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Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome

Nature Structural & Molecular Biology volume 11, pages 435–442 (2004)Cite this article

Abstract

HIV-1 deleted for the vif accessory gene encapsidates the cellular cytidine deaminase APOBEC3G. Upon infection, the encapsidated APOBEC3G induces G→A mutations in the viral reverse transcripts. The G→A mutations result either from C→U deamination of the minus strand or deamination of both strands followed by repair of the plus strand. We report here that minus-strand deamination occurred over the length of the virus genome, preferentially at CCCA sequences, with a graded frequency in the 5′→3′ direction. APOBEC3G induced previously undetected C→T mutations in the 5′ U3 and the primer-binding site, both of which become transiently single-stranded during reverse transcription. In vitro, APOBEC3G bound and deaminated single-stranded DNA (ssDNA) but not double-stranded DNA (dsDNA) or DNA-RNA hybrids. We propose that the requirement for ssDNA accounts for the minus-strand mutations, the 5′→3′ graded frequency of deamination and the rare C→T mutations.

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Figure 1: Graded frequency of G→A mutations induced by APOBEC3G.
Figure 2: Target sequence preference of APOBEC3G.
Figure 3: Analysis of integrated proviruses generated by Δvif APOBEC3G+ viruses.
Figure 4: Human APOBEC3G deaminates and binds ssDNA.
Figure 5: Proposed mechanism of APOBEC3G-mediated deamination of HIV reverse transcripts.

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Acknowledgements

We thank D. Chen, R. Mariani and B. Schröfelbauer for laboratory assistance. This work was funded by the US National Institutes of Health (AI058864, DA014494, AI27670, AI38858, AI43638, AI36214 and AI29164), the Universitywide AIDS Research Program of California (IS02-SI-704 and F03-SIBS-215), the Elizabeth Glaser Pediatric AIDS Foundation (EGPAF 28-PF-77491) and the Research Center for AIDS and HIV Infection of the San Diego Veterans Affairs Healthcare System. N.R.L. is an Elizabeth Glaser Scientist of the Pediatric AIDS Foundation.

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Authors and Affiliations

  1. Infectious Disease Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, 92037, California, USA

    Qin Yu, Renate König, Kristopher Chiles & Nathaniel R Landau

  2. Division of Biological Sciences, University of California, San Diego, La Jolla, 92093-0679, California, USA

    Satish Pillai

  3. HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, 21702, Maryland, USA

    Mary Kearney, Sarah Palmer & John M Coffin

  4. Departments of Pathology and Medicine, University of California, San Diego, La Jolla, 92093-0679, California, USA

    Douglas Richman

  5. Veterans Administration, San Diego Healthcare System, San Diego, 92161, California, USA

    Douglas Richman

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Correspondence to Nathaniel R Landau.

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Yu, Q., König, R., Pillai, S. et al. Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol 11, 435–442 (2004). https://doi.org/10.1038/nsmb758

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