Autophagy, a lysosomal degradation pathway in which the cell digests its own components, is an essential biological pathway that promotes organismal health and longevity and helps combat cancer and neurodegenerative diseases. Accordingly, the 2016 Nobel Prize in Physiology or Medicine was awarded for research in autophagy. Although autophagy has been extensively studied from yeast to mammals, the molecular events that underlie its induction and progression remain elusive. A highly conserved protein kinase, Atg1, plays a unique and essential role in initiating autophagy. However, the molecular mechanisms that enable the extensive remodelling of cellular membranes that occurs during autophagy is still completely undefined. A detailed knowledge of the inputs and outputs of the Atg1 kinase and the molecular events triggered, will enable us to provide a definitive mechanistic understanding of autophagy. To achieve this goal, we aim at reconstituting different steps of autophagy in vitro, to then dissect the underlying events in detail. As autophagy function is pivotal to prevent diseases such as cancer and neurodegeneration, understanding the molecular events of autophagy will also help to address its potential in therapeutics.