Protein acylation: mechanisms, biological functions and therapeutic targets

Abstract

Metabolic reprogramming is involved in the pathogenesis of not only cancers but also neurodegenerative diseases, cardiovascular diseases, and infectious diseases. With the progress of metabonomics and proteomics, metabolites have been found to affect protein acylations through providing acyl groups or changing the activities of acyltransferases or deacylases. Reciprocally, protein acylation is involved in key cellular processes relevant to physiology and diseases, such as protein stability, protein subcellular localization, enzyme activity, transcriptional activity, protein-protein interactions and protein-DNA interactions. Herein, we summarize the functional diversity and mechanisms of eight kinds of nonhistone protein acylations in the physiological processes and progression of several diseases. We also highlight the recent progress in the development of inhibitors for acyltransferase, deacylase, and acylation reader proteins for their potential applications in drug discovery.

Fig. 1

Timeline of the historical milestone for the discovery of protein acylation, and the chemical structures of acyl groups. Since acetylation was identified in 1960s, more than eight kinds of acylation modifications have been discovered, especially after 2009, because of the quick development of mass spectrometry and biochemistry technologies, as well as powerful algorithm methods. The eight kinds of protein acylations mentioned here can be divided into three groups according to their chemical structures. Acetyl- and crotonyl- are short-chain hydrophobic acyl groups. Myristoyl- and palmitoyl- are long-chain fatty acid hydrophobic acyl groups. β-hydroxybutyryl- and lactyl- belong to the polar acyl groups. Succinyl- and malonyl- belong to the negatively charged acidic acyl groups. The short-chain acylation mainly occurs at lysine residues. Whereas myristoylation often occurs at N-terminal glycine or lysine residues, and palmitoylation usually occurs at cysteine, serine or N-terminal amino acid residues

Fig. 2

Protein acetylation in shaping tumor metabolism and oncogenic signaling. Protein acetylation usually influence tumor progression via regulating metabolic enzymes and oncoproteins. a Protein acetylation in the regulation of tumor metabolism. Metabolic enzymes responsible for tumorigenesis and proliferation are regulated by acetylation. PGK1 is acetylated by PCAF at K323 to promote glucose uptake. GNPAT is acetylated by ACAT1 at K128 to inhibit FASN degradation and enhance lipid synthesis. SIRT2 degradation leads to succinate production and H3K4me3 activation. The above effects either provide energy source for tumor proliferation or activate tumor-specific gene transcription. Besides, protein acetylation can also occur on metabolic enzymes responsible for tumor metastasis. ENO2 is deacetylated by HDAC3 at K394 to increase its activity and glycolysis. IDH1 involved in glutamine metabolism is deacetylated at K224 to inhibit its enzymatic activity and HIF1α-SRC transcription axis. Enhanced glycolysis and HIF1α-SRC transcription axis is closely connected with tumor metastasis. b Acetylation of oncogenic signaling proteins relates to tumorigenesis, proliferation and metastasis. TRIB3 promotes KAT5-mediated SMAD3 acetylation at K333 to promote the transcriptional activity of SMAD3, which positively regulates transcription of the downstream TRIB3 and results in autophagy blockade. SIRT2 inhibits SMC1A acetylation at K579 to induce proper mitosis. SMAD3 recruits p300 to acetylate KLF5 at K369 and promote the expression of its target gene—CXCR4 and EMT. BRD4 recognizes CBP-acetylated Snail (K146 and K187) to enhance its protein stability and promote EMT. ACC1 is phosphorylated and inactivated by leptin or TGF-β signaling, resulting in increased acetyl-CoA and SMAD2 acetylation, which finally upregulates SMAD2 transcriptional activity and EMT

Fig. 3

Protein acylation in shaping tumor immune microenvironment. Protein acylation helps to shape immunosuppressive tumor microenvironment via regulating immune cell activation, infiltration and antigen presentation. a Protein acylation in immune braking or activation. HDAC2 inhibits PD-L1 acetylation to increase its nuclear localization and immune checkpoints activation. P300 mediates MEF2D acetylation to promote PD-L1 transcription. ZDHHC3 and ZDHHC9 mediate PD-L1 palmitoylation to inhibit its lysosomal degradation. The three events will induce T cells exhaustion. Rae-1 is acetylated by PCAF and GCN5 to enhance its stability and activate NK/T cells killing ability. b Protein acylation in immune infiltration. P300-mediated TRIB3 acetylation inhibits T cells infiltration through inhibiting CXCL10 transcription. SIRT1-mediated p53 deacetylation promotes TAM infiltration through secreting CXCL12. KAT6A-mediated SMAD3 acetylation results in its transactivation and the transcription of cytokines, including IL-6/IL-12/TNF-α and promotes MDSC infiltration. c Protein acylation in antigen presentation. OPTN interacts with AP3D1 to hinder its recognition of IFNGR1, thereby maintaining IFNGR1 stability and the integrity of downstream MHC-I signaling, promoting antigen presentation to T cells

Fig. 4

Protein succinylation and malonylation on metabolic enzymes or kinases in tumor, inflammatory, cardiovascular and metabolic diseases. The negatively charged acidic acyl groups including malonyl group derived from acetyl-CoA or malate, and succinyl group derived from α-KG or amino acids take part in the PTMs of metabolic enzymes in numerous kinds of diseases. a, e Protein Ksuc and Kmal in tumor. CPT1A mediated LDHA succinylation at K222 to inhibit its autophagic degradation via p62 to accelerate gastric cancer (a). Depletion or inhibition of FASN enhances malonyl-CoA level and promotes mTOR malonylation at K1218 to downregulate its kinase activity and the subsequent phosphorylation of p70S6K/4EBP1, promoting endothelial cells proliferation and tumor angiogenesis (e). b, f Protein succinylation and malonylation in metabolic enzymes play critical roles in LPS-induced inflammation of macrophages. LPS inhibits SIRT5 mediated desuccinylation of PKM2 at K311 to inhibit its kinase activity and increase its nuclear translocation by promoting PKM2 tetramer-to-dimer transition. The nucleus PKM2 interacts with HIF1α to promote IL-1β transcription and inflammation (b). LPS stimulation enhances malonyl-CoA level and promotes GAPDH malonylation at K213 in macrophages, leading to its increased enzymatic activity and dissociation from TNFα mRNA, promoting TNFα expression and inflammation (f). c, g Protein succinylation and malonylation in metabolic enzymes play critical roles in cardiovascular disease. Knockout of SIRT5 results in increased Ksuc in ECHA at K315, inhibiting its enzymatic activity and ATP production and promoting hypertrophic cardiomyopathy (c). IDH2 malonylation decreases its enzymatic activity and promotes cardiomyopathy (g). d, h Protein succinylation and malonylation in metabolic enzymes play critical roles in metabolic disease. HDAC1 inhibits SREBP1 succinylation and increases its protein stability, promoting hepatic steatosis (d). SIRT5 mediates several key metabolic enzymes malonylation to promote glycolysis and FAO, inhibiting hepatic steatosis (h)

Fig. 5

Lactate and protein lactylation contribute to the suppressive tumor immune microenvironment. Anaerobic glycolysis produces lactate in the cell cytoplasm, which is transported to the extracellular matrix (ECM) via MCT1/4, resulting in low pH tumor microenvironment (TME). The lactate in the ECM inhibits NK cells tumor infiltration and activity, reduces CD8⁺ T cells glycolysis, proliferation and cytotoxicity. Lactate also promotes the M2 polarization of macrophages and increases the release of anti-inflammatory cytokines from tumor-associated dendritic cells (TADCs). Besides, lactate enhances Treg cells function through promoting lactylation of MOESIN at the K72 residue in the cytoplasm, which upregulates TGF-β signaling via enhancing the interaction between MOESIN and TGF-βRI and increases expression of FOXP3

Fig. 6

Protein palmitoylation and myristoylation within tumor, infectious diseases and neurological diseases in affecting protein-membrane binding. In the protein palmitoylation process, DHHC domain of ZDHHCs binds to the palmitoyl-CoA located in the membrane and undergoes autopalmitoylation, which is followed by a transfer of the palmitate group to the cysteine residue of the substrate protein, promoting the membrane localization of the substrates. The myristoylation process is similar with palmitoylation. First, NMT binds the fatty acid chain of myristoyl-CoA to form the myristoyl-CoA-NMT complex accompanied by substrate-binding pocket exposure, allowing the substrate protein to bind. Second, the NMT catalyzes N-myristoylpeptide formation through chemical transformation and releases the myristoylpeptide and CoA. These two kinds of PTMs promote tumor progression through regulating oncogenic signaling pathways, autophagy, tumor metabolism, ER stress, and tumor immune microenvironment. Besides, they are also critical to the infection of COVID-19, Rhinovirus and HIV, and play important roles in neurological diseases, including Alzheimer’s disease (AD), Huntington’s disease (HD), Parkinson’s disease (PD), and depression

Fig. 7

Crosstalk between protein acylation and metabolism in human diseases. Protein acylation on the metabolic enzymes or transporters always modulate human diseases through affecting glycolysis, fatty acid, and amino acid metabolism. As described in the left, LDHA succinylation, LDHB, ENO2, and PGK1 acetylation, GAPDH malonylation, ENO1 crotonylation and GLUT1 palmitoylation (Spal) can regulate glycolysis. SHMT2 succinylation and IDH1 acetylation regulate amino acid (AA) metabolism. Besides, GNPAT acetylation, SREBP1c, ECHA, and PKM2 succinylation influence fatty acid metabolism. From the view of disease, succinylation of LDHA, SHMT2, acetylation of ENO2, PGK1, IDH1, and GNPAT, crotonylation of ENO1 and palmitoylation of GLUT1 are critical in tumor; acetylation of LDHB and succinylation of SREBP1c is critical in hepatic steatosis; malonylation of GAPDH and succinylation of PKM2 is critical in inflammation; succinylation of ECHA is critical in cardiovascular disease. As described in the right, cell intrinsic and extrinsic metabolism conditions will in turn affect the eight kinds of protein acylations