Specific and Unbiased Detection of Polyubiquitination via a Sensitive Non-Antibody Approach

Anal Chem. 2020 Jan 7;92(1):1074-1080. doi: 10.1021/acs.analchem.9b04092. Epub 2019 Dec 10.

Abstract

Polyubiquitination encompasses complex topologies through various linkage types to deliver diverse cellular signals, which has been recognized as a sophisticated ubiquitin code. Accurate comparison of polyubiquitination signals is critical for revealing the dynamic cellular ubiquitination-regulated events. Western blotting (WB) is the most widely used biochemical method to quantify proteins and posttranslational modifications under diverse physiological conditions. The accuracy and sensitivity of the WB mainly depend on the quality and specificity of the antibody. In this study, we found that the antiubiquitin antibodies exhibited different affinities to the eight linkage types of ubiquitin chains, with the highest sensitivity for the K63-linked chain, lower efficiency for M1 and K48, and very low affinity for the other types of chains. Herein, we introduced the tandem hybrid ubiquitin-binding domain (ThUBD)-based far-Western blotting (TUF-WB) to visualize the signal of synthetic ubiquitin chains or ubiquitinated conjugates on a solid membrane by utilizing the unbiased affinity of ThUBD to all types of ubiquitin linkages. As compared to antiubiquitin antibody detection, TUF-WB can accurately quantify the signal intensity to the mass amounts of all eight ubiquitin chains. Meanwhile, the sensitivity of this method in detecting complex ubiquitinated samples was 4-5-fold higher than those of antibodies. Consequently, TUF-WB allows accurate quantification of polyubiquitination signal on the membrane with great sensitivity and wider dynamic range.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blotting, Far-Western / methods*
  • Carrier Proteins / analysis
  • Carrier Proteins / chemistry
  • Carrier Proteins / metabolism
  • Escherichia coli / chemistry
  • HEK293 Cells
  • Humans
  • Membrane Proteins / analysis*
  • Membrane Proteins / chemistry
  • Membrane Proteins / metabolism*
  • Protein Domains
  • Protein Processing, Post-Translational*
  • Saccharomyces cerevisiae / chemistry
  • Saccharomyces cerevisiae Proteins / analysis
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism
  • Ubiquitination*

Substances

  • Carrier Proteins
  • Lsb1 protein, S cerevisiae
  • Membrane Proteins
  • Saccharomyces cerevisiae Proteins
  • ubiquinone-binding proteins