Twin gradients in APOBEC3 edited HIV-1 DNA reflect the dynamics of lentiviral replication

Nucleic Acids Research

Volumn 34, Issue 17, 2006, Pages 4677-4684

  Suspène, Rodolphe ^a   Rusniok, Christophe ^a   Vartanian, Jean Pierre ^a   Wain Hobson, Simon ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE 3F; APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE 3G; COMPLEMENTARY DNA; DNA; HETERODUPLEX; HYDROLASE; RNA; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; VIRUS DNA;

ARTICLE; CONTROLLED STUDY; DEAMINATION; GENE MUTATION; GENOME; HUMAN IMMUNODEFICIENCY VIRUS 1; IN VITRO STUDY; LENTIVIRINAE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; VIRUS REPLICATION;

CYTOSINE DEAMINASE; DNA REPLICATION; DNA, VIRAL; HIV-1; HUMANS; KINETICS; VIRUS REPLICATION;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33750210516     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl555     Document Type: Article

References (33)

1. Beale,R.C., Petersen-Mahrt,S.K., Watt,I.N., Harris,R.S., Rada,C. and Neuberger,M.S. (2004) Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: Correlation with mutation spectra in vivo. J. Mol. Biol., 337, 585-596.
2. Bishop,K.N., Holmes,R.K., Sheehy,A.M., Davidson,N.O., Cho,S.J. and Malim,M.H. (2004) Cytidine deamination of retroviral DNA by diverse APOBEC proteins. Curr. Biol., 14, 1392-1396.
3. Harris,R.S., Bishop,K.N., Sheehy,A.M., Craig,H.M., Petersen-Mahrt,S.K., Watt,I.N., Neuberger,M.S. and Malim,M.H. (2003) DNA deamination mediates innate immunity to retroviral infection. Cell, 113, 803-809.
4. Lecossier,D., Bouchonnet,F., Clavel,F. and Hance,A.J. (2003) Hypermutation of HIV-1 DNA in the absence of the Vif protein. Science, 300, 1112.
5. Liddament,M.T., Brown,W.L., Schumacher,A.J. and Harris,R.S. (2004) APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo. Curr. Biol., 14, 1385-1391.
6. Mangeat,B., Turelli,P., Caron,G., Friedli,M., Perrin,L. and Trono,D. (2003) Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature, 424, 99-103.
7. Mariani,R., Chen,D., Schrofelbauer,B., Navarro,F., Konig,R., Bollman,B., Munk,C., Nymark-McMahon,H. and Landau,N.R. (2003) Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif. Cell, 114, 21-31.
8. Suspene,R., Sommer,P., Henry,M., Ferris,S., Guetard,D., Pochet,S., Chester,A., Navaratnam,N., Wain-Hobson,S. and Vartanian,J.P. (2004) APOBEC3G is a single-stranded DNA cytidine deaminase and functions independently of HIV reverse transcriptase. Nucleic Acids Res., 32, 2421-2429.
9. Wiegand,H.L., Doehle,B.P., Bogerd,H.P. and Cullen,B.R. (2004) A second human antiretroviral factor, APOBEC3F, is suppressed by the HIV-1 and HIV-2 Vif proteins. EMBO J., 23, 2451-2458.
10. Yu,Q., Konig,R., Pillai,S., Chiles,K., Kearney,M., Palmer,S., Richman,D., Coffin,J.M. and Landau,N.R. (2004) Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nature Struct. Mol. Biol., 11, 435-442.
11. Zhang,H., Yang,B., Pomerantz,R.J., Zhang,C., Arunachalam,S.C. and Gao,L. (2003) The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA. Nature, 424, 94-98.
12. Zheng,Y.H., Irwin,D., Kurosu,T., Tokunaga,K., Sata,T. and Peterlin,B.M. (2004) Human APOBEC3F is another host factor that blocks human immunodeficiency virus type 1 replication. J. Virol., 78, 6073-6076.
13. Bonvin,M., Achermann,F., Greeve,I., Stroka,D., Keogh,A., Inderbitzin,D., Candinas,D., Sommer,P., Wain-Hobson,S., Vartanian,J.P. and Greeve,J. (2006) Interferon-inducible expression of APOBEC3 editing enzymes in human hepatocytes and inhibition of hepatitis B virus replication. Hepatology, 43, 1364-1374.
14. Peng,G., Lei,K.J., Jin,W., Greenwell-Wild,T. and Wahl,S.M. (2006) Induction of APOBEC3 family proteins, a defensive maneuver underlying interferon-induced anti-HIV-1 activity. J. Exp. Med., 203, 41-46.
15. Tanaka,Y., Marusawa,H., Seno,H., Matsumoto,Y., Ueda,Y., Kodama,Y., Endo,Y., Yamauchi,J., Matsumoto,T., Takaori-Kondo,A. et al. (2006) Anti-viral protein APOBEC3G is induced by interferon-alpha stimulation in human hepatocytes. Biochem. Biophys. Res. Commun., 341, 314-319.
16. Sheehy,A.M., Gaddis,N.C., Choi,J.D. and Malim,M.H. (2002) Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature, 418, 646-650.
17. Fitzgibbon,J.E., Mazar,S. and Dubin,D.T. (1993) A new type of G→A hypermutation affecting human immunodeficiency virus. AIDS Res. Hum. Retroviruses, 9, 833-838.
18. Gao,F., Yue,L., White,A.T., Pappas,P.G., Barchue,J., Hanson,A.P., Greene,B.M., Sharp,P.M., Shaw,G.M. and Hahn,B.H. (1992) Human infection by genetically diverse SIVSM-related HIV-2 in west Africa. Nature, 358, 495-499.
19. Perry,S.T., Flaherty,M.T., Kelley,M.J., Clabough,D.L., Tronick,S.R., Coggins,L., Whetter,L., Lengel,C.R. and Fuller,F. (1992) The surface envelope protein gene region of equine infectious anemia virus is not an important determinant of tropism in vitro. J. Virol., 66, 4085-4097.
20. Vartanian,J.P., Meyerhans,A., Asjo,B. and Wain-Hobson,S. (1991) Selection, recombination, and G→A hypermutation of human immunodeficiency virus type 1 genomes. J. Virol., 65, 1779-1788.
21. Wain-Hobson,S., Sonigo,P., Guyader,M., Gazit,A. and Henry,M. (1995) Erratic G→A hypermutation within a complete caprine arthritis-encephalitis virus (CAEV) provirus. Virology, 209, 297-303.
22. Langlois,M.A., Beale,R.C., Conticello,S.G. and Neuberger,M.S. (2005) Mutational comparison of the single-domained APOBEC3C and double-domained APOBEC3F/G anti-retroviral cytidine deaminases provides insight into their DNA target site specificities. Nucleic Acids Res., 33, 1913-1923.
23. Charneau,P., Alizon,M. and Clavel,F. (1992) A second origin of DNA plus-strand synthesis is required for optimal human immunodeficiency virus replication. J. Virol., 66, 2814-2820.
24. Kupiec,J.J., Tobaly-Tapiero,J., Canivet,M., Santillana-Hayat,M., Flugel,R.M., Peries,J. and Emanoil-Ravier,R. (1988) Evidence for a gapped linear duplex DNA intermediate in the replicative cycle of human and simian spumaviruses. Nucleic Acids Res., 16, 9557-9565.
25. Vartanian,J.P., Henry,M. and Wain-Hobson,S. (2002) Sustained G→A hypermutation during reverse transcription of an entire human immunodeficiency virus type 1 strain Vau group O genome. J. Gen. Virol., 83, 801-805.
26. Martinez,M.A., Vartanian,J.P. and Wain-Hobson,S. (1994) Hypermutagenesis of RNA using human immunodeficiency virus type 1 reverse transcriptase and biased dNTP concentrations. Proc. Natl Acad. Sci. USA, 91, 11787-11791.
27. Benjamin,J., Ganser-Pornillos,B.K., Tivol,W.F., Sundquist,W.I. and Jensen,G.J. (2005) Three-dimensional structure of HIV-1 virus-like particles by electron cryotomography. J. Mol. Biol., 346, 577-588.
28. Tovanabutra,S., Beyrer,C., Sakkhachornphop,S., Razak,M.H., Ramos,G.L., Vongchak,T., Rungruengthanakit,K., Saokhieo,P., Tejafong,K., Kim,B. et al. (2004) The changing molecular epidemiology of HIV type 1 among northern Thai drug users, 1999 to 2002. AIDS Res. Hum. Retroviruses, 20, 465-475.
29. Meyerhans,A., Vartanian,J.P. and Wain-Hobson,S. (1990) DNA recombination during PCR. Nucleic Acids Res., 18, 1687-1691.
30. Wurtzer,S., Goubard,A., Mammano,F., Saragosti,S., Lecossier,D., Hance,A.J. and Clavel,F. (2006) Functional central polypurine tract provides downstream protection of the human immunodeficiency virus type 1 genome from editing by APOBEC3G and APOBEC3B. J. Virol., 80, 3679-3683.
31. Chelico,L., Pham,P., Calabrese,P. and Goodman,M.F. (2006) APOBEC3G DNA deaminase acts processively 3′→5′ on single-stranded DNA. Nature Struct. Mol. Biol., 13, 392-399.
32. Klarmann,G.J., Chen,X., North,T.W. and Preston,B.D. (2003) Incorporation of uracil into minus strand DNA affects the specificity of plus strand synthesis initiation during lentiviral reverse transcription. J. Biol. Chem., 278, 7902-7909.
33. Simon,V., Zennou,V., Murray,D., Huang,Y., Ho,D.D. and Bieniasz,P.D. (2005) Natural variation in Vif: Differential impact on APOBEC3G/3F and a potential role in HIV-1 diversification. PLoS Pathog., 1, e6.