Palmitoylation of ULK1 by ZDHHC13 plays a crucial role in autophagy

S-palmitoylation coordinates the trafficking of ATG9A to mediate autophagy initiation

ABBREVIATION

17-ODYA: 17-octadecynoic acid; 293T: HEK293T; 2-BP: 2-bromopalmitate; 2CS: Cys155Ser and Cys156Ser; ABE: acyl-biotin exchange; AP: adaptor protein; APEX2: ascorbate peroxidase 2; ATG: autophagy related; baf A1: bafilomycin A1; CRISPR: clustered regularly interspaced short palindromic repeats; CTD: C-terminal domain; Cys: cysteine; DAB: 3,3'-diaminobenzidine; EV: empty vector; H2O2: hydrogen peroxide; IF: immunofluorescence; IP: immunoprecipitation; KO: knockout; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; NTD: N-terminal domain; PAS: phagophore assembly site; PBS: phosphate-buffered saline; PtdIns3K-CI: class III phosphatidylinositol 3-kinase complex I; PM: plasma membrane; PTM: post-translational modifications; Ser: serine; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy; TGN: trans-Golgi network; ULK1: unc-51 like autophagy activating kinase 1; WCL, whole cell lysates; WDR45/WIPI4: WD repeat domain 45; WT: wild-type; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1.

Dysregulation of autophagy during photoaging reduce oxidative stress and inflammatory damage caused by UV

Photoaging, the premature aging of skin due to chronic ultraviolet (UV) exposure, is a growing concern in dermatology and cosmetic science. While UV radiation is known to induce DNA damage, oxidative stress, and inflammation in skin cells, recent research unveils a promising countermeasure: autophagy. This review explores the intricate relationship between autophagy and photoaging, highlighting how this cellular recycling process can mitigate UV-induced damage. We begin by examining the differential impacts of UVA and UVB radiation on skin cells and the role of oxidative stress in accelerating photoaging. Next, we delve into the molecular mechanisms of autophagy, including its various forms and regulatory pathways. Central to this review is the discussion of autophagy's protective functions, such as the clearance of damaged organelles and proteins, and its role in maintaining genomic integrity. Furthermore, we address the current challenges in harnessing autophagy for therapeutic purposes, including the need for selective autophagy inducers and a deeper understanding of its context-dependent effects. By synthesizing recent advancements and proposing future research directions, this review underscores the potential of autophagy modulation as a novel strategy to prevent and treat photoaging. This comprehensive analysis aims to inspire further investigation into autophagy-based interventions, offering new hope for preserving skin health in the face of environmental stressors.

Protein lipidation in the tumor microenvironment: enzymology, signaling pathways, and therapeutics

Protein lipidation is a pivotal post-translational modification that increases protein hydrophobicity and influences their function, localization, and interaction network. Emerging evidence has shown significant roles of lipidation in the tumor microenvironment (TME). However, a comprehensive review of this topic is lacking. In this review, we present an integrated and in-depth literature review of protein lipidation in the context of the TME. Specifically, we focus on three major lipidation modifications: S-prenylation, S-palmitoylation, and N-myristoylation. We emphasize how these modifications affect oncogenic signaling pathways and the complex interplay between tumor cells and the surrounding stromal and immune cells. Furthermore, we explore the therapeutic potential of targeting lipidation mechanisms in cancer treatment and discuss prospects for developing novel anticancer strategies that disrupt lipidation-dependent signaling pathways. By bridging protein lipidation with the dynamics of the TME, our review provides novel insights into the complex relationship between them that drives tumor initiation and progression.

S-palmitoylation modulates ATG2-dependent non-vesicular lipid transport during starvation-induced autophagy

Lipid transfer proteins mediate the non-vesicular transport of lipids at membrane contact sites to regulate the lipid composition of organelle membranes. Despite significant recent advances in our understanding of the structural basis for lipid transfer, its functional regulation remains unclear. In this study, we report that S-palmitoylation modulates the cellular function of ATG2, a rod-like lipid transfer protein responsible for transporting phospholipids from the endoplasmic reticulum (ER) to phagophores during autophagosome formation. During starvation-induced autophagy, ATG2A undergoes depalmitoylation as the balance between ZDHHC11-mediated palmitoylation and APT1-mediated depalmitoylation. Inhibition of ATG2A depalmitoylation leads to impaired autophagosome formation and disrupted autophagic flux. Further, in cell and in vitro analyses demonstrate that S-palmitoylation at the C-terminus of ATG2A anchors the C-terminus to the ER. Depalmitoylation detaches the C-terminus from the ER membrane, enabling it to interact with phagophores and promoting their growth. These findings elucidate a S-palmitoylation-dependent regulatory mechanism of cellular ATG2, which may represent a broad regulatory strategy for lipid transport mediated by bridge-like transporters within cells.

Artemether relieves liver fibrosis by triggering ferroptosis in hepatic stellate cells via DHHC12-mediated S-palmitoylation of the BECN1 protein

Liver fibrosis, a pivotal stage in chronic liver disease progression, is driven by hepatic stellate cell (HSC) activation. Ferroptosis is a novel form of programmed cell death, which offers therapeutic potential for liver fibrosis. Although artemether (ART) exhibits antifibrotic properties, its mechanisms in liver fibrosis remain unclear. This study aimed to determine the therapeutic effects of ART on liver fibrosis and explore the role of S-palmitoylation in HSC ferroptosis.

METHODS

A mouse model of liver fibrosis was constructed by carbon tetrachloride (CCl4) injection. Transforming growth factor-β (TGF-β) was used for stimulating HSC activation in vitro. Histopathological and serological assays were performed to analyze the therapy effects of ART. Liquid Chromatography/Mass Spectrometry (LC/MS) and acyl-biotinyl exchange (ABE) were used to determine the role of S-palmitoylation in ART-induced HSC ferroptosis. Western blot and Co-Immunoprecipitation (Co-IP) were performed to examine the effects of autophagy in ART-induced HSC ferroptosis through regulating BECN1 S-palmitoylation.

RESULTS

ART ameliorated liver fibrosis by inducing HSC ferroptosis, and the ferroptosis inhibitor ferrostatin-1 (Fer-1) impaired the inhibitory effect of ART. Interestingly, the levels of S-palmitoylation were elevated by upregulating the palmitoyltransferase DHHC12 during ART-induced HSC ferroptosis. DHHC12 knockdown reduced S-palmitoylation levels and impaired ART-mediated HSC ferroptosis. RNA-seq analysis indicated that autophagy activation was essential for ART to induce HSC ferroptosis. 3-methyladenine (3-MA) suppressed autophagy and ART-induced HSC ferroptosis. Importantly, BECN1 S-palmitoylation by DHHC12 drove ART to activate autophagy. DHHC12 bound to the cysteine 21 residue of BECN1, thereby stabilizing the BECN1 protein and facilitating autophagy activation. Mutation of the cysteine 21 residue decreased BECN1 protein stability, autophagy activation and ferroptosis in ART-treated HSCs. In a mouse model of hepatic fibrosis, HSC-specific inhibition of BECN1 S-palmitoylation reversed ART-induced HSC ferroptosis and the improvement of fibrotic liver.

CONCLUSIONS

ART alleviates liver fibrosis by inducing HSC ferroptosis via DHHC12-mediated BECN1 protein S-palmitoylation.

The emerging roles of S-acylation in autophagy

Autophagy is an intracellular degradation system that delivers cytoplasmic materials to the lysosome. S-acylation, a reversible post-translational modification that attaches long-chain fatty acids to cysteine residues within proteins, has recently emerged as an important regulatory mechanism for autophagy. In this forum article, we review and discuss the emerging roles of S-acylation in autophagy.

Protein palmitoylation: biological functions, disease, and therapeutic targets

Protein palmitoylation, a reversible post-translational lipid modification, is catalyzed by the ZDHHC family of palmitoyltransferases and reversed by several acyl protein thioesterases, regulating protein localization, accumulation, secretion, and function. Neurological disorders encompass a spectrum of diseases that affect both the central and peripheral nervous system. Recently, accumulating studies have revealed that pathological protein associated with neurological diseases, such as β-amyloid, α-synuclein, and Huntingtin, could undergo palmitoylation, highlighting the crucial roles of protein palmitoylation in the onset and development of neurological diseases. However, few preclinical studies and clinical trials focus on the interventional strategies that target protein palmitoylation. Here, we comprehensively reviewed the emerging evidence on the role of protein palmitoylation in various neurological diseases and summarized the classification, processes, and functions of protein palmitoylation, highlighting its impact on protein stability, membrane localization, protein-protein interaction, as well as signal transduction. Furthermore, we also discussed the potential interventional strategies targeting ZDHHC proteins and elucidated their underlying pathogenic mechanisms in neurological diseases. Overall, an in-depth understanding of the functions and significances of protein palmitoylation provide new avenues for investigating the mechanisms and therapeutic approaches for neurological disorders.

ZDHHC3-LYPLA1 regulates PRRSV-2 replication through reversible palmitoylation

Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly contagious swine pathogen, causing respiratory problems in piglets and reproductive failure in sows. Palmitoylation, catalyzed by zinc finger Asp-His-His-Cys (ZDHHC) domain-containing palmitoyl acyltransferases, plays intricate roles in virus infection. However, whether palmitoylation regulates PRRSV replication is incompletely understood. Here, we report that inhibition of palmitoylation by 2-bromo palmitate (2-BP) promotes PRRSV multiplication. ZDHHC3 is identified as the key palmitoyl transferase regulating PRRSV replication in PAMs infection. Mechanistically, ZDHHC3 catalyzes nucleocapsid (N) protein palmitoylation at cysteine 90. This modification prevents the Nsp9-N protein interaction and subsequent viral RNA synthesis. Furthermore, LYPLA1 de-palmitoylates N protein, thus counteracting the ZDHHC3's activity on PRRSV replication. Meanwhile, the administration of small-molecule inhibitor ML348 targeting LYPLA1 could hinder PRRSV-2 replication. In summary, our results underscore the critical role of reversible palmitoylation in PRRSV replication. These findings might provide potential new anti-PRRSV strategies.

Mammalian nucleophagy: process and function

The nucleus is a highly specialized organelle that houses the cell's genetic material and regulates key cellular activities, including growth, metabolism, protein synthesis, and cell division. Its structure and function are tightly regulated by multiple mechanisms to ensure cellular integrity and genomic stability. Increasing evidence suggests that nucleophagy, a selective form of autophagy that targets nuclear components, plays a critical role in preserving nuclear integrity by clearing dysfunctional nuclear materials such as nuclear proteins (lamins, SIRT1, and histones), DNA-protein crosslinks, micronuclei, and chromatin fragments. Impaired nucleophagy has been implicated in aging and various pathological conditions, including cancer, neurodegeneration, autoimmune disorders, and neurological injury. In this review, we focus on nucleophagy in mammalian cells, discussing its mechanisms, regulation, and cargo selection, as well as evaluating its therapeutic potential in promoting human health and mitigating disease.Abbreviations: 5-FU: 5-fluorouracil; AMPK, AMP-activated protein kinase; ATG, autophagy related; CMA, chaperone-mediated autophagy; DRPLA: dentatorubral-pallidoluysian atrophy; ER, endoplasmic reticulum; ESCRT: endosomal sorting complex required for transport; HOPS, homotypic fusion and vacuole protein sorting; LIR: LC3-interacting region; MEFs: mouse embryonic fibroblasts; mRNA: messenger RNA; MTORC1: mechanistic target of rapamycin kinase complex 1; PCa: prostate cancer; PE: phosphatidylethanolamine; PI3K, phosphoinositide 3-kinase; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; rRNA: ribosomal RNA; SCI: spinal cord injury; SCLC: small cell lung cancer; SNARE: soluble N-ethylmaleimide-sensitive factor attachment protein receptor; SupraT: supraphysiological levels of testosterone; TOP1cc: TOP1 cleavage complexes.

MiR-192 and miR-731 synergically inhibit RGNNV infection by targeting ULK1-mediated autophagy in sea perch (Lateolabrax japonicus)

MicroRNAs (miRNAs) are crucial regulators of gene expression and are closely linked to viral infections. Nervous necrosis virus (NNV) poses a significant threat to global fish aquaculture. This study investigates the roles of miR-192 and miR-731 in controlling NNV infection and associated autophagy in sea perch (Lateolabrax japonicus). Our findings reveal that both miRNAs are upregulated in infected brain tissues and cells of sea perch, leading to reduced NNV replication. miR-192 and miR-731 synergistically reduce NNV replication by downregulating the RNA-dependent RNA polymerase and capsid protein genes, and disrupting autophagy by altering LC3 distribution and autophagy-related protein expressions. Additionally, L. japonicus unc-51 like autophagy activating kinase 1 protein (LjULK1) was identified as the target of miR-192 and miR-731. LjULK1 is integrally associated to the ULK-VAPs-Atg13 autophagic signaling, enhancing NNV-induced autophagy, and facilitating viral infection. Modulating LjULK1 expression counteracts the inhibitory effects of miR-192 and miR-731 on NNV, suggesting these miRNAs act as negative regulators of NNV infection by targeting LjULK1-mediated autophagy. Our findings reveal a novel miRNAs-regulated antiviral mechanism against NNV, offering insights into potential strategy to prevent NNV infection in fish.