Ubiquibodies, Synthetic E3 Ubiquitin Ligases Endowed with Unnatural Substrate Specificity for Targeted Protein Silencing

作者：Portnoff Alyse D; Stephens Erin A; Varner Jeffrey D; DeLisa Matthew P^*

来源：JOURNAL OF BIOLOGICAL CHEMISTRY, 2014, 289(11): 7844-7855.

DOI：10.1074/jbc.M113.544825

• Antibody Engineering
• E3 Ubiquitin Ligase
• Molecular Biology
• Proteasome
• Protein Degradation
• Protein Engineering
• Synthetic Biology
• Ubiquitin
• Ubiquitination
• Reverse Genetics

Background: Techniques that harness the power of the ubiquitin-proteasome pathway (UPP) for protein knock-out are limited to a narrow set of protein targets. Results: Engineered ubiquibodies specifically and systematically removed exogenous target proteins. Conclusion: Diverse protein targets can be redirected to the UPP using this new protein silencing method. Significance: Ubiquibodies offer a simple, reproducible, and customizable technique for selectively and controllably depleting cellular proteins.
The ubiquitin-proteasome pathway (UPP) is the main route of protein degradation in eukaryotic cells and is a common mechanism through which numerous cellular pathways are regulated. To date, several reverse genetics techniques have been reported that harness the power of the UPP for selectively reducing the levels of otherwise stable proteins. However, each of these approaches has been narrowly developed for a single substrate and cannot be easily extended to other protein substrates of interest. To address this shortcoming, we created a generalizable protein knock-out method by engineering protein chimeras called ubiquibodies that combine the activity of E3 ubiquitin ligases with designer binding proteins to steer virtually any protein to the UPP for degradation. Specifically, we reprogrammed the substrate specificity of a modular human E3 ubiquitin ligase called CHIP (carboxyl terminus of Hsc70-interacting protein) by replacing its natural substrate-binding domain with a single-chain Fv (scFv) intrabody or a fibronectin type III domain monobody that target their respective antigens with high specificity and affinity. Engineered ubiquibodies reliably transferred ubiquitin to surface exposed lysines on target proteins and even catalyzed the formation of biologically relevant polyubiquitin chains. Following ectopic expression of ubiquibodies in mammalian cells, specific and systematic depletion of desired target proteins was achieved, whereas the levels of a natural substrate of CHIP were unaffected. Taken together, engineered ubiquibodies offer a simple, reproducible, and customizable means for directly removing specific cellular proteins through accelerated proteolysis.

• 出版日期2014-3-14