The breadth of antiviral activity of Apobec3DE in chimpanzees has been driven by positive selection

Journal of Virology

Volumn 85, Issue 21, 2011, Pages 11361-11371

  Duggal, Nisha K ^a,b   Malik, Harmit S ^b   Emerman, Michael ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE DEAMINASE; PROTEIN APOBEC3DE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANTIVIRAL ACTIVITY; ARTICLE; CHIMPANZEE; CHLOROCEBUS; CONTROLLED STUDY; ENZYME ACTIVITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROPOSON; SIMIAN IMMUNODEFICIENCY VIRUS; VIRION; VIRUS GENOME;

ANIMALS; CELL LINE; CLUSTER ANALYSIS; CYTOSINE DEAMINASE; HUMANS; MOLECULAR SEQUENCE DATA; PAN TROGLODYTES; PHYLOGENY; RECOMBINATION, GENETIC; RETROELEMENTS; RETROVIRIDAE; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; VIRUS REPLICATION;

CERCOPITHECUS AETHIOPS; HUMAN IMMUNODEFICIENCY VIRUS 1; PAN; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 80055101936     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.05046-11     Document Type: Article

References (51)

1. Aguiar, R. S., N. Lovsin, A. Tanuri, and B. M. Peterlin. 2008. Vpr.A3A chimera inhibits HIV replication. J. Biol. Chem. 283:2518-2525.
2. Alisch, R. S., J. L. Garcia-Perez, A. R. Muotri, F. H. Gage, and J. V. Moran. 2006. Unconventional translation of mammalian LINE-1 retrotransposons. Genes Dev. 20:210-224.
3. Bartz, S. R., and M. A. Vodicka. 1997. Production of high-titer human immunodeficiency virus type 1 pseudotyped with vesicular stomatitis virus glycoprotein. Methods 12:337-342.
4. Batzer, M. A., and P. L. Deininger. 2002. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3:370-379.
5. Bennett, E. A., et al. 2008. Active Alu retrotransposons in the human genome. Genome Res. 18:1875-1883.
6. Bishop, K. N., et al. 2004. Cytidine deamination of retroviral DNA by diverse APOBEC proteins. Curr. Biol. 14:1392-1396.
7. Bogerd, H. P., B. P. Doehle, H. L. Wiegand, and B. R. Cullen. 2004. A single amino acid difference in the host APOBEC3G protein controls the primate species specificity of HIV type 1 virion infectivity factor. Proc. Natl. Acad. Sci. U. S. A. 101:3770-3774.
8. Bogerd, H. P., H. L. Wiegand, B. P. Doehle, K. K. Lueders, and B. R. Cullen. 2006. APOBEC3A and APOBEC3B are potent inhibitors of LTR-retrotransposon function in human cells. Nucleic Acids Res. 34:89-95.
9. Bogerd, H. P., et al. 2006. Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. Proc. Natl. Acad. Sci. U. S. A. 103:8780-8785.
10. Chen, H., et al. 2006. APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons. Curr. Biol. 16:480-485.
11. Dang, Y., et al. 2011. Identification of a single amino acid required for APOBEC3 antiretroviral cytidine deaminase activity. J. Virol. 85:5691-5695.
12. Dang, Y., X. Wang, W. J. Esselman, and Y. H. Zheng. 2006. Identification of APOBEC3DE as another antiretroviral factor from the human APOBEC family. J. Virol. 80:10522-10533.
13. Dereeper, A., et al. 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 36:W465-W469.
14. Dewannieux, M., C. Esnault, and T. Heidmann. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35:41-48.
15. Emerman, M., and H. S. Malik. 2010. Paleovirology-modern consequences of ancient viruses. PLoS Biol. 8:e1000301.
16. Gifford, R. J., et al. 2008. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc. Natl. Acad. Sci. U. S. A. 105:20362-20367.
17. Gilbert, C., D. G. Maxfield, S. M. Goodman, and C. Feschotte. 2009. Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLoS Genet. 5:e1000425.
18. Goila-Gaur, R., M. A. Khan, E. Miyagi, S. Kao, and K. Strebel. 2007. Targeting APOBEC3A to the viral nucleoprotein complex confers antiviral activity. Retrovirology 4:61.
19. Hedges, D. J., et al. 2004. Differential alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Res. 14:1068-1075.
20. Holmes, R. K., M. H. Malim, and K. N. Bishop. 2007. APOBEC-mediated viral restriction: not simply editing? Trends Biochem. Sci. 32:118-128.
21. Jarmuz, A., et al. 2002. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. Genomics 79:285-296.
22. Koning, F. A., et al. 2009. Defining APOBEC3 expression patterns in human tissues and hematopoietic cell subsets. J. Virol. 83:9474-9485.
23. Kosakovsky Pond, S. L., D. Posada, M. B. Gravenor, C. H. Woelk, and S. D. Frost. 2006. Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol. 23:1891-1901.
24. Li, M. M., L. I. Wu, and M. Emerman. 2010. The range of human APOBEC3H sensitivity to lentiviral Vif proteins. J. Virol. 84:88-95.
25. MacGinnitie, A. J., S. Anant, and N. O. Davidson. 1995. Mutagenesis of apobec-1, the catalytic subunit of the mammalian apolipoprotein B mRNA editing enzyme, reveals distinct domains that mediate cytosine nucleoside deaminase, RNA binding, and RNA editing activity. J. Biol. Chem. 270: 14768-14775.
26. Malim, M. H., and M. Emerman. 2008. HIV-1 accessory proteins-ensuring viral survival in a hostile environment. Cell Host Microbe 3:388-398.
27. Mangeat, B., et al. 2003. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature 424:99-103.
28. Mangeat, B., P. Turelli, S. Liao, and D. Trono. 2004. A single amino acid determinant governs the species-specific sensitivity of APOBEC3G to Vif action. J. Biol. Chem. 279:14481-14483.
29. Mariani, R., et al. 2003. Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif. Cell 114:21-31.
30. Miller, A. D., and G. J. Rosman. 1989. Improved retroviral vectors for gene transfer and expression. Biotechniques 7:980-990.
31. Mills, R. E., et al. 2006. Recently mobilized transposons in the human and chimpanzee genomes. Am. J. Hum. Genet. 78:671-679.
32. Miyagi, E., et al. 2010. Stably expressed APOBEC3F has negligible antiviral activity. J. Virol. 84:11067-11075.
33. Moran, J. V., R. J. DeBerardinis, and H. H. Kazazian, Jr. 1999. Exon shuffling by L1 retrotransposition. Science 283:1530-1534.
34. Mulder, L. C., et al. 2010. Moderate influence of human APOBEC3F on HIV-1 replication in primary lymphocytes. J. Virol. 84:9613-9617.
35. Niewiadomska, A. M., et al. 2007. Differential inhibition of long interspersed element 1 by APOBEC3 does not correlate with high-molecular-mass-complex formation or P-body association. J. Virol. 81:9577-9583.
36. OhAinle, M., J. A. Kerns, M. M. Li, H. S. Malik, and M. Emerman. 2008. Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. Cell Host Microbe 4:249-259.
37. OhAinle, M., J. A. Kerns, H. S. Malik, and M. Emerman. 2006. Adaptive evolution and antiviral activity of the conserved mammalian cytidine deaminase APOBEC3H. J. Virol. 80:3853-3862.
38. Refsland, E. W., et al. 2010. Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction. Nucleic Acids Res. 38:4274-4284.
39. Ribet, D., M. Dewannieux, and T. Heidmann. 2004. An active murine transposon family pair: retrotransposition of "master" MusD copies and ETn trans-mobilization. Genome Res. 14:2261-2267.
40. Sambrook, J., and D. W. Russell. 2006. Rapid amplification of 3' cDNA ends (3'-RACE). Cold Spring Harb. Protoc. doi:10.1101/pdb.prot3865.
41. Sawyer, S. L., M. Emerman, and H. S. Malik. 2004. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol. 2:E275.
42. Schrofelbauer, B., D. Chen, and N. R. Landau. 2004. A single amino acid of APOBEC3G controls its species-specific interaction with virion infectivity factor (Vif). Proc. Natl. Acad. Sci. U. S. A. 101:3927-3932.
43. Smith, J. L., and V. K. Pathak. 2010. Identification of specific determinants of human APOBEC3F, APOBEC3C, and APOBEC3DE and African green monkey APOBEC3F that interact with HIV-1 Vif. J. Virol. 84:12599-12608.
44. Stenglein, M. D., M. B. Burns, M. Li, J. Lengyel, and R. S. Harris. 2010. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat. Struct. Mol. Biol. 17:222-229.
45. Stenglein, M. D., and R. S. Harris. 2006. APOBEC3B and APOBEC3F inhibit L1 retrotransposition by a DNA deamination-independent mechanism. J. Biol. Chem. 281:16837-16841.
46. Tan, L., P. T. Sarkis, T. Wang, C. Tian, and X. F. Yu. 2009. Sole copy of Z2-type human cytidine deaminase APOBEC3H has inhibitory activity against retrotransposons and HIV-1. FASEB J. 23:279-287.
47. Wei, W., et al. 2001. Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell. Biol. 21:1429-1439.
48. Xu, H., et al. 2004. A single amino acid substitution in human APOBEC3G antiretroviral enzyme confers resistance to HIV-1 virion infectivity factorinduced depletion. Proc. Natl. Acad. Sci. U. S. A. 101:5652-5657.
49. Yamashita, M., and M. Emerman. 2004. Capsid is a dominant determinant of retrovirus infectivity in nondividing cells. J. Virol. 78:5670-5678.
50. Yang, Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591.
51. Yang, Z., W. S. Wong, and R. Nielsen. 2005. Bayes empirical bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22:1107-1118.