Principal Investigator, Research Group Leader – MPI for Biology of Ageing
Dr. Martin Graef
Max-Planck-Institut für Biologie des Alterns
Cells have evolved sophisticated homeostasis and quality control systems in order to cope with metabolic challenges and diverse stress conditions. One of these central systems is the evolutionarily highly conserved process termed “autophagy”. Autophagy allows cells the basal and inducible turnover of intracellular components ranging from whole dysfunctional organelles, e.g. mitochondria, to protein aggregates. Supporting a crucial role for cellular health, defects in autophagy are associated with ageing and age-associated diseases including neurodegeneration, metabolic disease, or cancer. A hallmark of (macro-)autophagy is the de novo formation of double-membrane vesicles termed autophagosomes. Driven by the concerted action of a complex core autophagy machinery and a number of other cellular processes, nascent autophagosomes encapsulate cytoplasmic cargoes of diverse size and nature and target them for lysosomal or vacuolar degradation and recycling. Cells have to carefully fine-tune the level of autophagy according to their current needs. However, we are just beginning to understand how cells integrate and transduce a multitude of information about their metabolic and functional state into an adequate autophagy response.
In our group, we address outstanding fundamental questions such as (1) how and where autophagomes form, (2) how cells integrate and transduce metabolic and functional information into a context- and stress-appropriate autophagy response, (3) what cellular functions are required for full regulatory capacity, and (4) how cellular dysfunction accumulating during ageing or disease affect the regulation of autophagy. In addition, we are interested in determining cellular mechanisms of ageing. Eukaryotic cells undergo only a limited number of cell divisions. Using yeast as a model system, we are currently pioneering the first system-wide approaches to explore the genetic and metabolic principles underlying replicative ageing.
In our past work, we made the fundamental observation that, as a conserved feature, autophagosomes form in spatial, physical, and functional association with ER exit sites, functionally specialized subregions of the endoplasmic reticulum (ER) that form COPII transport vesicles. These observations prompted us to analyse the functional relationship between the ER and autophagy in more detail and led to our recent discovery that lipid droplets, conserved storage compartments for neutral lipids, play a crucial role in autophagy regulation by maintaining ER homeostasis. Specifically, lipid droplets regulate the phospholipid composition of membranes and prevent ER stress by buffering de novo fatty acid synthesis in order to allow intact autophagosome formation in response to nutrient stress.
We are working towards a comprehensive understanding of the regulatory mechanisms of autophagy at mechanistic and system-wide level. As a long-term goal, we envision that uncovering fundamental principles will provide us with a unique opportunity to explore the therapeutic potential of intelligently modifying autophagy regulation for ageing and age-associated diseases in a targeted manner in higher organisms.
We use Saccharomyces cerevisiae and mammalian cell culture as model systems and employ an interdisciplinary approach ranging from biochemistry, genetics, fluorescence microscopy, synthetic biology to system-wide analyses including whole proteome profiling, protein interaction networks and automated high-throughput flow-cytometry.
Figure 1: ER exit site-linked autophagosome biogenes in vivo. Life-cell imaging of yeast cells harbouring fluorescently marked ER exit sites (ERES; Sec13-GFP, green) and autophagic membranes (mCherry-Atg8, red) during nutrient starvation. Bars, 1 mm. Images taken from: Graef et al. (2013). ER exit sites are phy-sical and functional core autophagosome biogenesis components. Mol. Biol. Cell 24, 2918-31.
Figure 2: Lipid droplet-deficiency causes severe defects in autophagosome formation in vivo. Life-cell imaging of wild type (wt) and lipid droplet-deficient (DLD) yeast cells harbouring fluorescently marked autophagic membranes (GFP-Atg8) during nutrient starvation. LD-deficient cells display impaired autophagosome biogenesis and accumulate multiple aberrant Atg8 puncta due to phospholipid changes and ER stress. Bars, 1 mm. Images taken from: Velázquez et al. (2016). Lipid droplet-mediated ER homeostasis regulates autophagy and cell survival during starvation. J. Cell Biol. 212, 621-631.