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The AID/APOBEC family of nucleic acid mutators.

Conticello SG - Genome Biol. (2008)

Bottom Line: The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine.APOBEC1 edits the mRNA for apolipoprotein B, a protein involved in lipid transport.A detailed understanding of the biological roles of the family is still some way off, however, and the functions of some members of the family are completely unknown.

View Article: PubMed Central - HTML - PubMed

Affiliation: Core Research Laboratory, Istituto Toscano Tumori, Florence, Via Cosimo il Vecchio 2, 50139 Firenze, Italy. silvo.conticello@ittumori.it

ABSTRACT
The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine. The ancestral AID/APOBECs originated from a branch of the zinc-dependent deaminase superfamily at the beginning of the vertebrate radiation. Other members of the family have arisen in mammals and present a history of complex gene duplications and positive selection. All AID/APOBECs have a characteristic zinc-coordination motif, which forms the core of the catalytic site. The crystal structure of human APOBEC2 shows remarkable similarities to that of the bacterial tRNA-editing enzyme TadA, which suggests a conserved mechanism by which polynucleotides are recognized and deaminated. The AID/APOBECs seem to have diverse roles. AID and the APOBEC3s are DNA mutators, acting in antigen-driven antibody diversification processes and in an innate defense system against retroviruses, respectively. APOBEC1 edits the mRNA for apolipoprotein B, a protein involved in lipid transport. A detailed understanding of the biological roles of the family is still some way off, however, and the functions of some members of the family are completely unknown. Given their ability to mutate DNA, a role for the AID/APOBECs in the onset of cancer has been proposed.

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Schematic representation of the evolutionary relationships between the AID/APOBECs and the rest of the zinc-dependent deaminases. The only other zinc-dependent deaminase families widely expressed in metazoans and from which the AID/APOBECs (shaded in red) could have originated are the cytidine deaminases (CDA), the dCMP deaminases (DCDT) or the tRNA adenosine deaminases (Tad/ADAT2) (all shown in orange). CDAs and DCDTs act on free pyrimidines in the salvage pathway, the Tad/ADAT2s edit adenosine 34 at the anticodon of various tRNAs to inosine and are essential in bacteria, yeast and metazoans [6]. AID/APOBECs are unlikely to have originated from CDAs because of the differences in gene organization and catalytic domain [7,10]; DCDTs, despite the similar secondary structure, differ substantially from the AID/APOBECs in their substrate (free nucleotides), dependency on Mg and dCTP, and aggregation into homohexamers [108]. Phylogenetic data [10], species representation, and structural/functional features favor the tRNA-editing enzymes as the origin of the AID/APOBECs [7,8], a model supported by the observation that ADAT2 from trypanosomes can deaminate DNA [9]. The tRNAAla adenosine 37 deaminases type 1 (ADAT1) and the mRNA adenosine deaminases 1, 2, and 3 (ADARs) (shaded in green) are thought to have originated from the Tad/ADAT2 family independently of the AID/APOBECs. CoDA, cytosine deaminases; RibD, riboflavin deaminases; GuanineD, guanine deaminases.
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Figure 1: Schematic representation of the evolutionary relationships between the AID/APOBECs and the rest of the zinc-dependent deaminases. The only other zinc-dependent deaminase families widely expressed in metazoans and from which the AID/APOBECs (shaded in red) could have originated are the cytidine deaminases (CDA), the dCMP deaminases (DCDT) or the tRNA adenosine deaminases (Tad/ADAT2) (all shown in orange). CDAs and DCDTs act on free pyrimidines in the salvage pathway, the Tad/ADAT2s edit adenosine 34 at the anticodon of various tRNAs to inosine and are essential in bacteria, yeast and metazoans [6]. AID/APOBECs are unlikely to have originated from CDAs because of the differences in gene organization and catalytic domain [7,10]; DCDTs, despite the similar secondary structure, differ substantially from the AID/APOBECs in their substrate (free nucleotides), dependency on Mg and dCTP, and aggregation into homohexamers [108]. Phylogenetic data [10], species representation, and structural/functional features favor the tRNA-editing enzymes as the origin of the AID/APOBECs [7,8], a model supported by the observation that ADAT2 from trypanosomes can deaminate DNA [9]. The tRNAAla adenosine 37 deaminases type 1 (ADAT1) and the mRNA adenosine deaminases 1, 2, and 3 (ADARs) (shaded in green) are thought to have originated from the Tad/ADAT2 family independently of the AID/APOBECs. CoDA, cytosine deaminases; RibD, riboflavin deaminases; GuanineD, guanine deaminases.

Mentions: All the AID/APOBECs share the structural and catalytic backbone of the zinc-dependent deaminases, a large gene superfamily encoding enzymes involved in the metabolism of purines and pyrimidines (Figure 1). Of these deaminases, the tRNA adenosine deaminases (Tad/ADAT2) edit adenosine to inosine at the anticodon of various tRNAs in both eukaryotes and prokaryotes [6] and are thought to be the group from which the AID/APOBEC family originated (Figure 1). Indeed, as well as having functional and structural similarities to the AID/APOBECs [7,8], ADAT2 from trypanosomes seems to be able to deaminate cytidine in DNA [9].


The AID/APOBEC family of nucleic acid mutators.

Conticello SG - Genome Biol. (2008)

Schematic representation of the evolutionary relationships between the AID/APOBECs and the rest of the zinc-dependent deaminases. The only other zinc-dependent deaminase families widely expressed in metazoans and from which the AID/APOBECs (shaded in red) could have originated are the cytidine deaminases (CDA), the dCMP deaminases (DCDT) or the tRNA adenosine deaminases (Tad/ADAT2) (all shown in orange). CDAs and DCDTs act on free pyrimidines in the salvage pathway, the Tad/ADAT2s edit adenosine 34 at the anticodon of various tRNAs to inosine and are essential in bacteria, yeast and metazoans [6]. AID/APOBECs are unlikely to have originated from CDAs because of the differences in gene organization and catalytic domain [7,10]; DCDTs, despite the similar secondary structure, differ substantially from the AID/APOBECs in their substrate (free nucleotides), dependency on Mg and dCTP, and aggregation into homohexamers [108]. Phylogenetic data [10], species representation, and structural/functional features favor the tRNA-editing enzymes as the origin of the AID/APOBECs [7,8], a model supported by the observation that ADAT2 from trypanosomes can deaminate DNA [9]. The tRNAAla adenosine 37 deaminases type 1 (ADAT1) and the mRNA adenosine deaminases 1, 2, and 3 (ADARs) (shaded in green) are thought to have originated from the Tad/ADAT2 family independently of the AID/APOBECs. CoDA, cytosine deaminases; RibD, riboflavin deaminases; GuanineD, guanine deaminases.
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Related In: Results  -  Collection

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Figure 1: Schematic representation of the evolutionary relationships between the AID/APOBECs and the rest of the zinc-dependent deaminases. The only other zinc-dependent deaminase families widely expressed in metazoans and from which the AID/APOBECs (shaded in red) could have originated are the cytidine deaminases (CDA), the dCMP deaminases (DCDT) or the tRNA adenosine deaminases (Tad/ADAT2) (all shown in orange). CDAs and DCDTs act on free pyrimidines in the salvage pathway, the Tad/ADAT2s edit adenosine 34 at the anticodon of various tRNAs to inosine and are essential in bacteria, yeast and metazoans [6]. AID/APOBECs are unlikely to have originated from CDAs because of the differences in gene organization and catalytic domain [7,10]; DCDTs, despite the similar secondary structure, differ substantially from the AID/APOBECs in their substrate (free nucleotides), dependency on Mg and dCTP, and aggregation into homohexamers [108]. Phylogenetic data [10], species representation, and structural/functional features favor the tRNA-editing enzymes as the origin of the AID/APOBECs [7,8], a model supported by the observation that ADAT2 from trypanosomes can deaminate DNA [9]. The tRNAAla adenosine 37 deaminases type 1 (ADAT1) and the mRNA adenosine deaminases 1, 2, and 3 (ADARs) (shaded in green) are thought to have originated from the Tad/ADAT2 family independently of the AID/APOBECs. CoDA, cytosine deaminases; RibD, riboflavin deaminases; GuanineD, guanine deaminases.
Mentions: All the AID/APOBECs share the structural and catalytic backbone of the zinc-dependent deaminases, a large gene superfamily encoding enzymes involved in the metabolism of purines and pyrimidines (Figure 1). Of these deaminases, the tRNA adenosine deaminases (Tad/ADAT2) edit adenosine to inosine at the anticodon of various tRNAs in both eukaryotes and prokaryotes [6] and are thought to be the group from which the AID/APOBEC family originated (Figure 1). Indeed, as well as having functional and structural similarities to the AID/APOBECs [7,8], ADAT2 from trypanosomes seems to be able to deaminate cytidine in DNA [9].

Bottom Line: The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine.APOBEC1 edits the mRNA for apolipoprotein B, a protein involved in lipid transport.A detailed understanding of the biological roles of the family is still some way off, however, and the functions of some members of the family are completely unknown.

View Article: PubMed Central - HTML - PubMed

Affiliation: Core Research Laboratory, Istituto Toscano Tumori, Florence, Via Cosimo il Vecchio 2, 50139 Firenze, Italy. silvo.conticello@ittumori.it

ABSTRACT
The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine. The ancestral AID/APOBECs originated from a branch of the zinc-dependent deaminase superfamily at the beginning of the vertebrate radiation. Other members of the family have arisen in mammals and present a history of complex gene duplications and positive selection. All AID/APOBECs have a characteristic zinc-coordination motif, which forms the core of the catalytic site. The crystal structure of human APOBEC2 shows remarkable similarities to that of the bacterial tRNA-editing enzyme TadA, which suggests a conserved mechanism by which polynucleotides are recognized and deaminated. The AID/APOBECs seem to have diverse roles. AID and the APOBEC3s are DNA mutators, acting in antigen-driven antibody diversification processes and in an innate defense system against retroviruses, respectively. APOBEC1 edits the mRNA for apolipoprotein B, a protein involved in lipid transport. A detailed understanding of the biological roles of the family is still some way off, however, and the functions of some members of the family are completely unknown. Given their ability to mutate DNA, a role for the AID/APOBECs in the onset of cancer has been proposed.

Show MeSH
Related in: MedlinePlus