The Molecular Basis of AID/APOBEC Deaminase Target Selection
AID/APOBEC cytosine deaminases play critical roles in adaptive and innate immunity. AID enzymes target cytosines in host immunoglobin locus genes to initiate class-switch recombination and somatic hypermutation, both of which contribute to antibody diversity. Of the APOBEC family, APOBEC1 targets the mRNA of the ApoB protein transcript to create a truncated protein involved in lipid transport, while APOBEC3 members contribute to innate immunity by targeting retroviruses and retroelements. These deaminases have several promising biotechnological applications, such as pairing with CRISPR systems to achieve more targeted base editing. However, AID/APOBECs have also been associated with pathogenic phenotypes and may play a role in tumor development.
This project’s objectives are to (1) synthesize existing knowledge on the biochemical basis of AID/APOBEC substrate selectivity and (2) decipher how this knowledge can be leveraged to improve biotechnological applications, such as genomic base editors. To do so, we will begin with deamination activity on the target cytosine, focusing on the impact of its structural analogues adenine and zebularine, the relevance of epigenetic modifications at the C5 position, and the identity of the nucleotide sugar. Since the binding of substrate to deaminase implicates more than just the target cytosine, we will then analyze the influence of surrounding nucleotides on deaminase sequence preferences, as well as the influence of the secondary structures in which these nucleotides are found.