Proteome analysis of nuclear Lipid‐Associated Promyelocytic Leukemia (PML) Structures (LAPS) Using Biotin Proximity Labelling

Abstract

Lipid droplets (LD) are organelles composed of a phospholipid monolayer surrounding a core of and triacylglycerol and cholesterol ester. LD have a primary role in energy homeostasis and lipotoxic stress through the regulated storage and release of fatty acids. While LD are cytoplasmic, lipoprotein secreting cells harbor nuclear LD (nLD) that associate with PML, the structural protein of PML nuclear bodies (PML‐NB) that regulate DNA repair and stress responses. Knockout studies in U2OS cells indicated that the 50% of nLDs contain PML isoform II (PML‐II) and have a unique lipid and protein composition marked by the lack of canonical PML‐NB‐associated proteins, such as DAXX, SP100 and SUMO. Owing to their unique composition, we term these subnuclear lipid:protein domains, lipid‐associated PML structures (LAPS). To gain insight into LAPS function, we conducted proximity labeling and mass spectrometry (MS) studies using PML‐I and PML‐II modified by fusion to the ascorbate peroxidase APEX2 that uses biotin‐phenol to biotinylate proteins. U2OS and Huh7 cells expressing PML‐APEX2 fusion proteins were treated with and without oleate, and biotinylated proteins were isolated and analyzed by LC‐MS/MS. Using standard filtering techniques (CRAPome, SAINT, Bayesian false discovery rate) we identified several high confidence interacting proteins associated with the COPII coatomer complex, including Sec24A, Sec23IP, Sec24B, and Sec23B. These Sec23/24 proteins were associated with PML‐I and, to a lesser extent, PML‐II under oleate‐treated conditions. Sec23B was observed to associate with both PML‐NBs as well as LAPS by immunofluorescence microscopy in U2OS cells expressing PML‐II‐APEX2. The COPII pathway has previously been implicated in protein delivery to cytoplasmic LD setting a precedence for the interaction we observed with LAPS. Thus, given our preliminary data showing interaction between Sec 23/24 heterodimer, PML‐NBs and LAPS we are now pursuing the hypothesis that lipid membrane deformation and/or cargo transport activity in the nucleus by COPII proteins could play a role in lipid homeostasis.