Autophagy is an indispensable process mediating bulk protein degradation and organelle turnover in eukaryotic cells. During autophagy, cytoplasmic organelles and proteins are engulfed into a double-lipid bilayer """"""""autophagosome"""""""" to be degraded in bulk upon autophagosome fusion with a lysosome. In addition to numerous proteins regulating autophagy, at least 15 distinct so-called """"""""Atg"""""""" proteins are core components for autophagic membrane formation common to many forms of autophagy. Among these key core components are two families of ubiquitin-like proteins (Atg8 and Atg12), and their noncanonical conjugation systems [a noncanonical E1 enzyme (Atg7), two noncanonical E2 enzymes (Atg3 and Atg10), and a noncanonical E3 enzyme partially composed of a UBL (the Atg12~Atg5 conjugate, here ~ refers to a covalent bond)]. Despite the essential roles of these UBL conjugation cascades in the process of autophagy, and the association of defects in these pathways with numerous disease processes, our knowledge of the detailed enzymatic bases for UBL conjugation in autophagy remains relatively rudimentary. We propose to apply our expertise in UBL conjugation cascades to the mechanisms and specificities of noncanonical enzymes that conjugate UBLs during autophagy. Our research plan will utilize structural biology and biochemistry to understand mechanisms underlying Atg7-mediated initiation of autophagy UBL cascades (Aim 1) and ligation of autophagy UBLs to their targets (Aim 2).
Autophagy is required to remove non-functional organelles and maintain protein homeostasis, and has been connected to numerous diseases, including cancers, diabetes, metabolic disorders, infections, and numerous debilitating processes associated with aging such as neurodegenerative disorders. Therefore, it is important to understand the molecular mechanisms underlying UBL conjugation in autophagy, both to provide insights into how defects in this pathway can lead to diseases, and because enzymes mediating UBL conjugation in autophagy are likely to be excellent targets for therapeutic agents.
|Qiu, Y; Zheng, Y; Taherbhoy, A M et al. (2017) Crystallographic Characterization of ATG Proteins and Their Interacting Partners. Methods Enzymol 587:227-246|
|Zheng, Y; Qiu, Y; Gunderson, J E C et al. (2017) Production of Human ATG Proteins for Lipidation Assays. Methods Enzymol 587:97-113|
|Kim, Myungjin; Sandford, Erin; Gatica, Damian et al. (2016) Mutation in ATG5 reduces autophagy and leads to ataxia with developmental delay. Elife 5:|
|Ordureau, Alban; Heo, Jin-Mi; Duda, David M et al. (2015) Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy. Proc Natl Acad Sci U S A 112:6637-42|
|Ordureau, Alban; Sarraf, Shireen A; Duda, David M et al. (2014) Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis. Mol Cell 56:360-75|
|Klionsky, Daniel J; Schulman, Brenda A (2014) Dynamic regulation of macroautophagy by distinctive ubiquitin-like proteins. Nat Struct Mol Biol 21:336-45|
|Hurley, James H; Schulman, Brenda A (2014) Atomistic autophagy: the structures of cellular self-digestion. Cell 157:300-311|
|Kaiser, Stephen E; Qiu, Yu; Coats, Julie E et al. (2013) Structures of Atg7-Atg3 and Atg7-Atg10 reveal noncanonical mechanisms of E2 recruitment by the autophagy E1. Autophagy 9:778-80|
|Qiu, Yu; Hofmann, Kay; Coats, Julie E et al. (2013) Binding to E1 and E3 is mutually exclusive for the human autophagy E2 Atg3. Protein Sci 22:1691-7|
|Lima, Christopher D; Schulman, Brenda A (2012) Structural biology: A protein engagement RING. Nature 489:43-4|
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