Mitophagy Research in the Ragusa Lab

Autophagy

In order for cells to maintain homeostasis, their long-lived and toxic cellular components must be degraded. However, large protein aggregates and organelles, due to their size, are inaccessible to the proteasome, the major protein degradation machinery in the cell. To address this issue, cells degrade large cytoplasmic components through a process called macroautophagy (hereafter, autophagy), in which double membrane vesicles engulf cytoplasmic material and mark it for delivery to the vacuole (in yeast) or lysosome (in higher eukaryotes), where it will be degraded. This process is conserved across eukaryotes, and numerous homologues are shared between yeast and humans.

Artist: Dr. Leary

Autophagy

Selective Autophagy

Autophagy can capture cargo using either a non-selective or a selective mechanism. Selective autophagy utilizes Selective Autophagy Receptors (SARs) that mark the surface of specific cytosolic cargos to be degraded. SARs can mark a range of cytosolic material including mitochondria, peroxisomes, lipid droplets, large protein aggregates and intracellular pathogens. Selective autophagy can be triggered by a variety of mechanisms including oxidative stress, changes in nutrient availability and damage to the cargo to be captured. Once selective autophagy initiation has occurred, SARs bind to the the selective autophagy initiation complex consisting of Atg1, Atg13 and Atg11. The selective autophagy initiation complex recruits the initial membrane required to generate a double-membrane autophagosome around the cargo along with additional autophagy proteins. Once formed, the autophagosome fuses with the vacuole (in yeast) or lysosome (in higher eukaryotes), leading to the degradation of the captured contents. While selective autophagy can capture a broad range of cargos we are using mitochondria-selective autophagy, or mitophagy, as a model system to study the mechanisms of the process.

The below figure is from a review written by lab alumna, Dr. Kelsie Leary; Characterization of Protein–Membrane Interactions in Yeast Autophagy; Cells 2022.

Dysfunctions in selective autophagy have been correlated with tumorigenesis, chronic infection and neurodegeneration. Therefore, gaining an understanding of the molecular mechanisms of selective autophagy will help us understand why this process fails in disease, and could lead to the development of novel therapeutics for the treatment of diseases that result from the dysfunction.

Atg Proteins

Autophagy-Related (Atg) proteins, though initially identified and named separately, in yeast are now classified under the 'Atg protein' family, and each is designated a number. The Atg proteins include kinases, ubiquitin-like proteins, scaffolding proteins, membrane binding proteins and others.

Autophagy-Related Proteins

Major Questions of Interest

Organizing
IM-SARs

How is the initiation complex organized by IM-SARs, and how does it develop? Which Atg proteins are involved, and what roles do they play? What are the inter-protein binding patterns?