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Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins.

Jónsson SR, Haché G, Stenglein MD, Fahrenkrug SC, Andrésdóttir V, Harris RS - Nucleic Acids Res. (2006)

Bottom Line: Retrovirus restriction is attributable to deaminase-dependent and -independent mechanisms, as deaminase-defective mutants retain significant anti-retroviral activity.These data indicate that DNA cytosine deamination; sub-cellular localization and retrovirus restriction activities are conserved in mammals, whereas active site location, local mutational preferences and Vif susceptibility are not.Together, these studies indicate that some properties of the mammal-specific, APOBEC3-dependent retroelement restriction system are necessary and conserved, but others are simultaneously modular and highly adaptable.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.

ABSTRACT
The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls: cattle, pigs and sheep. Like their human counterparts, APOBEC3F and APOBEC3G, the artiodactyl APOBEC3F proteins are DNA cytosine deaminases that locate predominantly to the cytosol and can inhibit the replication of HIV-1 and MLV. Retrovirus restriction is attributable to deaminase-dependent and -independent mechanisms, as deaminase-defective mutants retain significant anti-retroviral activity. However, unlike human APOBEC3F and APOBEC3G, the artiodactyl APOBEC3F proteins have an active N-terminal DNA cytosine deaminase domain, which elicits a broader dinucleotide deamination preference, and they are resistant to HIV-1 Vif. These data indicate that DNA cytosine deamination; sub-cellular localization and retrovirus restriction activities are conserved in mammals, whereas active site location, local mutational preferences and Vif susceptibility are not. Together, these studies indicate that some properties of the mammal-specific, APOBEC3-dependent retroelement restriction system are necessary and conserved, but others are simultaneously modular and highly adaptable.

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A comparison of artiodactyl A3F proteins. (A) A schematic of HsA3F, BtA3F, OaA3F and SsA3F. The conserved, zinc-binding deaminase domains are boxed (*) and those that are catalytically active are additionally shaded. The numbers on the right indicate the total polypeptide length. (B) HsA3F, BtA3F, OaA3F and SsA3F active site amino acid alignments [shaded regions from (A)]. The conserved HXE and PCXXC motifs are boxed. Amino acid positions are indicated on the right. (C) A neighbor-joining phylogenetic tree indicating the evolutionary relationship of several representative mammlian A3 family members. Branch lengths are proportional to the number of amino acid differences. Comparisons were done using the conserved Z domain amino acids, plus five additional residues on either side. The Z1a, Z1b and Z2 phylogenetic clusters are indicated. HsA3D and HsA3E represent the N- and C-terminal domains of HsA3DE. See the text for additional details. Bt, B.taurus (cow); Cf, Canis familiaris (dog); Hs, H.sapiens (human); Oa, O.aries (sheep); Pt, Pan troglodytes (chimpanzee); Rn, Rattus norvegicus (rat); Ss, S.scrofa (pig).
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fig1: A comparison of artiodactyl A3F proteins. (A) A schematic of HsA3F, BtA3F, OaA3F and SsA3F. The conserved, zinc-binding deaminase domains are boxed (*) and those that are catalytically active are additionally shaded. The numbers on the right indicate the total polypeptide length. (B) HsA3F, BtA3F, OaA3F and SsA3F active site amino acid alignments [shaded regions from (A)]. The conserved HXE and PCXXC motifs are boxed. Amino acid positions are indicated on the right. (C) A neighbor-joining phylogenetic tree indicating the evolutionary relationship of several representative mammlian A3 family members. Branch lengths are proportional to the number of amino acid differences. Comparisons were done using the conserved Z domain amino acids, plus five additional residues on either side. The Z1a, Z1b and Z2 phylogenetic clusters are indicated. HsA3D and HsA3E represent the N- and C-terminal domains of HsA3DE. See the text for additional details. Bt, B.taurus (cow); Cf, Canis familiaris (dog); Hs, H.sapiens (human); Oa, O.aries (sheep); Pt, Pan troglodytes (chimpanzee); Rn, Rattus norvegicus (rat); Ss, S.scrofa (pig).

Mentions: All known A3 proteins have either one or two conserved, zinc-binding deaminase domains, consisting of amino acids HXE-X23–28-PCX2–4C (X can be any amino acid) (2,5–7). The histidine and the two cysteines coordinate zinc and the glutamate participates directly in the C→U deamination reaction. NCBI BLAST searches using the human and mouse A3 deaminase domains as query polypeptides revealed several artiodactyl ESTs, which suggested the presence of at least one A3 protein in cattle and pigs. Corresponding cDNA clones were obtained, sequenced and shown to encode A3 proteins with two putative zinc-binding, cytosine deaminase domains (Figure 1A and Supplementary Figures S1 and S2; Materials and Methods). The orthologous sheep double domain A3 cDNA sequence was obtained using a combination of degenerate PCR and RACE (Figure 1A and Supplementary Figures S1 and S2). All three of these A3 proteins were similar in size to the 373 amino acid HsA3F protein, except the pig A3 protein, which was slightly longer due to a unique C-terminal, serine-rich extension (Figure 1A and Supplementary Figures S1 and S2).


Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins.

Jónsson SR, Haché G, Stenglein MD, Fahrenkrug SC, Andrésdóttir V, Harris RS - Nucleic Acids Res. (2006)

A comparison of artiodactyl A3F proteins. (A) A schematic of HsA3F, BtA3F, OaA3F and SsA3F. The conserved, zinc-binding deaminase domains are boxed (*) and those that are catalytically active are additionally shaded. The numbers on the right indicate the total polypeptide length. (B) HsA3F, BtA3F, OaA3F and SsA3F active site amino acid alignments [shaded regions from (A)]. The conserved HXE and PCXXC motifs are boxed. Amino acid positions are indicated on the right. (C) A neighbor-joining phylogenetic tree indicating the evolutionary relationship of several representative mammlian A3 family members. Branch lengths are proportional to the number of amino acid differences. Comparisons were done using the conserved Z domain amino acids, plus five additional residues on either side. The Z1a, Z1b and Z2 phylogenetic clusters are indicated. HsA3D and HsA3E represent the N- and C-terminal domains of HsA3DE. See the text for additional details. Bt, B.taurus (cow); Cf, Canis familiaris (dog); Hs, H.sapiens (human); Oa, O.aries (sheep); Pt, Pan troglodytes (chimpanzee); Rn, Rattus norvegicus (rat); Ss, S.scrofa (pig).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC1636497&req=5

fig1: A comparison of artiodactyl A3F proteins. (A) A schematic of HsA3F, BtA3F, OaA3F and SsA3F. The conserved, zinc-binding deaminase domains are boxed (*) and those that are catalytically active are additionally shaded. The numbers on the right indicate the total polypeptide length. (B) HsA3F, BtA3F, OaA3F and SsA3F active site amino acid alignments [shaded regions from (A)]. The conserved HXE and PCXXC motifs are boxed. Amino acid positions are indicated on the right. (C) A neighbor-joining phylogenetic tree indicating the evolutionary relationship of several representative mammlian A3 family members. Branch lengths are proportional to the number of amino acid differences. Comparisons were done using the conserved Z domain amino acids, plus five additional residues on either side. The Z1a, Z1b and Z2 phylogenetic clusters are indicated. HsA3D and HsA3E represent the N- and C-terminal domains of HsA3DE. See the text for additional details. Bt, B.taurus (cow); Cf, Canis familiaris (dog); Hs, H.sapiens (human); Oa, O.aries (sheep); Pt, Pan troglodytes (chimpanzee); Rn, Rattus norvegicus (rat); Ss, S.scrofa (pig).
Mentions: All known A3 proteins have either one or two conserved, zinc-binding deaminase domains, consisting of amino acids HXE-X23–28-PCX2–4C (X can be any amino acid) (2,5–7). The histidine and the two cysteines coordinate zinc and the glutamate participates directly in the C→U deamination reaction. NCBI BLAST searches using the human and mouse A3 deaminase domains as query polypeptides revealed several artiodactyl ESTs, which suggested the presence of at least one A3 protein in cattle and pigs. Corresponding cDNA clones were obtained, sequenced and shown to encode A3 proteins with two putative zinc-binding, cytosine deaminase domains (Figure 1A and Supplementary Figures S1 and S2; Materials and Methods). The orthologous sheep double domain A3 cDNA sequence was obtained using a combination of degenerate PCR and RACE (Figure 1A and Supplementary Figures S1 and S2). All three of these A3 proteins were similar in size to the 373 amino acid HsA3F protein, except the pig A3 protein, which was slightly longer due to a unique C-terminal, serine-rich extension (Figure 1A and Supplementary Figures S1 and S2).

Bottom Line: Retrovirus restriction is attributable to deaminase-dependent and -independent mechanisms, as deaminase-defective mutants retain significant anti-retroviral activity.These data indicate that DNA cytosine deamination; sub-cellular localization and retrovirus restriction activities are conserved in mammals, whereas active site location, local mutational preferences and Vif susceptibility are not.Together, these studies indicate that some properties of the mammal-specific, APOBEC3-dependent retroelement restriction system are necessary and conserved, but others are simultaneously modular and highly adaptable.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.

ABSTRACT
The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls: cattle, pigs and sheep. Like their human counterparts, APOBEC3F and APOBEC3G, the artiodactyl APOBEC3F proteins are DNA cytosine deaminases that locate predominantly to the cytosol and can inhibit the replication of HIV-1 and MLV. Retrovirus restriction is attributable to deaminase-dependent and -independent mechanisms, as deaminase-defective mutants retain significant anti-retroviral activity. However, unlike human APOBEC3F and APOBEC3G, the artiodactyl APOBEC3F proteins have an active N-terminal DNA cytosine deaminase domain, which elicits a broader dinucleotide deamination preference, and they are resistant to HIV-1 Vif. These data indicate that DNA cytosine deamination; sub-cellular localization and retrovirus restriction activities are conserved in mammals, whereas active site location, local mutational preferences and Vif susceptibility are not. Together, these studies indicate that some properties of the mammal-specific, APOBEC3-dependent retroelement restriction system are necessary and conserved, but others are simultaneously modular and highly adaptable.

Show MeSH
Related in: MedlinePlus