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Dev Cell. 2018 Jan 8;44(1):97-112.e7. doi: 10.1016/j.devcel.2017.11.020. Epub 2017 Dec 21.

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

Author information

1
Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA.
2
Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
3
SLAC National Accelerator Center, SSRL, Menlo Park, CA 94025, USA; Stanford Electrical Engineering Department, Stanford University, Stanford, CA 94305, USA.
4
Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
5
Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
6
Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: olzmann@berkeley.edu.

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.

KEYWORDS:

APEX; APEX2; ERAD; biotinylation; endoplasmic reticulum; lipid droplet; proteasome; proteome; proximity labeling; ubiquitin

PMID:
29275994
PMCID:
PMC5764092
DOI:
10.1016/j.devcel.2017.11.020
[Indexed for MEDLINE]
Free PMC Article

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