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. 2009 Dec;83(23):12611-21.
doi: 10.1128/JVI.01491-09. Epub 2009 Sep 23.

Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition

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Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition

"V体育安卓版" Yannick Bulliard et al. J Virol. 2009 Dec.

Abstract

Retroelements are important evolutionary forces but can be deleterious if left uncontrolled. Members of the human APOBEC3 family of cytidine deaminases can inhibit a wide range of endogenous, as well as exogenous, retroelements. These enzymes are structurally organized in one or two domains comprising a zinc-coordinating motif VSports手机版. APOBEC3G contains two such domains, only the C terminal of which is endowed with editing activity, while its N-terminal counterpart binds RNA, promotes homo-oligomerization, and is necessary for packaging into human immunodeficiency virus type 1 (HIV-1) virions. Here, we performed a large-scale mutagenesis-based analysis of the APOBEC3G N terminus, testing mutants for (i) inhibition of vif-defective HIV-1 infection and Alu retrotransposition, (ii) RNA binding, and (iii) oligomerization. Furthermore, in the absence of structural information on this domain, we used homology modeling to examine the positions of functionally important residues and of residues found to be under positive selection by phylogenetic analyses of primate APOBEC3G genes. Our results reveal the importance of a predicted RNA binding dimerization interface both for packaging into HIV-1 virions and inhibition of both HIV-1 infection and Alu transposition. We further found that the HIV-1-blocking activity of APOBEC3G N-terminal mutants defective for packaging can be almost entirely rescued if their virion incorporation is forced by fusion with Vpr, indicating that the corresponding region of APOBEC3G plays little role in other aspects of its action against this pathogen. Interestingly, residues forming the APOBEC3G dimer interface are highly conserved, contrasting with the rapid evolution of two neighboring surface-exposed amino acid patches, one targeted by the Vif protein of primate lentiviruses and the other of yet-undefined function. .

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Figures

FIG. 1.
FIG. 1.
Large-scale mutagenesis of A3G N-terminal domain residues and effects on steady-state levels of the proteins. (A) Amino acid sequence of human A3G positions 1 to 194, with mutated residues analyzed for restriction activity marked with an asterisk. (B) Steady-state levels of wild-type (WT) A3G in HEK293T cells transiently transfected with threefold dilutions of the wild type and the highest dose (1 μg) of mutant plasmid DNA, analyzed by Western blotting using HA-specific antibodies. Mutants with steady-state levels lower by threefold or more than that of the wild type are highlighted in bold. anti-Tub, antitubulin.
FIG. 2.
FIG. 2.
Functional analysis of wild-type (black bars) and mutant A3Gs against Δvif HIV-1 and Alu through single-round assays. (A) Dose-dependent inhibition of Δvif HIV-1 and Alu replication, with A2 serving as negative control, as described in Materials and Methods. Transfection with the Alu reporter in the absence of a LINE-1 helper plasmid (Alu w/o L1; w/o, without) was performed to control the LINE-1 dependency of neomycin resistance. (B to D) Relative restriction activities of stably expressed N-terminal domain mutants (B) and of N-terminal domain mutants with low steady-state levels before (dark gray) or after (light gray) normalization for expression levels (C), all expressed as a percentage of the wild-type activity. (D) Impact of C-terminal domain mutants on Δvif HIV-1 and Alu replication. Means and standard errors are representative of the results for independent duplicates from a single experiment (A and D) or from one to three different experiments (B and C). pCMV5, empty vector; WT, wild type; IU, infectious units; cpm, counts per minute; N.D., not done.
FIG. 3.
FIG. 3.
Small cellular RNA binding abilities of A3G N-terminal mutants. Extracts of HEK293T cells transiently transfected with plasmids expressing HA-tagged forms of A2 and wild-type and mutant A3G were either first immunoprecipitated (IP) with HA-specific antibodies (IP: anti-HA) or directly analyzed (Lysate) by Western blotting (for HA) or semiquantitative RT-PCR with primers specific for indicated small RNAs. Right panel shows results for 10-fold dilutions of human genomic DNA. “No RT” indicates control sample run in the absence of reverse transcriptase enzyme. WB, Western blotting.
FIG. 4.
FIG. 4.
A3G homodimerization is affected by N-terminal domain mutations but not by the presence of Vif C133S. (A) Indicated HA-tagged wild-type A3G and mutants were transiently coexpressed in HEK293T cells along with myc-tagged wild-type A3G (+). Cell lysate (Lysate) and immunoprecipitated material (IP: antimyc) were loaded onto SDS-PAGE gels, followed by Western blot analysis using HA- and myc-specific antibodies. A3G-HA alone served as control for nonspecific binding (first lane). (B) HA-tagged A3A, A3G, and A3G198-384 were cotransfected with A3G-myc (+) in HEK293T cells, and lysates were either directly loaded onto SDS-PAGE gels (Lysate) or used for immunoprecipitation using anti-HA-coated beads (IP: anti-HA). A3G-myc alone served as control for nonspecific binding. (C) Cells transiently expressing wild-type myc- and HA-tagged A3G in the presence or absence of Vif C133S were lysed and used for immunoprecipitation with anti-HA-coated beads. Vif C133S and A3G-myc alone served as controls for nonspecific binding. +, present.
FIG. 5.
FIG. 5.
Encapsidation and antiviral activities of packaging-defective A3G N-terminal domain mutants are rescued by fusion with Vpr14-88. Top, relative infectivity levels of Δvif HIV-1 exposed or not to wild-type or mutant A3G. Infectivity of viruses produced in the absence of A3G was given the arbitrary value of 100. Values represent means and standard errors of the results from independent duplicates. Bottom, Western blot analyses of cellular and viral extracts using HA-, tubulin- (anti-Tub), or p24-specific antibodies. (A) Results with native A3G. (B) Results with Vpr14-88-A3G fusion proteins.
FIG. 6.
FIG. 6.
Homology dimer model of A3G. (A) A3G N-terminal domain model based on homology with the crystal structure of the A3G C terminus. Residues affecting protein steady-state level when mutated are indicated as follows. Magenta, mutants are functionally defective even after normalization for expression levels (Fig. 2C); light blue, mutants are as active as the wild type after normalization for expression levels (Phe21, Glu85, Pro96, Leu108, Leu116, Leu123, Leu138, Met152, Cys160, and Phe164). (B and C) Nitrogen, oxygen, sulfur, and zinc atoms are depicted in blue, red, yellow, and magenta, respectively. (B) Top view of the dimer model, showing two N-terminal domains of A3G (one green and the other blue) in a head-to-head complex, as modeled from the A2 tetramer structure. Zinc-binding residues (His65, Glu67, Cys97, and Cys100) are shown in gray. (C) The predicted dimer interface in detail, with residues important for A3G oligomerization and Δvif/Alu restriction shown in orange. Intersubunit contacts of the aromatic side chains allow the formation of energetically favorable π-π interactions. (D) Space-filling visualization of A3G dimer. As in panel C, the surface of the residues important for oligomerization is depicted in orange. Yellow surfaces correspond to the residues found to be under positive selection in primate A3Gs. The side view evidences the 10-Å groove formed by the two monomers at the dimer interface, as well as the residues under positive selection that are close to the Vif-binding site comprising residues 128 to 130. Thr32 and Asp130 (labeled in white) are two conserved residues that both influence recognition by HIV-1 Vif.
FIG. 7.
FIG. 7.
Alignment of hominid and Old World monkey A3Gs. The alignment shows high conservation in predicted secondary structures deduced from the model (orange and green rectangles), as well as in loops containing the residues involved in restriction activity (orange-dashed boxes), as seen by the results in Fig. 2B. Alignment was performed using MUSCLE (20). Dark blue, >80% homology; blue, >60% homology; light blue, >40% homology; white, <40% homology; PANTR, Pan troglodytes; PANPA, Pan paniscus; GORGO, Gorilla gorilla; PONPY, Pongo pygmaeus; PAPAN, Papio anubis; MACMU, Macaca mulatta; MACNE, Macaca nemestrina; MACNG, Macaca nigra; MACFA, Macaca fascicularis; ERYPA, Erythrocebus patas; CERAE, Cercopithecus aethiops.

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