Lipid Droplets Are a Physiological Nucleoporin Reservoir

Abstract

Lipid Droplets (LD) are dynamic organelles that originate in the Endoplasmic Reticulum and mostly bud off toward the cytoplasm, where they store neutral lipids for energy and protection purposes. LD also have diverse proteins on their surface, many of which are necessary for the their correct homeostasis. However, these organelles also act as reservoirs of proteins that can be made available elsewhere in the cell. In this sense, they act as sinks that titrate key regulators of many cellular processes. Among the specialized factors that reside on cytoplasmic LD are proteins destined for functions in the nucleus, but little is known about them and their impact on nuclear processes. By screening for nuclear proteins in publicly available LD proteomes, we found that they contain a subset of nucleoporins from the Nuclear Pore Complex (NPC). Exploring this, we demonstrate that LD act as a physiological reservoir, for nucleoporins, that impacts the conformation of NPCs and hence their function in nucleo-cytoplasmic transport, chromatin configuration, and genome stability. Furthermore, our in silico modeling predicts a role for LD-released fatty acids in regulating the transit of nucleoporins from LD through the cytoplasm and to nuclear pores.

Uip4p modulates nuclear pore complex function in Saccharomyces cerevisiae

“…Apart from aggregation of NPCs at the NE, we also observed presence of cytosolic spots of nups in uip4 Δ (Fig2D). Although cytosolic pool of nucleoporins in wild type cells has been reported earlier (Colombi et al, 2013; Makio et al, 2013; Kumanski et al, 2021), this fraction of cell population was at least three-fold higher in uip4 Δ cells (FigS2B). Complementation with a plasmid borne copy of UIP4 expressed from endogenous promoter could rescue the phenotype in uip4 Δ (FigS2B).…”

“…While some of the NPC components might assemble in the cytosol, they are not recruited at the NE until the transmembrane and scaffold nups have created pore site for insertion. In yeast some of these cytoplasmic spots are pools of nups and remain associated with lipid droplets (Kumanski et al, 2021). While in other cases, these components are retained to prevent incorporation of damaged nups at the NE thereby protecting NE integrity (Webster et al, 2014).…”

The Many Faces of Lipids in Genome Stability (and How to Unmask Them)

“…Both pockets are located at strategic sites mastering the 3D conformation of these nucleoporins. Genetic experiments and fluorescence microscopy suggested that FA binding may help solubilize these proteins to escort them for assembly at the nuclear membrane [ 77 ]. Thus, FA binding bears a strong potential for ruling very divergent nuclear phenomena.…”

“…To add to this, we recently exploited published LD proteomes from S. cerevisiae cells [ 120 ] to validate thus enlarge the catalog of nuclear proteins whose presence onto LD is physiologically relevant. While reported hits such as condensin or cohesin complex subunits could not be validated [ 132 ], we discovered the ability of cytoplasmic LD to harbor nucleoporins in a manner concerted with cell metabolism [ 77 ]. Thus, active cycling is coupled to nucleoporin release from LD to conform active pores and, reciprocally, storage of nucleoporins onto LD permits nuclear pores to modify their stoichiometry under low-cycling conditions [ 77 ].…”

New Activities of the Nuclear Pore Complexes

“…Despite our knowledge of the NPC structure, the molecular mechanisms underlying its regulatory roles remain to be understood [1,3]. Using high-speed atomic force microscopy (HS-AFM), we showed that FG-Nups are in a liquid-liquid phase separated (LLPS) state [10,11] in which rapid and transient intermediates of FG filaments and sometimes co-exist with a central plug during conformational changes in cancer cells and organoids [12]. The real-time HS-AFM images also suggested that the NPC central channel has a moist cobweb-like structure [13].…”