메뉴 건너뛰기




Volumn 287, Issue 19, 2012, Pages 15826-15835

Single-stranded DNA scanning and deamination by APOBEC3G cytidine deaminase at single molecule resolution

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE DEAMINASE; IN-VITRO; IN-VIVO; MECHANISTIC STUDIES; MOTIF SEQUENCE; RESONANCE ENERGY TRANSFER; SCANNING TRAJECTORY; SINGLE MOLECULE; SINGLE-MOLECULE RESOLUTION; SINGLE-STRANDED (SS) DNA; SINGLE-STRANDED DNA; SMALL TARGETS;

EID: 84860855710     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M112.342790     Document Type: Article
Times cited : (52)

References (34)
  • 1
    • 10944251591 scopus 로고    scopus 로고
    • Repair and genetic consequences of endogenous DNA base damage in mammalian cells
    • DOI 10.1146/annurev.genet.38.072902.092448
    • Barnes, D. E., and Lindahl, T. (2004) Repair and genetic consequences of endogenousDNAbase damage in mammalian cells. Annu. Rev. Genet. 38, 445-476 (Pubitemid 40013735)
    • (2004) Annual Review of Genetics , vol.38 , pp. 445-476
    • Barnes, D.E.1    Lindahl, T.2
  • 2
    • 77953654163 scopus 로고    scopus 로고
    • Detection of damaged DNA bases by DNA glycosylase enzymes
    • Friedman, J. I., and Stivers, J. T. (2010) Detection of damaged DNA bases by DNA glycosylase enzymes. Biochemistry 49, 4957-4967
    • (2010) Biochemistry , vol.49 , pp. 4957-4967
    • Friedman, J.I.1    Stivers, J.T.2
  • 4
    • 70350463566 scopus 로고    scopus 로고
    • Biochemical basis of immunological and retroviral responses to DNA-targeted cytosine deamination by activation-induced cytidine deaminase and APOBEC3G
    • Chelico, L., Pham, P., Petruska, J., and Goodman, M. F. (2009) Biochemical basis of immunological and retroviral responses to DNA-targeted cytosine deamination by activation-induced cytidine deaminase and APOBEC3G. J. Biol. Chem. 284, 27761-27765
    • (2009) J. Biol. Chem. , vol.284 , pp. 27761-27765
    • Chelico, L.1    Pham, P.2    Petruska, J.3    Goodman, M.F.4
  • 5
    • 0038004471 scopus 로고    scopus 로고
    • The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA
    • DOI 10.1038/nature01707
    • 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 (Pubitemid 36834848)
    • (2003) Nature , vol.424 , Issue.6944 , pp. 94-98
    • Zhang, H.1    Yang, B.2    Pomerantz, R.J.3    Zhang, C.4    Arunachalam, S.C.5    Gao, L.6
  • 7
    • 34249671724 scopus 로고    scopus 로고
    • Virion-associated uracil DNA glycosylase-2 and apurinic/apyrimidinic endonuclease are involved in the degradation of APOBEC3G-edited nascent HIV-1 DNA
    • DOI 10.1074/jbc.M606864200
    • Yang, B., Chen, K., Zhang, C., Huang, S., and Zhang, H. (2007) Virion-associated uracil DNA glycosylase-2 and apurinic/apyrimidinic endonuclease are involved in the degradation of APOBEC3G-edited nascent HIV-1 DNA. J. Biol. Chem. 282, 11667-11675 (Pubitemid 47100658)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.16 , pp. 11667-11675
    • Yang, B.1    Chen, K.2    Zhang, C.3    Huang, S.4    Zhang, H.5
  • 8
    • 33645807371 scopus 로고    scopus 로고
    • A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
    • Blainey, P. C., van Oijen, A. M., Banerjee, A., Verdine, G. L., and Xie, X. S. (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl. Acad. Sci. U.S.A. 103, 5752-5757
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 5752-5757
    • Blainey, P.C.1    Van Oijen, A.M.2    Banerjee, A.3    Verdine, G.L.4    Xie, X.S.5
  • 9
    • 0038681023 scopus 로고    scopus 로고
    • Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts
    • DOI 10.1038/nature01709
    • Mangeat, B., Turelli, P., Caron, G., Friedli, M., Perrin, L., and Trono, D. (2003) Broad antiretroviral defense by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature 424, 99-103 (Pubitemid 36834849)
    • (2003) Nature , vol.424 , Issue.6944 , pp. 99-103
    • Mangeat, B.1    Turelli, P.2    Caron, G.3    Friedli, M.4    Perrin, L.5    Trono, D.6
  • 10
    • 66349132212 scopus 로고    scopus 로고
    • Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance
    • Jern, P., Russell, R. A., Pathak, V. K., and Coffin, J. M. (2009) Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance. PLoS Pathog. 5, e1000367
    • (2009) PLoS Pathog. , vol.5
    • Jern, P.1    Russell, R.A.2    Pathak, V.K.3    Coffin, J.M.4
  • 11
    • 42649120310 scopus 로고    scopus 로고
    • The APOBEC3 cytidine deaminases: An innate defensive network opposing exogenous retroviruses and endogenous retroelements
    • Chiu, Y. L., and Greene, W. C. (2008) The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu. Rev. Immunol. 26, 317-353
    • (2008) Annu. Rev. Immunol. , vol.26 , pp. 317-353
    • Chiu, Y.L.1    Greene, W.C.2
  • 12
    • 13844270834 scopus 로고    scopus 로고
    • Complementary function of the two catalytic domains of APOBEC3G
    • DOI 10.1016/j.virol.2005.01.011
    • Navarro, F., Bollman, B., Chen, H., König, R., Yu, Q., Chiles, K., and Landau, N. R. (2005) Complementary function of the two catalytic domains of APOBEC3G. Virology 333, 374-386 (Pubitemid 40250119)
    • (2005) Virology , vol.333 , Issue.2 , pp. 374-386
    • Navarro, F.1    Bollman, B.2    Chen, H.3    Konig, R.4    Yu, Q.5    Chiles, K.6    Landau, N.R.7
  • 13
    • 15744390742 scopus 로고    scopus 로고
    • The retroviral hypermutation specificity of APOBEC3F and APOBEC3G is governed by the C-terminal DNA cytosine deaminase domain
    • DOI 10.1074/jbc.M500382200
    • Haché, G., Liddament, M. T., and Harris, R. S. (2005) The retroviral hypermutation specificity of APOBEC3F andAPOBEC3Gis governed by the C-terminal DNA cytosine deaminase domain. J. Biol. Chem. 280, 10920-10924 (Pubitemid 40418393)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.12 , pp. 10920-10924
    • Hache, G.1    Liddament, M.T.2    Harris, R.S.3
  • 15
    • 33745067722 scopus 로고    scopus 로고
    • APOBEC3G DNA deaminase acts processively 3′ → 5′ on single-stranded DNA
    • DOI 10.1038/nsmb1086, PII N1086
    • Chelico, L., Pham, P., Calabrese, P., and Goodman, M. F. (2006) APOBEC3G DNA deaminase acts processively 3′→5′ on single-stranded DNA. Nat. Struct. Mol. Biol. 13, 392-399 (Pubitemid 43881578)
    • (2006) Nature Structural and Molecular Biology , vol.13 , Issue.5 , pp. 392-399
    • Chelico, L.1    Pham, P.2    Calabrese, P.3    Goodman, M.F.4
  • 16
    • 46649114007 scopus 로고    scopus 로고
    • A model for oligomeric regulation of APOBEC3G cytosine deaminase-dependent restriction of HIV
    • Chelico, L., Sacho, E. J., Erie, D. A., and Goodman, M. F. (2008) A model for oligomeric regulation of APOBEC3G cytosine deaminase-dependent restriction of HIV. J. Biol. Chem. 283, 13780-13791
    • (2008) J. Biol. Chem. , vol.283 , pp. 13780-13791
    • Chelico, L.1    Sacho, E.J.2    Erie, D.A.3    Goodman, M.F.4
  • 17
    • 33750210516 scopus 로고    scopus 로고
    • Twin gradients in APOBEC3 edited HIV-1 DNA reflect the dynamics of lentiviral replication
    • DOI 10.1093/nar/gkl555
    • Suspène, R., Rusniok, C., Vartanian, J. P., and Wain-Hobson, S. (2006) Twin gradients in APOBEC3-edited HIV-1 DNA reflect the dynamics of lentiviral replication. Nucleic Acids Res. 34, 4677-4684 (Pubitemid 44605614)
    • (2006) Nucleic Acids Research , vol.34 , Issue.17 , pp. 4677-4684
    • Suspene, R.1    Rusniok, C.2    Vartanian, J.-P.3    Wain-Hobson, S.4
  • 18
    • 77952399342 scopus 로고    scopus 로고
    • Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G
    • Chelico, L., Prochnow, C., Erie, D. A., Chen, X. S., and Goodman, M. F. (2010) Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G. J. Biol. Chem. 285, 16195-16205
    • (2010) J. Biol. Chem. , vol.285 , pp. 16195-16205
    • Chelico, L.1    Prochnow, C.2    Erie, D.A.3    Chen, X.S.4    Goodman, M.F.5
  • 19
    • 0037057630 scopus 로고    scopus 로고
    • Initiation and reinitiation of DNA unwinding by the Escherichia coli Rep helicase
    • Ha, T., Rasnik, I., Cheng, W., Babcock, H. P., Gauss, G. H., Lohman, T. M., and Chu, S. (2002) Initiation and reinitiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419, 638-641
    • (2002) Nature , vol.419 , pp. 638-641
    • Ha, T.1    Rasnik, I.2    Cheng, W.3    Babcock, H.P.4    Gauss, G.H.5    Lohman, T.M.6    Chu, S.7
  • 20
    • 77957157863 scopus 로고    scopus 로고
    • Single-molecule FRET of protein-nucleic acid and protein-protein complexes: Surface passivation and immobilization
    • Lamichhane, R., Solem, A., Black, W., and Rueda, D. (2010) Single-molecule FRET of protein-nucleic acid and protein-protein complexes: surface passivation and immobilization. Methods 52, 192-200
    • (2010) Methods , vol.52 , pp. 192-200
    • Lamichhane, R.1    Solem, A.2    Black, W.3    Rueda, D.4
  • 21
    • 70349281455 scopus 로고    scopus 로고
    • RNA folding dynamics by single-molecule fluorescence resonance energy transfer
    • Zhao, R., and Rueda, D. (2009) RNA folding dynamics by single-molecule fluorescence resonance energy transfer. Methods 49, 112-117
    • (2009) Methods , vol.49 , pp. 112-117
    • Zhao, R.1    Rueda, D.2
  • 22
    • 33746747438 scopus 로고    scopus 로고
    • Analysis of single-molecule FRET trajectories using hidden Markov modeling
    • DOI 10.1529/biophysj.106.082487
    • McKinney, S. A., Joo, C., and Ha, T. (2006) Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys. J. 91, 1941-1951 (Pubitemid 44352455)
    • (2006) Biophysical Journal , vol.91 , Issue.5 , pp. 1941-1951
    • McKinney, S.A.1    Joo, C.2    Ha, T.3
  • 23
    • 79960145089 scopus 로고    scopus 로고
    • Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity
    • Pham, P., Calabrese, P., Park, S. J., and Goodman, M. F. (2011) Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity. J. Biol. Chem. 286, 24931-24942
    • (2011) J. Biol. Chem. , vol.286 , pp. 24931-24942
    • Pham, P.1    Calabrese, P.2    Park, S.J.3    Goodman, M.F.4
  • 24
    • 0037926476 scopus 로고    scopus 로고
    • Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation
    • DOI 10.1038/nature01760
    • Pham, P., Bransteitter, R., Petruska, J., and Goodman, M. F. (2003) Processive AID-catalyzed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 424, 103-107 (Pubitemid 36834850)
    • (2003) Nature , vol.424 , Issue.6944 , pp. 103-107
    • Pham, P.1    Bransteitter, R.2    Petruska, J.3    Goodman, M.F.4
  • 25
    • 10944223445 scopus 로고    scopus 로고
    • Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase
    • DOI 10.1074/jbc.M408135200
    • Bransteitter, R., Pham, P., Calabrese, P., and Goodman, M. F. (2004) Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase. J. Biol. Chem. 279, 51612-51621 (Pubitemid 40017912)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.49 , pp. 51612-51621
    • Bransteitter, R.1    Pham, P.2    Calabrese, P.3    Goodman, M.F.4
  • 28
    • 79953853888 scopus 로고    scopus 로고
    • Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis
    • Torella, J. P., Holden, S. J., Santoso, Y., Hohlbein, J., and Kapanidis, A. N. (2011) Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis. Biophys. J. 100, 1568-1577
    • (2011) Biophys. J. , vol.100 , pp. 1568-1577
    • Torella, J.P.1    Holden, S.J.2    Santoso, Y.3    Hohlbein, J.4    Kapanidis, A.N.5
  • 29
    • 0028963346 scopus 로고
    • Enthalpy-entropy compensation in DNA melting thermodynamics
    • Petruska, J., and Goodman, M. F. (1995) Enthalpy-entropy compensation in DNA melting thermodynamics. J. Biol. Chem. 270, 746-750
    • (1995) J. Biol. Chem. , vol.270 , pp. 746-750
    • Petruska, J.1    Goodman, M.F.2
  • 30
    • 0029929717 scopus 로고    scopus 로고
    • Archaebacterial DNA polymerases tightly bind uracil-containing DNA
    • DOI 10.1074/jbc.271.30.17692
    • Lasken, R. S., Schuster, D. M., and Rashtchian, A. (1996) Archaebacterial DNA polymerases tightly bind uracil-containing DNA. J. Biol. Chem. 271, 17692-17696 (Pubitemid 26250739)
    • (1996) Journal of Biological Chemistry , vol.271 , Issue.30 , pp. 17692-17696
    • Lasken, R.S.1    Schuster, D.M.2    Rashtchian, A.3
  • 31
    • 0036894880 scopus 로고    scopus 로고
    • Structural basis for uracil recognition by archaeal family B DNA polymerases
    • DOI 10.1038/nsb867
    • Fogg, M. J., Pearl, L. H., and Connolly, B. A. (2002) Structural basis for uracil recognition by archaeal family B DNA polymerases. Nat. Struct. Biol. 9, 922-927 (Pubitemid 35417061)
    • (2002) Nature Structural Biology , vol.9 , Issue.12 , pp. 922-927
    • Fogg, M.J.1    Pearl, L.H.2    Connolly, B.A.3
  • 32
    • 3042579602 scopus 로고    scopus 로고
    • How do site-specific DNA-binding proteins find their targets?
    • DOI 10.1093/nar/gkh624
    • Halford, S. E., and Marko, J. F. (2004) How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32, 3040-3052 (Pubitemid 39022995)
    • (2004) Nucleic Acids Research , vol.32 , Issue.10 , pp. 3040-3052
    • Halford, S.E.1    Marko, J.F.2
  • 33
    • 35649018595 scopus 로고    scopus 로고
    • Dynamic Basis for One-Dimensional DNA Scanning by the Mismatch Repair Complex Msh2-Msh6
    • DOI 10.1016/j.molcel.2007.09.008, PII S1097276507006181
    • Gorman, J., Chowdhury, A., Surtees, J. A., Shimada, J., Reichman, D. R., Alani, E., and Greene, E. C. (2007) Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol. Cell 28, 359-370 (Pubitemid 350030566)
    • (2007) Molecular Cell , vol.28 , Issue.3 , pp. 359-370
    • Gorman, J.1    Chowdhury, A.2    Surtees, J.A.3    Shimada, J.4    Reichman, D.R.5    Alani, E.6    Greene, E.C.7
  • 34
    • 53549107186 scopus 로고    scopus 로고
    • Hypermutation by intersegmental transfer of APOBEC3G cytidine deaminase
    • Nowarski, R., Britan-Rosich, E., Shiloach, T., and Kotler, M. (2008) Hypermutation by intersegmental transfer of APOBEC3G cytidine deaminase. Nat. Struct. Mol. Biol. 15, 1059-1066
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 1059-1066
    • Nowarski, R.1    Britan-Rosich, E.2    Shiloach, T.3    Kotler, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.