AirID, a novel proximity biotinylation enzyme, for analysis of protein-protein interactions

Elife. 2020 May 11;9:e54983. doi: 10.7554/eLife.54983.

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-IκBα 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-IκBα showed top-level biotinylation of RelA proteins. These results indicate that AirID is a novel enzyme for analyzing protein-protein interactions.

Keywords: A. thaliana; BioID; ancestral sequence reconstruction; biochemistry; cell biology; cell-free; chemical biology; enzymatic engineering; human; protein-protein interaction; proximity labeling.

Plain Language Summary

Proteins in a cell need to interact with each other to perform the many tasks required for organisms to thrive. A technique called proximity biotinylation helps scientists to pinpoint the identity of the proteins that partner together. It relies on attaching an enzyme (either BioID or TurboID) to a protein of interest; when a partner protein comes in close contact with this construct, the enzyme can attach a chemical tag called biotin to it. The tagged proteins can then be identified, revealing which molecules interact with the protein of interest. Although BioID and TurboID are useful tools, they have some limitations. Experiments using BioID take more than 16 hours to complete and require high levels of biotin to be added to the cells. TurboID is more active than BioID and is able to label proteins within ten minutes. However, under certain conditions, it is also more likely to be toxic for the cell, or to make mistakes and tag proteins that do not interact with the protein of interest. To address these issues, Kido et al. developed AirID, a new enzyme for proximity biotinylation. Experiments were then conducted to test how well AirID would perform, using proteins of interest whose partners were already known. These confirm that AirID was able to label partner proteins in human cells; compared with TurboID, it was also less likely to mistakenly tag non-partners or to kill the cells, even over long periods. The results by Kido et al. demonstrate that AirID is suitable for proximity biotinylation experiments in cells. Unlike BioID and TurboID, the enzyme may also have the potential to be used for long-lasting experiments in living organisms, since it is less toxic for cells over time.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biotin / chemistry
  • Biotin / metabolism
  • Biotinylation
  • Carbon-Nitrogen Ligases / chemistry*
  • Carbon-Nitrogen Ligases / genetics
  • Cell Survival
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • HEK293 Cells
  • Humans
  • Mutation
  • Protein Engineering*
  • Protein Interaction Mapping
  • Protein Interaction Maps
  • Recombinant Fusion Proteins / chemistry*
  • Recombinant Fusion Proteins / genetics
  • Repressor Proteins / chemistry*
  • Repressor Proteins / genetics

Substances

  • Escherichia coli Proteins
  • Recombinant Fusion Proteins
  • Repressor Proteins
  • Biotin
  • Carbon-Nitrogen Ligases
  • birA protein, E coli