Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast

Abstract

The mechanism of autophagy relies on complex cell signaling and regulatory processes. Each cell contains many proteins that lack a rigid 3-dimensional structure under physiological conditions. These dynamic proteins, called intrinsically disordered proteins (IDPs) and protein regions (IDPRs), are predominantly involved in cell signaling and regulation. Yet, very little is known about their presence among proteins of the core autophagy machinery. In this work, we characterized the autophagy protein Atg3 from yeast and human along with 2 variants to show that Atg3 is an IDPRs-containing protein and that disorder/order predicted for these proteins from their amino acid sequence corresponds to their experimental characteristics. Based on this consensus, we applied the same prediction methods to all known Atg proteins from Saccharomyces cerevisiae. The data presented here provide an insight into the structural dynamics of each Atg protein. They also show that intrinsic disorder at various levels has to be taken into consideration for about half of the Atg proteins. This work should become a useful tool that will facilitate and encourage exploration of protein intrinsic disorder in autophagy.

Keywords: :

• Atg3
• autophagy
• intrinsically disordered protein
• stress
• vacuole
• yeast

Disclosure of Potential Conflicts of Interests

No potential conflicts of interests were disclosed.

Acknowledgments

We thank Dr DR Southworth (University of Michigan) for assistance with dynamic light scattering, Drs Y Qiu, AM Taherbhoy, SE Kaiser, and BA Schulman (St. Jude Children’s Research Hospital) for providing protein samples, and Dr CK Yip (University of British Columbia) for helpful comments. This work was supported by NIH grant R01GM053396 to DJK, and through the Protein Folding Diseases FastForward Initiative, University of Michigan.