A Proximity Labeling Strategy Provides Insights into the Composition and Dynamics of Lipid Droplet Proteomes

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Abstract

Lipid droplet (LD) functions are regulated by a complement of integral and peripheral proteins that associate with the bounding LD phospholipid monolayer. Defining the composition of the LD proteome has remained a challenge due to the presence of contaminating proteins in LD-enriched buoyant fractions. To overcome this limitation, we developed a proximity labeling strategy that exploits LD-targeted APEX2 to biotinylate LD proteins in living cells. Application of this approach to two different cell types identified the vast majority of previously validated LD proteins, excluded common contaminating proteins, and revealed new LD proteins. Moreover, quantitative analysis of LD proteome dynamics uncovered a role for endoplasmic reticulum-associated degradation in controlling the composition of the LD proteome. These data provide an important resource for future LD studies and demonstrate the utility of proximity labeling to study the regulation of LD proteomes. Lipid droplets (LDs) are dynamic neutral lipid storage organelles. Bersuker et al. employ an APEX2-based proximity labeling strategy to define high-confidence LD proteomes from human cells. They reveal a role for endoplasmic reticulum-associated degradation in controlling the levels of an LD protein identified here that regulates LD lipid composition.

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Bersuker, K., Peterson, C. W. H., To, M., Sahl, S. J., Savikhin, V., Grossman, E. A., … Olzmann, J. A. (2018). A Proximity Labeling Strategy Provides Insights into the Composition and Dynamics of Lipid Droplet Proteomes. Developmental Cell, 44(1), 97-112.e7. https://doi.org/10.1016/j.devcel.2017.11.020

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