c Lipid droplets (LDs) are ubiquitous organelles that serve as a neutral lipid reservoir and a hub for lipid metabolism. Manipulating LD formation, evolution, and mobilization in oleaginous species may lead to the production of fatty acid-derived biofuels and chemicals. However, key factors regulating LD dynamics remain poorly characterized. Here we purified the LDs and identified LD-associated proteins from cells of the lipid-producing yeast Rhodosporidium toruloides cultured under nutrient-rich, nitrogen-limited, and phosphorus-limited conditions. The LD proteome consisted of 226 proteins, many of which are involved in lipid metabolism and LD formation and evolution. Further analysis of our previous comparative transcriptome and proteome data sets indicated that the transcription level of 85 genes and protein abundance of 77 proteins changed under nutrient-limited conditions. Such changes were highly relevant to lipid accumulation and partially confirmed by reverse transcription-quantitative PCR. We demonstrated that the major LD structure protein Ldp1 is an LD marker protein being upregulated in lipid-rich cells. When overexpressed in Saccharomyces cerevisiae, Ldp1 localized on the LD surface and facilitated giant LD formation, suggesting that Ldp1 plays an important role in controlling LD dynamics. Our results significantly advance the understanding of the molecular basis of lipid overproduction and storage in oleaginous yeasts and will be valuable for the development of superior lipid producers.
Lipid droplets (LDs), intracellular organelles with deposits of neutral lipids and involved in many cellular activities, are widely present in both eukaryotic and prokaryotic cells (1-4). These organelles consist of a neutral lipid core surrounded by a phospholipid monolayer and associated proteins (3, 5). It has been known that LDs serve as the energy reservoir of cells, which may increase the adaptation by mobilization and degradation of lipids during nutrient deprivation, and also connect with other cellular processes, including lipid transport, membrane biogenesis, lipotoxicity relief, protein storage and degradation, pathogenicity, and autophagy (6-9). Because the biology of LDs is closely linked to some diseases, such as obesity, type 2 diabetes, and atherosclerosis, great progress has been made in elucidating the cellular trafficking, dynamics, and biogenesis of LDs in mammalian cells (2, 7, 10). However, there have been few studies on LDs in other species, especially naturally lipid-producing microorganisms (11-13). Analysis of these microorganisms is motivated by the fact that microbial lipid production holds a great promise to convert waste materials, including lignocellulosic biomass, into fatty acid-derived fuel molecules and chemicals in a scenario of biorefinery and sustainable development (14, 15).The major components of LDs are neutral lipids, including triacylglycerols (TAGs), sterol esters, and ether lipids (16). Neutral lipids constitute more than 90% of LDs by weight, but the ratio of TAGs to ste...