Engineering degrons of yeast ornithine decarboxylase as vehicles for efficient targeted protein degradation

Ornithine decarboxylase (ODC), which catalyzes the first step of polyamine biosynthesis, undergoes rapid targeted degradation (TPD) with the help of its two degron sequences, namely the N-terminal 50 residues (N50) and α/β domain (α/β) housing antizyme binding element (AzBE), in response to increased polyamine levels. Antizyme binds to AzBE of ODC and delivers it to proteasome for degradation. Entire ODC was used as a tag to demonstrate TPD of chimeric proteins.

Here we fashioned three peptide sequences from yeast ODC to test their capability to act as degrons, namely N50, α/β and Nα/β (a combination of N50 and α/β), and monitored their degradation potentials in chimeric proteins. We have examined the correlation between degradation potentials and structural integrity of the peptides, to find mechanistic explanations.

Nα/β with two signals in tandem is a better degron, under the regulation of antizyme. N50 like N44 reported earlier could drive chimeric proteins to degradation, while α/β could not act as an independent degron. Strong correlation was observed between functional efficacy of the peptides and their structural integrity. N50, which was believed to be unstructured, displayed propensity for helical conformation. Nα/β exhibited optimal structure, while α/β failed to adopt native like conformation.

Functional efficacy of the degron Nα/β is a consequence of its structural integrity. Nα/β and N50 could target chimeric proteins to degradation. However, α/β failed in the quest. Nα/β, regulated by antizyme, is better suited than N50 for TPD to understand the function of novel proteins.