TOOLS AND RESOURCES AirID, a novel proximity biotinylation enzyme, for analysis of protein–protein interactions Kohki Kido1, Satoshi Yamanaka1, Shogo Nakano2, Kou Motani3, Souta Shinohara1, Akira Nozawa1, Hidetaka Kosako3, Sohei Ito2, Tatsuya Sawasaki1* 1Division of Cell-Free Life Science, Proteo-Science Center, Matsuyama, Japan; 2Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan; 3Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan Abstract Proximity biotinylation based on Escherichia coli BirA enzymes such as BioID (BirA*) and TurboID is a key technology for identifying proteins that interact with a target protein in a cell or organism. However, there have been some improvements in the enzymes that are used for that purpose. Here, we demonstrate a novel BirA enzyme, AirID (ancestral BirA for proximity-dependent biotin identification), which was designed de novo using an ancestral enzyme reconstruction algorithm and metagenome data. AirID-fusion proteins such as AirID-p53 or AirID-IkBa indicated biotinylation of MDM2 or RelA, respectively, in vitro and in cells, respectively. AirID-CRBN showed the pomalidomide-dependent biotinylation of IKZF1 and SALL4 in vitro. AirID-CRBN biotinylated the endogenous CUL4 and RBX1 in the CRL4CRBN complex based on the streptavidin pull-down assay. LC-MS/MS analysis of cells that were stably expressing AirID-IkBa showed top-level biotinylation of RelA proteins. These results indicate that AirID is a novel enzyme for analyzing protein–protein interactions. *For correspondence:
[email protected] Introduction Competing interests: The Many cellular proteins function under the control of biological regulatory systems. Protein–protein authors declare that no interactions (PPIs) comprise part of the biological regulation system for proteins.