Synthetic Control of Protein Degradation during Cell Proliferation and Developmental Processes

Abstract

Synthetic tools for the control of protein function are valuable for biomedical research to characterize cellular functions of essential proteins or if a rapid switch in protein activity is necessary. The ability to tune protein activity precisely opens another level of investigations that is not available with gene deletion mutants. Control of protein stability is a versatile approach to influence the activity of a target protein by its cellular abundance. Diverse strategies have been developed to achieve efficient proteolysis using external inducers or differentiation-coupled signals. The latter is especially important for the inactivation of a protein during a developmental process. Recently, several approaches to achieve this have been engineered. In this article, we present current synthetic tools for regulation of protein stability that allow fine-tuning of protein abundance, their advantages and disadvantages with an emphasis on methods applicable in the context of cell differentiation and development. We give an outlook toward future developments and discuss main applications of these tools.

Predator: A novel method for targeted protein degradation

“…A comprehensive understanding of cellular processes requires different kinds of tools to identify the function of proteins in the context of cells and organisms (33). Genetic methods (3)(4)(5)(6)20) and methods targeting RNA level (7,14) have been widely used in researches. However, these methods dependents on the turnover of the target protein for not working at the protein level directly, which can be powerless and problematic when studying long-lived proteins or highly dynamic processes (1, 8).…”

“…The general usage of many current TPD methods that hijack UPS like DeGradFP, AID, and conditional degrons in higher eukaryotes are limited due to their requirement of the prior modification at endogenous protein targets (9,20). In recent years, PROTAC has emerged as a very promising and powerful approach to degrade POI directly both in vitro and in vivo, however, the time-consuming process for PROTAC design and development, universality, offtarget effect and hook effect are major disadvantages (14,(34)(35)(36)(37).…”

“…Generally, these results indicated that the GCGR predator significantly impairs hepatocyte glucagon sensitivity in vitro by affecting metabolic programs downstream of GCGR. Clinical application potential of current protein degradation techniques such as Trim-Away, AID, and deGradFP was thought to be limited by their technique complexity (8,10,11,16,20). To further explore the clinical potential of our Predator system, the GCGR Predator system was constructed into an adenovirus-based gene therapy vector that is widely used in pre-clinical applications, and primary hepatocytes were selected for degradation and downstream phenotypic validation of the GCGR Predator system as it is closer to normal physiological condition.…”

“…Then, Trim21 recruits the ubiquitin-proteasome system to antibodybound antigens, leading to their destruction (17)(18)(19). This method showed an acute and rapid degradation for target protein exactly at the protein level, but the short lifespan of injectedantibody, the high cost of antibody production, and the technique complexity limit its wide application, especially for clinical usage (11,16,20).…”

Degradation of integral membrane proteins modified with the photosensitive degron module requires the cytosolic endoplasmic reticulum–associated degradation pathway

“…It consists of a peptide of 37 amino acids without secondary structure comprising a cysteine–alanine motif, which is important for proteasomal degradation (Erales and Coffino, 2014). The LOV2 domain exposes cODC1 upon illumination with blue light, which triggers degradation of the whole protein by the proteasome (Renicke et al , 2013; Trauth et al , 2019). The degron cODC1 was successfully utilized to target two membrane proteins for degradation, the ER membrane protein Sec62 from Saccharomyces cerevisiae and the membrane protein synaptotagmin (SNT1) from Caenorhabditis elegans (Renicke et al , 2013; Hermann et al , 2015).…”