MBE Advance Access published online on October 20, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi026
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
* To whom correspondence should be addressed. The AID/APOBEC family (comprising AID, APOBEC1, APOBEC2 and APOBEC3 subgroups) contains members that can deaminate cytidine in RNA and/or DNA and exhibit diverse physiological functions (AID and APOBEC3 deaminating DNA to trigger pathways in adaptive and innate immunity; APOBEC1 mediating apolipoprotein B RNA editing). The founder member APOBEC1, which has been used as a paradigm, is an RNA-editing enzyme with proposed antecedents in yeast. Here we have undertaken phylogenetic analysis in order to glean insight into the primary physiological function of the AID/APOBEC family. We find that whilst the family forms part of a larger superfamily of deaminases distributed throughout the biological world, the AID/APOBEC family itself is restricted to vertebrates with homologues of AID (a DNA deaminase that triggers antibody gene diversification) and of APOBEC2 (unknown function) identifiable in sequence databases from bony fish, birds, amphibians and mammals. The cloning of an AID homologue from dogfish reveals that AID extends at least as far back as cartilaginous fish. Like mammalian AID, the pufferfish AID homologue can trigger deoxycytidine deamination in DNA but, consistent with its coldblooded origin, is thermolabile. The fine specificity of its mutator activity and the biased codon usage in pufferfish IgV genes appear broadly similar to that of their mammalian counterparts, consistent with a co-evolution of the antibody mutator and its substrate for the optimal targeting of somatic mutation during antibody maturation. By contrast, APOBEC1 and APOBEC3 are later evolutionary arrivals with orthologues not found in pufferfish (although synteny with mammals is maintained in respect of the flanking loci). We conclude that AID and APOBEC2 are likely to be the ancestral members of the AID/APOBEC family (going back to the beginning of vertebrate speciation) with APOBEC1 and APOBEC3 both being mammal-specific derivatives of AID, with a complex set of domain shuffling underpinning the expansion and evolution of the primate APOBEC3s. *These two authors made equal contributions
Research Article
Evolution of the AID/APOBEC Family of Polynucleotide (Deoxy)Cytidine Deaminases
Silvestro G. Conticello, E-mail: silvoc{at}mrc-lmb.cam.ac.uk
Abstract
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