Molecular cell biology of autophagy

Lead Research Organisation: The Francis Crick Institute


The cells that make up the organ and immune systems of our body have to maintain the ability to work properly and survive under any adverse conditions, conditions which come both from within the body and from outside the body. To do this they have a dedicated process that helps keep them healthy and ensure their survival called autophagy, or self-eating. Autophagy acts in many ways, for instance it can remove parts of the cell contents and recycle then to make basic components, or it can identify and remove harmful components in the cell. The ability of autophagy to do these things helps prevent diseases such as neurodegeneration, cancer, and infection. Thus, autophagy is considered an important process to manipulate to keep cells healthy and prevent disease. Autophagy works through the remobilization of building blocks, such proteins and lipids, already present in the cell. This remobilization creates a new cellular structure, or compartment, called an autophagosome that does the job. My laboratory aims to understand how autophagy works by understanding where the proteins and lipids come from during adverse conditions to make an autophagosome. Working at the level of the basic building blocks of proteins and lipids we aim to identify those which are required for autophagy (new targets) and develop approaches to manipulate the target and pathway to ensure cells are kept healthy no matter what adversity they encounter.

Technical Summary

This work was supported by the Francis Crick Institute which receives its core funding from the UK Medical Research Council (FC001000), the Wellcome Trust (FC001000),and Cancer Research UK (FC001000)

The focus of my laboratory’s research is mammalian macroautophagy, an intracellular degradative pathway mediated by lysosomes. Macroautophagy, which is called autophagy, is fundamentally a sequestration process during which cytosolic solutes, proteins, and organelles are engulfed and sequestered into autophagosomes, followed by fusion of the autophagosomes with lysosomes and degradation of the sequestered material. The function of autophagy is to maintain intracellular homeostasis (through removal of damaged cytosolic components) under normal conditions, and to enable survival under stress (through replenishment of amino acids and metabolites). Many of the proteins required for autophagy, first identified in yeast and called Atg (autophagy related) proteins, have now been identified in mammals. However, their molecular function remains largely unknown and it is their molecular function we aim to understand. Importantly, autophagy has been shown to play a role in human diseases including cancer. My laboratory aims to understand the process of autophagosome formation and maturation at a molecular level building upon our identification of three essential mammalian Atg proteins, ULK1, Atg9 and WIPI2, and new regulatory or accessory molecules that my lab has recently identified. Specifically, our studies involve a molecular dissection of 1) the earliest event, autophagosome formation and 2) regulatory mechanisms controlling expansion, and maturation of autophagosomes. ULK1 is the kinase contained within a multi-subunit complex which initiates autophagy, and it controls the multi-spanning membrane protein Atg9 which is required for autophagy. WIPI2 is the main effector of the lipid Phosphatidylinositol 3-Phosphate produced by the class III PtdIns 3-kinase. We are studying the subcellular localization, and interdependence of these Atg proteins. We are also seeking to identify post-translational modifications that activate and allow recruitment of these proteins upon induction of autophagy, including phosphorylation. These experiments provide a platform for our second aim, to identify and understand at a structural level how the proteins required for autophagy function to generate the autophagosome membrane. We speculate that these regulatory molecules control or fine-tune membrane formation, shaping and composition. In addition to the core ATG machinery, regulatory proteins and candidates obtained through our proteomic analysis, and screens, will be studied. Understanding both the essential and accessory machinery, and how it is regulated will direct future research towards understanding key functional complexes required for autophagy.


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