Endoplasmic Reticulum Architecture and Inter-Organelle Communication in Metabolic Health and Disease

Abstract

The endoplasmic reticulum (ER) is a key organelle involved in the regulation of lipid and glucose metabolism, proteostasis, Ca²⁺ signaling, and detoxification. The structural organization of the ER is very dynamic and complex, with distinct subdomains such as the nuclear envelope and the peripheral ER organized into ER sheets and tubules. ER also forms physical contact sites with all other cellular organelles and with the plasma membrane. Both form and function of the ER are highly adaptive, with a potent capacity to respond to transient changes in environmental cues such as nutritional fluctuations. However, under obesity-induced chronic stress, the ER fails to adapt, leading to ER dysfunction and the development of metabolic pathologies such as insulin resistance and fatty liver disease. Here, we discuss how the remodeling of ER structure and contact sites with other organelles results in diversification of metabolic function and how perturbations to this structural flexibility by chronic overnutrition contribute to ER dysfunction and metabolic pathologies in obesity.

Figure 1.

Distinct endoplasmic reticulum (ER) architecture across specialized cell types. Transmission electron microscopy images of specialized cells in their native tissue environment. (From left to right) Pancreatic acinar cells, intestinal Goblet cells, hepatocytes, enterocytes, adipocytes from white adipose tissue, and Leydig cells from testis. The images are derived from lean healthy mouse tissues and were acquired by authors Dr. Arruda and Dr. Parlakgül. (The cartoons representing the tissues were adapted from images from Servier Medical Art [smart.servier.com], which are licensed under a Creative Commons Attribution 3.0 Unported License.)

Figure 2.

Structure and function of peripheral endoplasmic reticulum (ER) sheets and ER tubules. (A) (Left side) Membrane-shaping proteins such as Climp-63, p180 (RRBP1), and kinectin regulate the formation and stabilization of ER sheets. (Right side) ER sheets are the preferential site for membrane-bound polysome and translocon complex localization. Therefore, protein cotranslation and translocation preferentially occurs at this ER subdomain. First, the signal recognition particle (SRP) binds to a ribosome containing a nascent polypeptide. Next, the SRP-ribosome-nascent polypeptide complex interacts with the SRP receptor in the ER membrane. The nascent polypeptide chain is imported into the ER lumen through the translocon channel (SEC61 and associated proteins), where chaperones like BIP assist in protein folding. (B) (Left side) The high curvature of the tubular ER membranes is maintained by proteins containing the reticulon homology domain (RHD), such as reticulons and REEP5. (Right side) The ER tubules are enriched in proteins involved in lipid metabolism and are the main site of LD formation and budding, where seipin protein is localized. Another protein enriched in ER tubules is the glucose-6-phosphatase (G6Pase), an enzyme involved in the conversion of glucose-6-phosphate (G6P) to glucose. The catalytic domain of G6Pase is located in the ER lumen. Therefore, this reaction requires G6P to be imported from the cytosol to the ER lumen and then glucose to be exported from the ER lumen to the cytosol by a transporter. Hydrolysis of G6P is the last step of glucose production from gluconeogenesis and glycogenolysis.

Figure 3.

Functions of endoplasmic reticulum (ER) membrane contact sites. (A) Examples of split biochemical pathways for which enzymes are located in different organelles requiring trafficking of metabolites through inter-organelle contact sites. Phospholipid synthesis: The phosphatidylserine (PS) present in the ER membrane is shuttled to the inner mitochondria membrane, where it is decarboxylated by the PS decarboxylase (PSD1) generating phosphatidylethanolamine (PE). Mitochondrial PE can be then shuttled back to the ER and be converted to phosphatidylcholine (PC) through the phosphatidylethanolamine N-methyltransferase (PEMT) (Vance 1990). Steroidogenesis: Steroid hormones originate from cholesterol and require the shuttling of intermediates across the ER and mitochondria (Miller 2007). Cholesterol gets into the inner mitochondrial membrane through the steroidogenic acute regulatory protein (StAR), which is shown to be located at the mitochondria-associated membranes (MAMs) (Prasad et al. 2015). In the mitochondria, the cholesterol side-chain cleavage enzyme (P450scc) catalyzes the conversion of cholesterol into pregnenolone. Next, pregnenolone is converted to progesterone by the enzyme 3β-hydroxysteroid dehydrogenase (3βHSD). In the next step, 17α-hydroxylation of progesterone occurs, which is catalyzed by the enzyme CYP17A1 in the ER. Steroid 21-hydrolase (P450c21) then converts 17α-hydroxyprogesterone into 11-deoxycorticosterone and 11-dexycortisol, respectively. Last, 11β-hydroxylase (P450c11β1) completes the synthesis of cortisol in the mitochondria. Alterations in proteins such as ATAD3, which stabilize MAMs in steroidogenic cells, have been shown to result in decreased hormone-stimulated steroid hormone synthesis (Issop et al. 2015). (B) Ca²⁺ flux at the MAMs: Ca²⁺ transport from ER to mitochondria occurs through the IP3R, located in the ER membrane, the mitochondrial anion transporter (VDAC), located at the outer mitochondrial membrane, and the MCU, located in the inner mitochondrial membrane. In the mitochondria, Ca²⁺ regulates the TCA cycle dehydrogenases, thus modulating the rate of NADH production and ATP synthesis. Excess Ca²⁺ flux from ER to mitochondria leads to mitochondrial Ca²⁺ overload and apoptosis. ER Ca²⁺ levels are also regulated through the store-operated Ca²⁺ entry (SOCE) at ER-PM contact sites. SOCE is mediated by the physical coupling between STIM, an ER protein, and Orai, a Ca²⁺ channel located at the PM, which allows Ca²⁺ entry from the extracellular compartment to the cytosol, and then into the ER through SERCA. (C) Regulation of organelle fission at ER contact sites: Sites of physical interactions between ER and mitochondria are shown to recruit key proteins involved in mitochondria fission such as DRP1. At the MAMs, DRP1 homo-oligomerizes, forming rings that help the ER tubule to constrict the mitochondria, leading to mitochondria fission.

Figure 4.

Obesity leads to loss of parallel endoplasmic reticulum (ER) sheets and predominance of ER tubules in the liver. (Left panel) Three-dimensional (3D) reconstruction of segmented ER morphology from livers derived from lean (upper panel) and obese (ob/ob) (lower panel) mice (1000 × 1000 × 400 pixels—8 × 8 × 3.2 μm³). (Middle panel) Reconstruction of hepatic ER and mitochondria segmentation on raw FIB-SEM images of lean (upper panel) and obese (ob/ob) mice (lower panel). (Right panel) The cartoon depicts the transition of ER subdomains promoted by obesity. Obesity leads to decreased parallel organized rough ER sheets and increased smooth ER tubules, resulting in a decreased ER sheet-to-tubule ratio. These alterations are accompanied by changes in the expression of ER-shaping proteins. While Climp-63 and RRBP1 (p180) levels are decreased, the expression levels of Reticulon 4 (Rtn4) and REEP5 are increased. Accordingly, obesity leads to decreased membrane-bound-polysome content. On the other hand, de novo lipogenesis and lipid droplet accumulation are increased in obesity. (The left and middle images shown in this figure are reprinted from Parlakgül et al. 2022; with permission from the authors through an agreement with Springer Nature 2022.)

Figure 5.

Obesity-driven alterations in endoplasmic reticulum (ER) contact sites in the liver. Obesity leads to chronic enrichment in mitochondria-associated membranes (MAMs) and increased expression of MAM proteins such as the inositol trisphosphate receptor isoform 1 (IP3R1) and phosphofurin acidic cluster sorting protein 2 (PACS-2). Increased MAMs and IP3Rs contributes to lower ER Ca²⁺ levels and higher mitochondrial Ca²⁺, which leads to higher ROS production and mitochondrial dysfunction. Increased IP3R1 activity in obesity also leads to increased cytosolic Ca²⁺ and phosphorylation of CaMKII, which in turn phosphorylates FOXO, with a direct impact on gluconeogenesis. Obesity leads to alterations in sphingolipid composition of the MAMs, driven by the enrichment of ceramide synthase CerS6 at these contact sites. Increased C_16:0 sphingolipids binding to the mitochondrial fission factor (Mff) leads to the recruitment of DRP1 to the mitochondria triggering mitochondrial fragmentation and dysfunction. Down-regulation of CerS6 in the liver protects from obesity and insulin resistance. Obesity also affects processes at the ER-PM contact sites, such as store-operated Ca²⁺ entry (SOCE). In obesity, SOCE is dysregulated due to defective STIM1 translocation, caused, at least in part, by aberrant STIM1 O-GlycNAcylation, a post-translational modification involving the addition of O-linked N-acetylglucosamine (GlcNac) to serine and threonine amino acids.