Refining S-acylation: Structure, regulation, dynamics, and therapeutic implications

Abstract

With a limited number of genes, cells achieve remarkable diversity. This is to a large extent achieved by chemical posttranslational modifications of proteins. Amongst these are the lipid modifications that have the unique ability to confer hydrophobicity. The last decade has revealed that lipid modifications of proteins are extremely frequent and affect a great variety of cellular pathways and physiological processes. This is particularly true for S-acylation, the only reversible lipid modification. The enzymes involved in S-acylation and deacylation are only starting to be understood, and the list of proteins that undergo this modification is ever-increasing. We will describe the state of knowledge on the enzymes that regulate S-acylation, from their structure to their regulation, how S-acylation influences target proteins, and finally will offer a perspective on how alterations in the balance between S-acylation and deacylation may contribute to disease.

Figure 1.

The protein S-acylation cycle. (A) Schematic representation of the S-acylation cycle. A medium-long chain fatty acid moiety from an acyl-CoA is added to a cytosolic cysteine of the target protein by an acyltransferase (ZDHHC). The enlarged view shows different domains of an acyltransferase. The thioester linkage formed between the acyl chain and the thiol group is hydrolyzed by an acyl-protein thioesterase (APT). (B) Number of ZDHHC acyltranferases in different model organisms. (C) Structures of acylating and deacylating enzymes. Left panel: Ribbon diagram of ZDHHC20, schematically showing that it leads to membrane deformation to expose its catalytic site to the cytosolic milieu (Stix et al., 2020b). Right panel: Ribbon diagram of APT2, schematically showing that it deforms the lipid monolayer to which it binds, facilitating the extraction of the acyl chain, which is covalently attached to the APT2 substrate, from the membrane for hydrolysis (Abrami et al., 2021). The extracted acyl chain is shown in the green space field.

Figure 2.

Phylogenetic tree of human ZDHHC enzymes. Multiple sequence alignment of human ZDHHCs was performed using Clustal Omega (Sievers et al., 2011). The tree was constructed using the neighbor-joining method and was visualized using iTOL (Letunic and Bork, 2011). ZDHHCs are color-coded based on their reported subcellular localization(s) (Abrami et al., 2017, 2021; Ernst et al., 2018; Sandoz et al., 2023), and examples of substrates for each enzyme are shown in black (for a complete list of reported S-acylated proteins visit https://www.swisspalm.org/ [Blanc et al., 2015]).

Figure 3.

Degradation of S-acylated proteins in lysosomes. S-acylated proteins, whether cytosolic or transmembrane, can reach late endosomes/lysosomes via three routes: (1) by the classical endosomal trafficking route, (2) by the autophagic pathway, or (3) by interorganelle vesicular trafficking, when proteins are targeted for degradation, for example via ERLAD (ER to lysosome associate degradation; Rudinskiy and Molinari, 2023). It is only at the last step, when the membranes present in the lysosomal lumen lose their integrity, that the acylated cysteines are exposed to luminal PPT1 for deacylation. At this stage, proteins might already have been fragmented into peptides.