Mechanism of lipid droplet formation by the yeast Sei1/Ldb16 Seipin complex

Abstract

Lipid droplets (LDs) are universal lipid storage organelles with a core of neutral lipids, such as triacylglycerols, surrounded by a phospholipid monolayer. This unique architecture is generated during LD biogenesis at endoplasmic reticulum (ER) sites marked by Seipin, a conserved membrane protein mutated in lipodystrophy. Here structural, biochemical and molecular dynamics simulation approaches reveal the mechanism of LD formation by the yeast Seipin Sei1 and its membrane partner Ldb16. We show that Sei1 luminal domain assembles a homooligomeric ring, which, in contrast to other Seipins, is unable to concentrate triacylglycerol. Instead, Sei1 positions Ldb16, which concentrates triacylglycerol within the Sei1 ring through critical hydroxyl residues. Triacylglycerol recruitment to the complex is further promoted by Sei1 transmembrane segments, which also control Ldb16 stability. Thus, we propose that LD assembly by the Sei1/Ldb16 complex, and likely other Seipins, requires sequential triacylglycerol-concentrating steps via distinct elements in the ER membrane and lumen.

Seipin forms a flexible cage at lipid droplet formation sites

“…Because we found no density of Ldb16 in our yeast structure, our study does not address this question. However, a recent report showing crosslinking of Ldb16 to the central helix in yeast provides support for this hypothesis 32 .…”

“…Core elements of the seipin structure appear to be evolutionarily conserved in yeast, fly and human proteins 18 , 19 , 31 , 32 . The lumenal α/β-sandwich fold domain is well resolved and has similar features in all species analyzed, except for the centrally located hydrophobic helix.…”

Touch and Go: Membrane Contact Sites Between Lipid Droplets and Other Organelles

“…Interestingly, yeast seipin lacks the HH domain found in human or Drosophila seipins. However, yeast seipin binds to Ldb16 (low dye binding 16), which contains HH-like regions and supports HH function in the yeast seipin complex ( Klug et al, 2021 ).…”

Insights Into the Biogenesis and Emerging Functions of Lipid Droplets From Unbiased Molecular Profiling Approaches

“…It is difficult to overstate the contribution of yeast systematic genetics approaches to our current understanding of eukaryotic lipid metabolism and LD biology ( Radulovic et al, 2013 ). A few recent examples include: insights onto the regulated dynamics and spatial positioning of LDs during nutrient stress conditions to supply free fatty acids ( Henne et al, 2018 ; Hariri et al, 2019 ); the first mechanistic and structural descriptions of the seipin complex driving LD budding from the ER ( Klug et al, 2021 ; Arlt et al, 2022 ), and systematic screens for its regulatory partners ( Eisenberg-Bord et al, 2018 ); the description of specific mechanisms by which LDs contribute to manage protein aggregates ( see also below ) ( Moldavski et al, 2015 ); or the discovery of a new class of LDs stemming from nuclear membranes ( Romanauska and Köhler, 2018 ). Innovative applications of imaging technologies for automated screening, such as 3D imaging ( Lv et al, 2019 ), have also been reported in this system.…”