Nε-lysine acetylation in the endoplasmic reticulum - a novel cellular mechanism that regulates proteostasis and autophagy

Abstract

Protein post-translational modifications (PTMs) take many shapes, have many effects and are necessary for cellular homeostasis. One of these PTMs, Nε-lysine acetylation, was thought to occur only in the mitochondria, cytosol and nucleus, but this paradigm was challenged in the past decade with the discovery of lysine acetylation in the lumen of the endoplasmic reticulum (ER). This process is governed by the ER acetylation machinery: the cytosol:ER-lumen acetyl-CoA transporter AT-1 (also known as SLC33A1), and the ER-resident lysine acetyltransferases ATase1 and ATase2 (also known as NAT8B and NAT8, respectively). This Review summarizes the more recent biochemical, cellular and mouse model studies that underscore the importance of the ER acetylation process in maintaining protein homeostasis and autophagy within the secretory pathway, and its impact on developmental and age-associated diseases.

Keywords: Autophagy; Endoplasmic reticulum; Lysine acetylation; Secretory pathway.

Fig. 1.

Metabolic pathways that maintain acetyl-coenzyme A levels in the cell. See also Box 1. Abbreviations: ACAA1, 3-ketoacyl-CoA thiolase; ACAA2, mitochondrial 3-ketoacyl-CoA thiolase; ACDH, 3-hydroxy acyl-CoA dehydrogenase; AceAld, acetaldehyde; AceCS1, cytoplasmic/nuclear acetyl-coenzyme A synthetase; AceCS2, mitochondrial acetyl-coenzyme A synthetase; ACLY, ATP-citrate lyase; ACOT, acyl-CoA thioesterase; ACOX, peroxisomal acyl-CoA oxidase 1; ADH1B, alcohol dehydrogenase 1B; ALDH1, acetaldehyde dehydrogenase; ALDH2, aldehyde dehydrogenase 2; BCAA, branched-chain amino acids; BCAT2, mitochondrial branched-chain amino acid aminotransferase; BCKDC, branched-chain α-keto acid dehydrogenase complex; BDH1, beta-hydroxybutyrate dehydrogenase; B-OH, beta-hydroxybutyric acid; Cit, citrate; CoA, coenzyme A; CPT1, carnitine palmitoyltransferase 1; CPT2 carnitine palmitoyltransferase 2; CS, citrate synthase; DPCK, dephosphocoenzyme A kinase; ECH, 2,3 enoyl-CoA hydrase; ECHD, enoyl-CoA hydratase; ER, endoplasmic reticulum; EtOH, ethanol; FFA, medium/short chain free fatty acid; GDH, glutamate dehydrogenase; Gln, glutamine; GLS, glutaminase; Glu, glutamate; HADH, mitochondrial hydroxyacyl-coenzyme A dehydrogenase; HADH, 3-hydroxyacyl-CoA dehydrogenase; HMG-CoA lyase, 3-hydroxy-3-methylylglutaryl-CoA lyase; HMG-CoA synthase, hydroxymethyl glutaryl-CoA synthase; LC-FACS, long chain fatty acyl-CoA synthetase; LC-FFA, long chain free fatty acid; Mal, malate; MC-CoA, medium chain coenzyme A; MDH, malate dehydrogenase; OAA, oxaloacetate; PANK, pantothenic acid kinase; PDH, pyruvate dehydrogenase; PPAT, phosphopantetheine adenylyl transferase; PPCDC, phosphopantothenoylcysteine decarboxylase; PPCS, phosphopantothenoylcysteine synthetase; Pyr, pyruvate; SLC13A5, solute carrier family 13A5; SLC25A1, solute carrier family 25A1; AT-1 (SLC33A1), solute carrier family 33A1/acetyl-CoA transporter protein 1; TCA, tricarboxylic acid cycle; VLC-FACS, very long chain fatty acyl-CoA synthetase; VLC-FFA, very long chain free fatty acid.

Fig. 2.

The ER acetylation machinery. Acetyl-CoA is synthesized in the cytosol through a multi-step process and is then transported into the ER lumen by the ER membrane transporter AT-1. In the ER lumen, acetyl-CoA is used by two ER-based acetyltransferases, ATase1 and ATase2, to acetylate ER-cargo and -resident proteins. Both ATase1 and ATase2 are type-II membrane proteins with the catalytic domain facing the lumen of the organelle.

Fig. 3.

The ER acetylation machinery is an integral component of ER quality control and regulates the efficiency of the secretory pathway. Secretory membrane or lumenal proteins are synthesized close to the ER and enter the organelle through the translocon (SEC61–SEC62–SEC63) complex (1). Proteins with an N-x-S/T consensus sequence (yellow circles) for N-glycosylation that is 14 or 15 amino acids (∼40 Å) away from the inner membrane, are recognized by the oligosaccharyltransferase (OST) complex, which interacts with the translocon and transfers a preassembled GlcNAc₂Man₉Glc₃ oligosaccharide (branched lines) to the asparagine residue of the nascent glycoprotein (2). Correctly folded glycoproteins are then recognized by the ATases, which interact with the OST to acetylate specific lysine residues (3). The acetylated lysine residues act as a positive marker that allows correctly folded glycoproteins to advance toward the Golgi (4). Unfolded or misfolded glycoproteins, although N-glycosylated, are not recognized by the ATases (5), and, as a result, are prevented from reaching the Golgi and are disposed of (6). Although supported by a number of publications (see text), the above is only a working model for how the ER acetylation machinery might regulate the secretory pathway.

Fig. 4.

The ER acetylation machinery regulates the induction of reticulophagy. ATG9A is acetylated on two lysine residues (K359 and K363) that face the lumen of the ER. The acetylation status of ATG9A regulates its ability to interact with SEC62 and FAM134B. Both SEC62 and FAM134B appear to act as reticulophagy receptors by engaging with cytosolic LC3β, whereas ATG9A appears to act as an ER acetylation sensor. In its acetylated form, ATG9A is unable to interact with either SEC62 or FAM134B, thus impeding further engagement of LC3β and inhibiting the induction of reticulophagy (upper half). In contrast, when non-acetylated, ATG9A is able to interact with SEC62 and FAM134B, which engage LC3β and induce reticulophagy (lower half). Although supported by a number of publications (see text), the above is only a working model for how the ER acetylation machinery might regulate the induction of reticulophagy.