallo D.E., Hope T.J. Knockdown of MAP4 and DNAL1 produces a post-fusion and pre-nuclear translocation impairment in HIV-1 replication. Virology 2012, 422:13-21.
20. Gifford R.J. Viral evolution in deep time: lentiviruses and mammals. Trends Genet. 2012, 28:89-100.
21. Goff S.P. Host factors exploited by retroviruses. Nat. Rev. Microbiol. 2007, 5:253-263.
22. Goff S.P. Knockdown screens to knockout HIV-1. Cell 2008, 135:417-420.
23. Goldman N., Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 1994, 11:725-736.
24. Gupta R.K., Hué S., Schaller T., Verschoor E., Pillay D., Towers G.J. Mutation of a single residue renders human tetherin resistant to HIV-1 Vpu-mediated depletion. PLoS Pathol. 2009, 5:e1000443.
25. Hirsch A.J. The use of RNAi-based screens to identify host proteins involved in viral replication. Future Microbiol. 2010, 5:303-311.
26. Hopkins A.L., Groom C.R. The druggable genome. Nat. Rev. Drug Discov. 2002, 1:727-730.
27. Houzet L., Jeang K.T. Genome-wide screening using RNA interference to study host factors in viral replication and pathogenesis. Exp. Biol. Med. 2011, 236:962-967.
28. Hsu T.-H., Spindler K.R. Identifying host factors that regulate viral infection. PLoS Pathol. 2012, 8:e1002772. (R.C. Condit, Ed.).
29. Humes D., Emery S., Laws E., Overbaugh J. A species-specific amino acid difference in the macaque CD4 receptor restricts replication by global circulating HIV-1 variants representing viruses from recent infection. J. Virol. 2012, 86:12472-12483.
30. Jäger S., Cimermancic P., Gulbahce N., Johnson J.R., McGovern K.E., Clarke S.C., Shales M., Mercenne G., Pache L., et al. Global landscape of HIV-human protein complexes. Nature 2012, 481:365-370.
31. Kaelber J.T., Demogines A., Harbison C.E., Allison A.B., Goodman L.B., Ortega A.N., Sawyer S.L., Parrish C.R. Evolutionary reconstructions of the transferrin receptor of caniforms supports canine parvovirus being a re-emerged and not a novel pathogen in dogs. PLoS Pathol. 2012, 8:e1002666. (L. Villarreal, Ed.).
32. Kirmaier A., Wu F., Newman R.M., Hall L.R., Morgan J.S., O'Connor S., Marx P.A., Meythaler M., Goldstein S., et al. TRIM5 suppresses cross-species transmission of a primate immunodeficiency virus and selects for emergence of resistant variants in the new species. PLoS Biol. 2010, 8:e1000462.
33. König R., Zhou Y., Elleder D., Diamond T.L., Bonamy G.M.C., Irelan J.T., Chiang C.-Y., Tu B.P., De Jesus P.D., et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 2008, 135:49-60.
34. König R., Stertz S., Zhou Y., Inoue A., Hoffmann H.-H., Bhattacharyya S., Alamares J.G., Tscherne D.M., Ortigoza M.B., et al. Human host factors required for influenza virus replication. Nature 2010, 463:813-817.
35. Kwong P.D., Wyatt R., Robinson J., Sweet R.W., Sodroski J., Hendrickson W.A. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 1998, 393:648-659.
36. Laguette N., Rahm N., Sobhian B., Chable-Bessia C., Munch J., Snoeck J., Sauter D., Switzer W.M., Heneine W., et al. Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe 2012, 11:205-217.
37. Lee K., Mulky A., Yuen W., Martin T.D., Meyerson N.R., Choi L., Yu H., Sawyer S.L., KewalRamani V.N. HIV-1 capsid-targeting domain of cleavage and polyadenylation specificity factor 6. J. Virol. 2012, 86:3851-3860.
38. Lim E.S., Malik H.S., Emerman M. Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. J. Virol. 2010, 84:7124-7134.
39. Lim E.S., Fregoso O.I., McCoy C.O., Matsen F.A., Malik H.S., Emerman M. The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe 2012, 11:194-204.
40. Malim M.H., Bieniasz P.D. HIV restriction factors and mechanisms of evasion. Cold Spring Harb. Perspect. Med. 2012, 2:a006940.
41. Malim M.H., Emerman M. HIV-1 accessory proteins-ensuring viral survival in a hostile environment. Cell Host Microbe 2008, 3:388-398.
42. Martin C., Buckler-White A., Wollenberg K., Kozak C.A. The avian XPR1 gammaretrovirus receptor is under positive selection and is disabled in bird species in contact with virus-infected wild mice. J. Virol. 2013, 87:10094-10104.
43. Matreyek K.A., Engelman A. The requirement for nucleoporin NUP153 during Human Immunodeficiency Virus Type 1 infection is determined by the viral capsid. J. Virol. 2011, 85:7818-7827.
44. Matreyek K.A., Yücel S.S., Li X., Engelman A. Nucleoporin NUP153 phenylalanine-glycine motifs engage a common binding pocket within the HIV-1 capsid protein to mediate lentiviral infectivity. PLoS Pathol. 2013, 9:e1003693.
45. McCarthy K.R., Schmidt A.G., Kirmaier A., Wyand A.L., Newman R.M., Johnson W.E. Gain-of-sensitivity mutations in a Trim5-resistant primary isolate of pathogenic SIV identify two independent conserved determinants of Trim5α specificity. PLoS Pathol. 2013, 9:e1003352.
46. McNatt M.W., Zang T., Hatziioannou T., Bartlett M., Fofana I.B., Johnson W.E., Neil S.J.D., Bieniasz P.D. Species-specific activity of HIV-1 Vpu and positive selection of tetherin transmembrane domain variants. PLoS Pathol. 2009, 5:e1000300. (T.J. Hope, Ed.).
47. Meyerson N.R., Sawyer S.L. Two-stepping through time: mammals and viruses. Trends Microbiol. 2011, 19:286-294.
48. O'Brien S.J., Nelson G.W. Human genes that limit AIDS. Nat. Genet. 2004, 36:565-574.
49. OhAinle M., Kerns J.A., Malik H.S., Emerman M. Adaptive evolution and antiviral activity of the conserved mammalian cytidine deaminase APOBEC3H. J. Virol. 2006, 80:3853-3862.
50. Ortiz M., Guex N., Patin E., Martin O., Xenarios I., Ciuffi A., Quintana-Murci L., Telenti A. Evolutionary trajectories of primate genes involved in HIV pathogenesis. Mol. Biol. Evol. 2009, 26:2865-2875.
51. Park H., Kim J.-I., Ju Y.S., Gokcumen O., Mills R.E., Kim S., Lee S., Suh D., Hong D., et al. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat. Genet. 2010, 42:400-405.
52. Parmley J.L., Hurst L.D. How Common Are Intragene Windows with K A>K S Owing to Purifying Selection on Synonymous Mutations. J. Mol. Evol. 2007, 64:646-655.
53. Radtke K., Dohner K., Sodeik B. Viral interactions with the cytoskeleton: a hitchhiker[U+05F3]s guide to the cell. Cell Microbiol. 2006, 8:387-400.
54. Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs R.A., Rogers J., Katze M.G., Bumgarner R., Weinstock G.M., Mardis E.R., Remington K.A., Strausberg R.L., et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007, 316:222-234.
55. Sawyer S.L., Malik H.S. Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis. Proc. Natl. Acad. Sci. USA 2006, 103:17614-17619.
56. Sawyer S.L., Emerman M., Malik H.S. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol. 2004, 2:E275.
57. Sawyer S.L., Wu L.I., Emerman M., Malik H.S. Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. Proc. Natl. Acad. Sci. USA 2005, 102:2832-2837.
58. Schaller T., Ocwieja K.E., Rasaiyaah J., Price A.J., Brady T.L., Roth S.L., Hué S., Fletcher A.J., Lee K., et al. HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathol. 2011, 7:e1002439.
59. Schmid K., Yang Z. The trouble with sliding windows and the selective pressure in BRCA1. PLoS One 2008, 3:e3746.
60. Shaw M.L. The host interactome of influenza virus presents new potential targets for antiviral drugs. Rev. Med. Virol. 2011, 21:358-369. (The host interactome of influenza virus).
61. Stoye J.P. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat. Rev. Microbiol. 2012, 10:395-406.
62. Telenti A., Johnson W.E. Host genes important to HIV replication and evolution. Cold Spring Harb. Perspect. Med. 2012, 2:a007203.
63. Watanabe T., Watanabe S., Kawaoka Y. Cellular networks involved in the influenza virus life cycle. Cell Host Microbe 2010, 7:427-439.
64. Whitehead K.A., Dahlman J.E., Langer R.S., Anderson D.G. Silencing or stimulation? siRNA delivery and the immune system. Annu. Rev. Chem. Biomol. Eng. 2011, 2:77-96.
65. Woodward C.L., Prakobwanakit S., Mosessian S., Chow S.A. Integrase interacts with nucleoporin NUP153 to mediate the nuclear import of Human Immunodeficiency Virus Type 1. J. Virol. 2009, 83:6522-6533.
66. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 1997, 13:555-556.
67. Yeung M.L., Houzet L., Yedavalli V.S.R.K., Jeang K.-T. A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication. J. Biol. Chem. 2009, 284:19463-19473.
68. Zhang Z.D., Weinstock G., Gerstein M. Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates. J. Mol. Evol. 2008, 66:446-456.
69. Zhou H., Xu M., Huang Q., Gates A.T., Zhang X.D., Castle J.C., Stec E., Ferrer M., Strulovici B., et al. Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 2008, 4:495-504.