Degradation signals

Identification and characterization of degradation signals

A failure to maintain cell homeostasis is associated with the pathogenesis of many human diseases, such as malignancies and neurodegenerative disorders. The ubiquitin-proteasome system plays a critical role in maintaining the cellular environment by removing misfolded proteins from the cell. One of our research interests is understanding how misfolded substrates are recognized for degradation by the ubiquitin system. In general, every protein has the potential to undergo misfolding and therefore to become a substrate for ubiquitin-mediated degradation. However, what is recognized as “misfolded” by the ubiquitin system is largely unknown.

In order to better understand how misfolded proteins are recognized for degradation we adopted a misfolded substrate model in yeast, termed Ndc10. We found that the C-terminal region of the protein contains a hidden degron, termed DegAB, composed of two amphipathic helices, followed by an unstructured tail (Furth et al., 2011)(See below). 

We further show that the hydrophobic regions of the helices provide the signal for the ubiquitin system while the unstructured tail is essential for degradation by the proteasome (Alfassy et al., 2013). Importantly, we find that mild structural changes in the degradation signal that exposes the hydrophobic surface of the amphipathic helices are sufficient to trigger degradation, suggesting that the recognition by the ubiquitin system takes place at early stages of protein misfolding when the protein secondary structure is still intact.

Mutation that disrupt the hydrophobic interactions in DegA expose a hydrophobic surface, thereby triggering degradation

Currently we perform a new study for large scale identification of degrons in yeast. Using growth assays, combined with deep sequencing, we measure a quantitative degradation potency for thousands of polypeptides in yeast simultaneously (Novel methodology – See methods section). We utilize this assay for the identification of degradation signals involved in protein quality control. The new research system we developed will enable researchers to examine the stability of the proteome of multiple organisms, from yeast to human.  On a broader perspective, we anticipate this work to be a first step toward a complete assessment of the general and specific degradation requirements for each and every protein of interest.