Nuclear ATGs in the regulation of nucleophagy
Autophagy is a highly conserved mechanism that can mediate either the bulk or selective degradation of substrates through the lysosome in response to stress signals. In both scenarios the activity of autophagy-related (ATG) proteins mediates the nucleation and expansion of a specialized membrane domain that encloses the substrates into so-called autophagosomes. These vesicles later on fuse with the lysosome, where the contents are degraded and basic metabolites recycled back to the cytoplasm. Among ATG proteins, the ULK1 complex (composed of the ULK1 kinase, ATG13, FIP200 and ATG101) stands at the very top of the autophagy signaling pathway by integrating metabolic and environmental signals and initiating autophagy through the ULK1 kinase- mediated phosphorylation of downstream targets. These events lead to the conjugation of members of the ubiquitin-like ATG8 protein family to the autophagosomal membrane, a key step for cargo selection and autophagosome biogenesis, maturation and fusion with the lysosome.
In contrast to bulk autophagy, during selective autophagy a specific cargo (aggregated proteins, defective organelles and others) is recognized by a protein receptor and targeted for lysosomal degradation. Remarkably, recent evidence shows that the nucleus can serve as a selective autophagy substrate. Exposure to genotoxic stress can trigger this "nucleophagy", which is morphologically visible as a blebbing of the nuclear membrane and its adjacent DNA that results in their extrusion to the cytoplasm and encapsulation within autophagosomes. In the last years nucleophagy has received increasing attention because it can contribute to the establishment of cellular senescence, and therefore constitutes a potentially relevant mechanism during ageing and in the context of cancer progression.
Importantly, key ATG proteins exist also as nuclear pools with so far poorly characterized functions. Evidence suggests that ULK1 kinase participates in the DNA damage response induced by oxidative damage, while LC3B, a member of the ATG8 family, interacts with the nuclear lamina protein LaminB1 and mediates its nucleophagic degradation. By making use of mammalian cell culture and biochemical, microscopy and cell biology methods we aim to:
1) explore whether the ULK protein family is involved in nuclear signaling during DNA damage,
2) identify nuclear ULK-dependent phosphorylation targets and characterize their possible role in the nucleophagy program, and
3) identify nuclear ATG8-interacting proteins that may represent novel nucleophagy substrates.
Altogether, we are working to understand if- and how - re-purposing of these important ATG proteins impacts nuclear signaling, the selection of nucleophagy targets and ultimately nuclear homeostasis during steady-state and disease conditions.