Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function

Cells respond to fluctuating nutrient supply by adaptive changes in organelle dynamics and in metabolism. How such changes are orchestrated on a cell-wide scale is unknown. We show that endosomal signaling lipid turnover by MTM1, a phosphatidylinositol 3-phosphate [PI(3)P] 3-phosphatase mutated in X-linked centronuclear myopathy in humans, controls mitochondrial morphology and function by reshaping the endoplasmic reticulum (ER). Starvation-induced endosomal recruitment of MTM1 impairs PI(3)P-dependent contact formation between tubular ER membranes and early endosomes, resulting in the conversion of ER tubules into sheets, the inhibition of mitochondrial fission, and sustained oxidative metabolism. Our results unravel an important role for early endosomal lipid signaling in controlling ER shape and, thereby, mitochondrial form and function to enable cells to adapt to fluctuating nutrient environments. Description A lipid-triggered signal in starvation Nutrient starvation triggers changes in metabolism that are coordinated across the cell and its organelles. Jang et al. studied how endosomal signaling lipid turnover through MTM1, a phosphoinositide 3-phosphatase mutated in X-linked centronuclear myopathy in humans, reshapes the endoplasmic reticulum to control mitochondrial morphology and oxidative metabolism (see the Perspective by Zanellati and Cohen). A lipid-controlled organellar relay transmits nutrient-triggered changes in endosomal signaling lipid levels to mitochondria to enable metabolic rewiring. —SMH Cell-wide organellar rewiring through endosomal lipid signaling enables cells to adapt to altering nutrient supplies. INTRODUCTION Cells need to react appropriately to nutritional cues. Defects in the rewiring of metabolism in response to alterations in nutrient supply have been linked to human diseases ranging from diabetes to muscle atrophy. Starvation represses anabolic pathways and facilitates catabolic ones, such as the degradation of macromolecules by autophagy and endolysosomes. Starvation also promotes the β-oxidation of fatty acids in mitochondria to produce adenosine triphosphate (ATP). Within cells, organelles including lysosomes and mitochondria undergo changes in shape and dynamics. These processes are often regulated by phosphoinositide lipids. Phosphoinositides are also involved in the formation of membrane contacts between organelles and in the response of cells and tissues to growth and nutrient signals. How the adaptive changes that protect mammalian cells and tissues from starvation-induced damage are coordinated on a cell-wide scale is unknown. RATIONALE Endolysosomal membrane dynamics and function are controlled by phosphoinositide signaling lipids, most notably by the synthesis and turnover of phosphatidylinositol 3-phosphate [PI(3)P]. Patients carrying mutations in the gene encoding the lipid phosphatase MTM1, an enzyme that mediates endosomal PI(3)P turnover, suffer from X-linked centronuclear myopathy (XLCNM), a severe neuromuscular disease characterized by muscle atrophy, disorganization of mitochondria, and defects in the organization of the muscle endoplasmic reticulum (ER). Given that PI(3)P is a hallmark of endosomes, we hypothesized that the control of early endosomal PI(3)P by MTM1 might serve to orchestrate adaptive changes in the dynamics of the ER and mitochondria in response to altering nutrient supply. RESULTS Working with XLCNM patient–derived myoblasts and engineered cell lines, we found that nutrient starvation (for example, lack of amino acids) induced the hydrolysis of PI(3)P by endosomal recruitment of MTM1. Concomitantly, tubular ER membranes were observed to be converted into ER sheets by live super-resolution light microscopy. Mechanistically, loss of early endosomal PI(3)P upon starvation was found to reduce membrane contacts between peripheral ER tubules and early endosomes. These contacts function as physical tethers that may transmit pulling forces from highly motile peripheral endosomes to the tubular ER. Using proximity labeling proteomic and functional cell biological experiments we demonstrated that the ER–endosome contacts were mediated by binding of the related ER membrane proteins RRBP1 and kinectin 1 to PI(3)P on endosomes. To study the role of starvation-induced reshaping of tubular ER membranes into sheets on mitochondrial form and function, we combined live imaging with three-dimensional focused ion beam milling scanning electron microscopy (FIB-SEM) and proteomic analysis. We found that starvation-induced ER reshaping by MTM1 reduced the rate of mitochondrial fission and promoted the formation of a hyperfused mitochondrial network. Genetic manipulations that resulted in ER sheet expansion caused the formation of an enlarged mitochondrial network even in fed cells. Conversely, impaired ER reshaping and reduced mitochondrial network formation were observed in starved myoblasts from XLCNM patients. Mitochondrial network formation appeared to be critical for the delivery of fatty acids from lipid droplets to mitochondria and for oxidative ATP production to sustain energy supply in nutrient-deprived cells. CONCLUSION Our data unravel a crucial role for early endosomal lipid signaling in controlling ER morphology and, thereby, mitochondrial form and function to orchestrate the adaptive response of cells to alterations in nutrient (e.g., amino acid) supply. This mechanism operates independent of autophagy, a cellular self-eating process typically induced by prolonged starvation. Rather, it resembles an organellar conveyor belt, in which the tubular ER serves as a membrane conduit that transmits nutrient-triggered changes in endosomal PI(3)P levels to metabolic organelles to enable metabolic rewiring. How early endosomal PI(3)P levels and MTM1 function are controlled by cellular nutrient status is currently unknown. Defects in ER shape, mitochondrial morphogenesis, and cellular ATP depletion caused by loss of MTM1 function can explain the observed myofiber hypotrophy and defective ER organization in animal models of XLCNM and in human patients who often appear undernourished. We therefore hypothesize that dysregulated organelle remodeling may underlie XLCNM caused by MTM1 mutations in humans. Role of MTM1-mediated endosomal PI(3)P signaling in mitochondrial metabolic rewiring through reshaping of the ER in response to starvation. In fed cells, early endosomes form contacts with ER tubules. Tubular ER membranes facilitate mitochondrial fission and serve as a source for lipid droplet formation. Nutrient starvation–induced hydrolysis of endosomal PI(3)P by MTM1 reduces membrane contacts between the tubular ER and early endosomes. The resulting loss of peripheral ER tubules induces mitochondrial network formation and the delivery of fatty acids to mitochondria to sustain cellular energy supply. EE, early endosome; MT, microtubule; FA, fatty acid; LD, lipid droplet.