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

Suspène, Rodolphe; Rusniok, Christophe; Vartanian, Jean‐Pierre; Wain‐Hobson, Simon

doi:10.1093/nar/gkl555

Cited by 105 publications

(138 citation statements)

References 34 publications

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“…The features of processivity and polarity are determined by the CD1 domain of the monomer, thus revealing the overriding importance of the non-catalytic CD1 in the spatial properties of deamination and in imposing an asymmetric catalytic constraint on full-length Apo3G. These properties are responsible for generating 3Ј35Ј deamination gradients on ssDNA in vitro, which correspond to mutational gradients in HIV RNA observed in vivo (16,22,23,51).…”

Section: Discussionmentioning

confidence: 98%

Structural Model for Deoxycytidine Deamination Mechanisms of the HIV-1 Inactivation Enzyme APOBEC3G

Chelico

Prochnow

Erie

et al. 2010

Journal of Biological Chemistry

108

244

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APOBEC3G (Apo3G) is a single-stranded DNA-dependent deoxycytidine deaminase, which, in the absence of the human immunodeficiency virus (HIV) viral infectivity factor, is encapsulated into HIV virions. Subsequently, Apo3G triggers viral inactivation by processively deaminating C3 U, with 335 polarity, on nascent minus-strand cDNA. Apo3G has a catalytically inactive N-terminal CD1 domain and an active C-terminal CD2 domain. Apo3G exists as monomers, dimers, tetramers, and higher order oligomers whose distributions depend on DNA substrate and salt. Here we use multiangle light scattering and atomic force microscopy to identify oligomerization states of Apo3G. A double mutant (F126A/W127A), designed to disrupt dimerization at the predicted CD1-CD1 dimer interface, predominantly converts Apo3G to a monomer that binds singlestranded DNA, Alu RNA, and catalyzes processive C3 U deaminations with 335 deamination polarity, similar to native Apo3G. The CD1 domain is essential for both processivity and polarity. We propose a structure-based model to explain the scanning and catalytic behavior of Apo3G.

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Section: Discussionmentioning

confidence: 98%

Structural Model for Deoxycytidine Deamination Mechanisms of the HIV-1 Inactivation Enzyme APOBEC3G

Chelico

Prochnow

Erie

et al. 2010

Journal of Biological Chemistry

108

244

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“…4, A, B, E, and F) suggest that in vivo A3G has the potential to catalyze sizable numbers of processive deaminations on (Ϫ)-cDNA within the limited time that it is single-stranded. Notably, in vivo data reveal twin 5Ј 3 3Ј G to A mutational gradients of the HIV-1 genome, which means that deaminations are increasing toward the 5Ј-end of the (Ϫ)-cDNA in two regions marked by reverse transcription primer sites on the (Ϫ)-cDNA (17,18). It has been suggested that the mutational gradients are attributable to the temporal effects of reverse transcription acting in combination with RNase H, so that regions that remain singlestranded over the longest time frame are most susceptible to A3G-catalyzed deaminations (17,18).…”

Section: Discussionmentioning

confidence: 99%

“…Directional deamination is an intrinsic property of A3G, occurring in the absence of an obvious source of energy (e.g. ATP or GTP) (15) and can in principle contribute to the HIV-1 G 3 A mutational bias, increasing in a 3Ј-direction in the RNA genome (17,18). A3G processivity appears consistent with a three-dimensional facilitated diffusion process involving sliding and jumping motions along the DNA (15), where jumping involves microscopic dissociation and reassociation events occurring with the same DNA molecule, rather than diffusion into the surrounding bulk solution (19 -21).…”

Section: Apobec3g (A3g) Restricts Hiv-1 Infection By Catalyzingmentioning

confidence: 99%

A Model for Oligomeric Regulation of APOBEC3G Cytosine Deaminase-dependent Restriction of HIV

Chelico

Sacho

Erie

et al. 2008

Journal of Biological Chemistry

218

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APOBEC3G (A3G) restricts HIV-1 infection by catalyzingprocessive C 3 U deaminations on single-stranded DNA (ssDNA) with marked 3 3 5 deamination polarity. Here we show that A3G exists in oligomeric states whose composition is dictated primarily by interactions with DNA, with salt playing an important, yet secondary, role. Directional deaminations correlate with the presence of dimers, tetramers, and larger oligomers observed by atomic force microscopy, and random deaminations appear to correlate mainly with monomers. The presence of a 30-nt weakly deaminated "dead" zone located at the 3-ssDNA end implies the presence of a preferred asymmetric direction for A3G catalysis. Single turnover reaction rates reveal a salt-dependent inhibition of C deamination toward the 3-ssDNA region, offering a molecular basis underlying A3G deamination polarity. Presteady state analysis demonstrates rapid diffusionlimited A3G-ssDNA binding, a slower salt-dependent conformational change, possibly indicative of DNA wrapping, and long (5-15 min) protein-DNA complex lifetimes. We suggest that diverse A3G oligomerization modes contribute to the human immunodeficiency virus, type 1, proviral DNA mutational bias.In 2002, Sheehy et al.(1) determined that APOBEC3G (A3G), originally called CEM15, a proposed cytidine deaminase based on sequence analysis, is the nonpermissive host factor that blocks virion infectivity factor-defective (⌬vif) HIV-1 infection of T cells. The experimental determination that CEM15 was a cytidine deaminase belonging to the APOBEC family followed soon after with experiments demonstrating G 3 A-induced hypermutation of proviral DNA in a ⌬vif HIV-1 virion (2, 3). A3G has a duplicated deaminase domain structure, but only the C-terminal domain is responsible for the single-stranded DNA (ssDNA) 2 deamination activity (4, 5).Apart from A3G-catalyzed deamination, A3G may also have the capacity for blocking reverse transcription, (ϩ)-DNA synthesis, and provirus formation either by interacting with RNA or DNA of HIV-1 (6 -8) or by possibly interacting with HIV-1 proteins (9, 10). However, these noncatalytic effects on HIV inhibition may be attributable to the overexpression of A3G and may not be occurring during normal infection (11-13).It is important to bear in mind that any actions of A3G on DNA, catalytic and possibly noncatalytic, are balanced in vivo against cellular RNA binding, which forms a high molecular mass A3G-RNA complex, which may prevent A3G incorporation into virions (7, 14 -16), and against HIV RNA binding, which forms an intravirion A3G complex in which A3G must be activated by HIV RNase H for DNA deamination to ensue (16).We have shown that A3G-catalyzed deamination occurs processively while exhibiting a 3Ј 3 5Ј polarity favoring deamination toward the 5Ј-region of ssDNA (15). Directional deamination is an intrinsic property of A3G, occurring in the absence of an obvious source of energy (e.g. ATP or GTP) (15) and can in principle contribute to the HIV-1 G 3 A mutational bias, increasing in a 3Ј-direction ...

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“…The env region was chosen for analyses because several studies have confirmed that A3 exhibits a pronounced 59 to 39 editing gradient, resulting in a particular susceptibility to A3 cytidine deaminase activity (38,39). Sixty different clones were sequenced, and the total numbers of bp investigated were 51,000.…”

Section: Peg Ifn-a2b Induces G-to-a Hypermutation In Mddcs Infected Wmentioning

confidence: 99%

IFN-α Induces APOBEC3G, F, and A in Immature Dendritic Cells and Limits HIV-1 Spread to CD4+ T Cells

Mohanram

Sköld

Bächle

et al. 2013

The Journal of Immunology

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Cytokines and IFNs, such as TNF-α and IFN-α, upregulate costimulatory molecules in monocyte-derived dendritic cells (MDDCs), enabling effective Ag presentation to T cells. This activation of MDDCs is often accompanied by upregulation of apolipoprotein B mRNA–editing, enzyme-catalytic, polypeptide-like 3 (APOBEC3) (A3) family proteins that are able to restrict HIV-1 replication in MDDCs by inducing hypermutations in the viral genome. In this study, we show that TNF-α upregulates costimulatory molecules and are able to restrict HIV-1BaL replication in MDDCs without significant induction of A3G, A3A, or A3F. Conversely, low quantities of IFN-α failed to upregulate costimulatory molecules, did not induce IL-12p40 or migration, but significantly induced A3G, A3A, and A3F mRNA expression and restricted viral replication in MDDCs. We also showed that transmission of HIV-1 from MDDCs to autologous T cells was significantly reduced in the presence of IFN-α. Sequence analyses detected the induction of high frequency of G-to-A hypermutations in the env genes from HIV-1BaL–infected MDDCs treated with low quantities of IFN-α2b. These findings show that low quantities of IFN-α can induce functional A3 family proteins and restrict HIV-1 replication in MDDCs while keeping an immature nonmigratory phenotype, supporting further investigations of modalities that enhance retroviral restriction factors. In addition, the findings highlight the role of IFN-α as a double-edged sword in HIV-1 infection, and we show that IFN-α can be powerful in reducing HIV-1 infection both in MDDCs and T cells.

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

Cited by 105 publications

References 34 publications

Structural Model for Deoxycytidine Deamination Mechanisms of the HIV-1 Inactivation Enzyme APOBEC3G

Structural Model for Deoxycytidine Deamination Mechanisms of the HIV-1 Inactivation Enzyme APOBEC3G

A Model for Oligomeric Regulation of APOBEC3G Cytosine Deaminase-dependent Restriction of HIV

IFN-α Induces APOBEC3G, F, and A in Immature Dendritic Cells and Limits HIV-1 Spread to CD4+ T Cells

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