In a new paper published in eLife, my colleagues in the Denic Lab and I investigated how budding yeast (S. cerevisiae) breaks down damaged peroxisome organelles through a type of autophagy called “pexophagy.” Researchers who study “selective autophagy” processes, where only certain organelles are targeted for destruction, have long wondered how the cell selects the correct target for autophagy.
This key selection process usually depends on a class of proteins called autophagy receptors, which target a diverse range of organelles and other targets for autophagic degradation. We wanted to understand how the autophagy receptor proteins are able to distinguish damaged organelles from their undamaged counterparts. In some cases, autophagy receptors are selectively recruited by membrane ligands that only appear on the surface of organelles following local damage. However, some other autophagy receptors natively residing on the membrane don’t fit this pattern recognition paradigm and need different mechanisms to describe their regulatory role in selective autophagy.
In this work, we resolve this paradox for one such autophagy receptor – the yeast peroxisome autophagy receptor, Atg36 – by showing how organelle-autonomous factors locally regulate the ability of Atg36 to drive pexophagy.
Peroxisomes are single-layer membrane sphere-shape organelles that participate in many metabolic functions across different organisms. They’re not essential in the budding yeast, which makes yeast peroxisomes an excellent case study for how cells break down damaged organelles via selective autophagy. The pexophagy receptor Atg36 starts the pexophagy process when it is phosphorylated, so we sought to understand what regulates Atg36’s phosphorylation.
One of the known players in regulating pexophagy is a protein kinase called Hrr25, which acts as “the watchman” and phosphorylates Atg36 under pexophagic conditions so that triggers the autophagic destruction of peroxisome. Under normal conditions, the Atg36 phosphoractivation by Hrr25 is repressed. We were surprised to find that a AAA+ (ATPases Associated with diverse cellular Activities) complex Pex1/6, which is known to aid protein import into the peroxisome, has a second job of preventing Atg36’s phosphorylation. Thus, Pex1/6 watches the watchmen (Hrr25) in yeast pexophagy.
Taking the advantages of quantitative proteomic approaches (immunoprecipitation + mass spectrometry [IP/MS]), we first identified the repressors involved in Atg36 phosphor-inhibition. Next, we validated the minimum components in the repression of Atg36 phosphorylation. These minimum components are the AAA+ Pex1/6 and its peroxisomal anchor Pex15. Pex15 only promotes Pex1/6’s proximity to Atg36 and can be replaced by the rapamycin-dependent FRB/FKBP heterodimerization system. Further, we provided complementary in vivo and in vitro evidence that Pex1/6’s repression on Atg36 phosphorylation requires its ATPase activity. Lastly, the direct binding between Atg36 and Pex1/6 were established in yeast-two-hybrid analysis and pexophagy assays.
Our work provides a model by which the cells keep quality control on their internal organelles. It will help us define a broadly conserved regulatory mechanism of selective autophagy. Our understanding on yeast peroxisome and selective autophagy here will pave the way for future efforts to cure some diseases caused by peroxisome disorder, such as Zellweger Syndrome and rhizomelic chondrodysplasia punctata type 1 (RCDP1).
The authors would like to dedicate this paper to the memory of the late Peter Arvidson who had administratively supported our lab for many years.
This work was supported by grants from the NIH and NSF.