Protein lipidation in health and disease: molecular basis, physiological function and pathological implication

Abstract

Posttranslational modifications increase the complexity and functional diversity of proteins in response to complex external stimuli and internal changes. Among these, protein lipidations which refer to lipid attachment to proteins are prominent, which primarily encompassing five types including S-palmitoylation, N-myristoylation, S-prenylation, glycosylphosphatidylinositol (GPI) anchor and cholesterylation. Lipid attachment to proteins plays an essential role in the regulation of protein trafficking, localisation, stability, conformation, interactions and signal transduction by enhancing hydrophobicity. Accumulating evidence from genetic, structural, and biomedical studies has consistently shown that protein lipidation is pivotal in the regulation of broad physiological functions and is inextricably linked to a variety of diseases. Decades of dedicated research have driven the development of a wide range of drugs targeting protein lipidation, and several agents have been developed and tested in preclinical and clinical studies, some of which, such as asciminib and lonafarnib are FDA-approved for therapeutic use, indicating that targeting protein lipidations represents a promising therapeutic strategy. Here, we comprehensively review the known regulatory enzymes and catalytic mechanisms of various protein lipidation types, outline the impact of protein lipidations on physiology and disease, and highlight potential therapeutic targets and clinical research progress, aiming to provide a comprehensive reference for future protein lipidation research.

Fig. 1

The main commonly studied posttranslational modifications (PTMs) that are associated with various diseases. PTMs play a critical role in a broad spectrum of biological processes. Here, we conclude that 25 common types of PTMs and dysregulation of those PTMs are strongly associated with the pathogenesis of a variety of diseases

Fig. 2

The timeline of protein lipidation discoveries. The figure illustrates the timeline of protein lipidation research from their origin to the most advanced scientific discoveries, including regulatory enzymes, important protein substrates, clinical trials and the development of inhibitors

Fig. 3

Catalytic mechanisms of DHHC palmitoyl S-acyltransferases (DHHC-PATs) and depalmitoylases. Some DHHC-PATs go through two steps (ping-pong kinetic mechanisms) to catalyse substrate protein S-palmitoylation. First, DHHC-PAT undergoes autopalmitoylation, linking palmitoyl-CoA to Cys156 in the DHHC domain to form an acyl-enzyme transfer intermediate. Subsequently, the palmitoyl chain is transferred to the putative cysteine residue on the substrate protein to complete S-palmitoylation. For depalmitoylases, three categories of depalmitoylases are subject to being palmitoylated to arrive at proper positions to function. A portion of palmitoylated APT1 and APT2 localise to the Golgi, and APT1 is capable of depalmitoylating itself and APT2, which allows them to be released into the cytosol to ensure the steady-state distribution of APTs in the Golgi and the cytosol. A large proportion of palmitoylated proteins are depalmitoylated by APT1 and APT2 on the plasma membrane or in the cytosol. Some palmitoylated proteins on the plasma membrane could also be depalmitoylated by ABHDs. PPT1 and PPT2 are mainly responsible for depalmitoylation of substrate proteins that localise in lysosomes. There are two fates for substrate proteins after depalmitoylation. One of them returns to catalytic positions, such as the Golgi, to undergo repalmitoylation, and the other enters the lysosome to be degraded

Fig. 4

S-palmitoylation is involved in the regulation of multiple cellular signal transduction pathways. We summarised several crucial and well-established signalling pathways that are under the control of S-palmitoylation. The majority of proteins are subjected to S-palmitoylation at the ER or Golgi by the respective DHHC-PATs. Some protein substrates could traffic from the ER to the Golgi or Golgi to the plasma membrane after being palmitoylated to activate the corresponding signalling cascades (e.g., EGFR pathway, N-Ras/H-Ras pathway, GPCR pathway, AGK-Akt-mTORC1 pathway, STING pathway and LRP6 pathway). In some cases, protein substrates anchor at the original organelle after being palmitoylated. Once S-palmitoylation is blocked, these protein substrates detach from the original organelle to abnormally activate the corresponding signalling pathway (e.g., SCRIB pathway and FLT3-ITD pathway). In addition to regulating protein trafficking, some proteins are protected from degradation in lysosomes after being palmitoylated to further activate the corresponding signalling pathway (e.g., Fas pathway and PD-L1 pathway). In addition, S-palmitoylation can regulate the activation of signalling pathways by regulating protein‒protein interactions (e.g., the PCSK9-PI3K-Akt pathway). Furthermore, some protein substrates are under dynamic palmitoylation-depalmitoylation regulation, abnormally activating signalling pathways by increasing palmitate turnover (e.g., the STAT3 pathway). ER endoplasmic reticulum

Fig. 5

The catalytic mechanism and process of protein N-myristoylation. a Cotranslational myristoylation usually occurs on the glycine at the N-terminal end of nascent proteins after the methionine initiator has been removed by MetAP2. The catalytic mechanism follows the Bi–Bi mechanism. Conformational changes were induced after NMTs bound to the fatty acid chain of the myristoyl-CoA binding site. Then, the substrate binds to the NMTs and produces myristoylpeptide via a myristoyl transfer reaction. Finally, the NMTs release the myristoylpeptide and restore its conformation. b Posttranslational protein N-myristoylation often occurs during apoptosis. After the internal glycine of the substrate protein is exposed by caspase cleavage, NMTs catalyse the attachment of myristic acid to the glycine residue of the substrate. c Reversible protein N-myrisotylation occurs on the Nε-side chain of lysine residues instead of glycine residues, which is reversed by sirtuins or HDACs

Fig. 6

N-myristoylation is involved in the regulation of multiple cellular signal transduction pathways. We briefly summarised several well-established signalling pathways that are under the control of N-myristoylation, including the Scr-meditating oncogenetic pathway, Wnt pathway, Akt pathway, STING-autophagy pathway, Notch signalling pathway, TCR activation signalling pathway, TLR4 inflammatory responses, AMPK signalling pathway and B-cell receptor pathway

Fig. 7

The catalytic process of protein S-prenylation and postprenylation reactions. Most substrate proteins have a characteristic CAAX motif, which is the enzyme recognition site. First, a 15-carbon farnesyl or a 20-carbon geranylgeranyl isoprenoid lipid is attached to the cysteine residues on the CAAX motif of the substrate by FTase or GGTase-I, respectively. Then, the prenylated proteins translocate to the ER and undergo removal of the AAX motif by RCE1 and methylation by ICMT. After that, proteins such as Ras may be directly trafficked to the plasma membrane or undergo additional S-palmitoylation. Other proteins, such as RHO GTPases, bind to RHO guanine nucleotide dissociation inhibitors (GDIs) to assist in their trafficking. GDIs guanine nucleotide dissociation inhibitors, ER endoplasmic reticulum

Fig. 8

S-prenylation is involved in the regulation of multiple cellular signal transduction pathways. We briefly summarised several well-established signalling pathways of the main small GTPase family. The prenylation and post prenylation of these proteins often occur on the ER. K-Ras and N-Ras can be either farnesylated or geranylgeranylated, while H-Ras can only be farnesylated. N-Ras, H-Ras and K-Ras4a undergo S-palmitoylation before anchoring at the plasma membrane and activating downstream signalling. Other proteins, such as Rho, can switch membrane-bound states through binding to RhoGDI. Overall, protein prenylation mediates downstream signalling by regulating protein trafficking and protein‒protein interactions. ER endoplasmic reticulum, MAM mitochondria-associated endoplasmic reticulum membrane, RE recycling endosome

Fig. 9

Biosynthesis and maturation of GPI-anchored proteins (GPI-APs). N Nascent proteins first translocate to the ER following the N-terminal signal. After arriving at the ER, the N-terminal signal is removed. Subsequently, GPI-T recognises the amino acid at the ω position and catalyses the attachment of GPI at the ω position, followed by fatty acid remodelling of GPI with or without GalNAc side chain modification of the ER and Golgi. Finally, mature GPI-APs are trafficked to the plasma membrane and associate with raft microdomains. ER endoplasmic reticulum

Fig. 10

Glycosylphosphatidylinositol anchor proteins (GPI-APs) play a role in several cellular signal transduction pathways. In this section, we describe several classical GPI-APs and their roles in cellular signal transduction. CD109 negatively regulates TGF‐β signalling, while it can activate the Jak-STAT3 pathway to drive tumour metastasis. CD14 can activate TLR4 to trigger signalling pathways, including INF, tnf-α and IL-6 signalling, to initiate the immune response. Folate binds to FOLR1 to activate MEK/ERK signalling and the Jak-STAT3 pathway. ART could trigger NAD + -induced cell death. uPAR binds to Upa to stimulate the association of EGFR and β1 integrin to activate MEK/ERK signalling. ER endoplasmic reticulum

Fig. 11

Mechanism of hedgehog (Hh) and smoothened (SMO) cholesterylation. a Autoprocessing nucleophilic attack between C258 of Hh and G257 induces the formation of a labile thioester intermediate. Subsequently, the activated intermediate undergoes cleavage, and cholesterol attaches to HhH to complete HhH cholesterylation. b The autoprocessing nucleophilic attack between D95 and Y130 of SMO induces the formation of a high-energy intermediate, followed by ester exchange from D95–Y130 to D95–cholesterol. C258: Cystine 258; G257: Glycine 257. D95: Aspartic acid 95; Y130: Tyrosine 130

Fig. 12

The role of cholesterylation in Hedgehog (Hh) signalling. The Hh protein undergoes cholesterylation and O-palmitoylation on the ER and Golgi membrane before targeting the plasma membrane (PM). Subsequently, it is secreted into the extracellular space and trafficked with the help of Dispathed and Scube. After arriving at the Hh-receiving cell, Hh binds to PATCH1, resulting in the degradation of PATCH1, which reduces cholesterol efflux and activates smoothened (SMO). Cholesterylated SMO traffics to the PM and then activates the downstream oncogenic GLI signalling pathway. ER endoplasmic reticulum