{"title":"The human autophagy-initiating complexes ULK1C and PI3KC3-C1.","authors":"Minghao Chen,James Hurley","doi":"10.1016/j.jbc.2025.110391","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110391","url":null,"abstract":"The unc-51-like kinase complex (ULK1C) and the class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) are the key regulators of macroautophagy initiation. Understanding the assembly and coordination of these two complexes is essential for deciphering their cellular regulation and targeting them for therapeutic enhancement. This review highlights recent advances in our understanding of the structural organization and activation mechanisms of ULK1C and PI3KC3-C1 at the molecular level and discusses their roles within the protein interaction network governing autophagy initiation.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"147 1","pages":"110391"},"PeriodicalIF":4.8,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Silencing PIM1 inhibits ENO1-induced AKT activation and attenuates fibrillogenesis during spinal cord injury-induced skeletal muscle atrophy.","authors":"Xiao Yu,Jiang Cao,Binyu Wang,Jiaju Fu,Jingcheng Liu,Tao Sui,Zi Wang,Chaoqin Wu,Jie Chang,Xiaojian Cao,Shaohua Zhang","doi":"10.1016/j.jbc.2025.110398","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110398","url":null,"abstract":"Spinal cord injury (SCI) induces rapid and extensive skeletal muscle atrophy. During skeletal muscle atrophy, numerous extracellular matrix (ECM) and fibroblasts accumulate, impairing muscle function. The pro-viral Integration site for moloney murine leukaemia virus kinases-1(PIM1) is considered a positive regulator of inflammation. In our study, we found that PIM1 was overexpressed in the fibrotic regions of the skeletal muscle following SCI. We then explored the effects of the selective PIM1 inhibitor TP-3654 on fibrosis. TP-3654 decreased fibrosis by promoting fibroblast apoptosis, reducing proliferation and migration, and inhibiting tumor growth factor (TGF)-β classical and non-classical signaling pathways. In vivo PIM1 pharmacological inhibition with TP-3654 alleviates skeletal muscle fibrosis, mitigating skeletal muscle atrophy by decreasing ECM formation, enhancing the cross-sectional area of muscle fibers, and increasing muscle weight. Furthermore, we found a potential interaction between PIM1 and the enolase (ENO1)/protein kinase B (AKT) pathway. Downregulation of PIM1 expression in fibroblasts using drugs or siRNA leads to decreased ENO1 expression, concurrent with AKT phosphorylation reduction and suppressor of mothers against decapentaplegic (Smad)2/3 dephosphorylation within the TGF-β classical pathway. In summary, PIM1 might be an important target gene for future skeletal muscle atrophy treatments.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"244 1","pages":"110398"},"PeriodicalIF":4.8,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Functional insights into Plasmodium actin depolymerizing factor interactions with phosphoinositides.","authors":"Devaki Lasiwa, Inari Kursula","doi":"10.1016/j.jbc.2025.110399","DOIUrl":"10.1016/j.jbc.2025.110399","url":null,"abstract":"<p><p>Malaria is caused by protozoan parasites, Plasmodium spp., that belong to the phylum Apicomplexa. The life cycle of these parasites depends on two different hosts; the definitive host, or vector, is a mosquito, and the intermediate host is a vertebrate, such as human. Malaria parasites use a unique form of substrate-dependent motility for host cell invasion and egress, which is dependent on an actomyosin motor complex called the glideosome. Apicomplexa have a small set of actin regulators, which are poorly conserved compared to their equivalents in higher eukaryotes. Actin depolymerizing factors (ADFs) are key regulators responsible for accelerating actin turnover in eukaryotic cells. The activity of ADFs is regulated by membrane phosphoinositides. Malaria parasites express two ADF isoforms at different life stages. ADF1 differs substantially from canonical ADF/cofilins and from Plasmodium ADF2 in terms of both structure and function. Here, we studied the interaction of both Plasmodium ADFs with phosphoinositides using biochemical and biophysical methods and mapped their binding sites on ADF1. Both Plasmodium ADFs bind to different phosphoinositides, and binding in vitro requires the formation of vesicles or micelles. Interaction with phosphoinositides increases the α-helical content of the parasite ADFs, and the affinities are in the micromolar range. The binding site for PI(4,5)P<sub>2</sub> in PfADF1 involves a small, positively charged surface patch.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"110399"},"PeriodicalIF":4.0,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jianxin Zhao,Zheng Zhao,Wen Zhou,Jianzhi Zhang,Jinfeng Chen,Jianwei Sun,Jing Li
{"title":"YEATS2 O-GlcNAcylation Promotes Chromatin Association of the ATAC Complex and Lung Cancer Tumorigenesis.","authors":"Jianxin Zhao,Zheng Zhao,Wen Zhou,Jianzhi Zhang,Jinfeng Chen,Jianwei Sun,Jing Li","doi":"10.1016/j.jbc.2025.110388","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110388","url":null,"abstract":"The intracellular O-linked N-acetylglucosamine (O-GlcNAc) modification is known to be enriched in the nucleus and on chromatin, but many of its chromatin targets remain to be identified. Herein we demonstrate the O-GlcNAcylation of YEATS Domain Containing 2 (YEATS2), a subunit of the chromatin Ada-two-A-containing (ATAC) complex and a reader of histone H3K27ac. We show that YEATS2 interacts with the O-GlcNAc transferase (OGT) and further pinpoint its major O-GlcNAcylation site to be Thr604 using electron transfer dissociation mass spectrometry. O-GlcNAcylation promotes the chromatin association of YEATS2, and the affinity between YEATS2 and other ATAC components on chromatin, such as ZZZ3, GCN5 and PCAF. Downstream, YEATS2-T604A mutants attenuated the ATAC-dependent histone H3K9ac levels and inactivated the expression of essential ribosomal genes as shown in chromatin immunoprecipitation assays. Further, xenograft experiments show that YEATS2 O-GlcNAcylation promotes lung cancer tumorigenesis. Our work reveals the critical role of YEATS2 O-GlcNAcylation in stabilizing the ATAC complex on chromatin and expands the chromatin substrates of OGT.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"179 1","pages":"110388"},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144335305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Austin Tedman, Muskan Goel, Sohan Shah, Jonathan P. Schlebach
{"title":"Unifying Perspectives on the Activity and Genotypic Targeting of Pharmacological Chaperones","authors":"Austin Tedman, Muskan Goel, Sohan Shah, Jonathan P. Schlebach","doi":"10.1016/j.jbc.2025.110375","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110375","url":null,"abstract":"Several diseases of protein misfolding can now be treated with an emerging class of therapeutics known as pharmacological chaperones, pharmacochaperones, or correctors. These small molecules exploit the universal thermodynamic coupling between ligand binding and protein folding to suppress conformational defects that disrupt protein homeostasis. While the mechanistic basis of their activity is quite simple in theory, their nuanced proteostatic effects can vary depending on the intrinsic properties of their target proteins and the cellular context. Deviations in activity are especially pronounced across panels of pathogenic variants of the target protein. In this perspective, we explore the factors that shape the potency of pharmacochaperones and the intrinsic sensitivity of different target proteins in relation to various theoretical considerations and experimental observations. We discuss how emerging technologies have provided general insights into the molecular basis of the variant-specific effects of certain pharmacochaperones. We also highlight ongoing efforts to identify existing drugs that stabilize misfolded variants and to repurpose them as pharmacochaperones. Finally, we discuss how the chaperone activity of current drugs could potentially contribute to complex pharmacology and deviations in therapeutic efficacy across patient cohorts. Together, these principles provide a coherent framework that may help guide the discovery and precision targeting of next generation pharmacochaperones for both current and new targets involved in proteostasis diseases.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"16 1","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144341322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qiufeng Pan,Changmin Zou,Zhigen Lin,Hao Tang,Zepu Long,Longwang Wang
{"title":"TFAP2C Drives Cisplatin Resistance in Bladder Cancer by Upregulating YAP and Activating β-Catenin Signaling.","authors":"Qiufeng Pan,Changmin Zou,Zhigen Lin,Hao Tang,Zepu Long,Longwang Wang","doi":"10.1016/j.jbc.2025.110387","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110387","url":null,"abstract":"Cisplatin-based chemotherapy is a conventional therapy for muscle-invasive bladder cancer (BC); However, its efficacy is often limited by the emergence of resistance to cisplatin. Yes-associated protein (YAP) and β-catenin are involved in this resistance, yet their upstream regulators are not well defined. This study investigates the role of TFAP2C in regulating YAP expression and its impact on cisplatin resistance in BC. The Cancer Genome Atlas (TCGA) gene expression data and GSE231835 dataset were analyzed to identify potential transcription factors regulating YAP. Assessed TFAP2C and YAP expression in clinical samples and cell lines. Functional assays were performed following TFAP2C knockdown. Dual-luciferase reporter assays and Chromatin immunoprecipitation (ChIP) confirmed TFAP2C binding to the YAP promoter. An mouse model evaluated the effects of TFAP2C silencing on tumor growth and cisplatin resistance. The results showed that TFAP2C was identified as an upstream activator of YAP, with elevated expression in cisplatin-resistant BC cell lines and positive correlation with YAP expression. Silencing TFAP2C reduced malignant behaviors, decreased YAP, phosphorylated YAP (p-YAP), and β-catenin levels, and increased apoptosis in both cisplatin-sensitive and resistant BC cells. Besides, TFAP2C directly binds to the YAP promoter, enhancing its transcription. In the xenograft model, TFAP2C silencing significantly inhibited tumor growth and reduced cisplatin resistance. TFAP2C promotes cisplatin resistance and malignant behavior in BC by upregulating YAP and activating the β-catenin signaling pathway. Targeting TFAP2C offers a novel therapeutic strategy to overcome cisplatin resistance in BC, representing a new discovery in combating chemoresistance.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"24 1","pages":"110387"},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144335359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Julia Tanquary,Ian J Pavelich,Marcin Grabowicz,Christine M Dunham
{"title":"The Escherichia coli RelB antitoxin C-terminus is essential for RelE toxin suppression and transcriptional repression.","authors":"Julia Tanquary,Ian J Pavelich,Marcin Grabowicz,Christine M Dunham","doi":"10.1016/j.jbc.2025.110389","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110389","url":null,"abstract":"Bacterial type II toxin-antitoxin (TA) systems exhibit high specificity within each pair to ensure precise recognition of the toxin by its cognate antitoxin to inhibit toxicity of the free toxin. Despite high structural similarity among some TAs, crosstalk between non-cognate TA pairs is rare. To determine how the E. coli RelB antitoxin suppresses its cognate RelE toxin, we engineered C-terminal truncations of RelB and tested their functional effects on toxin suppression in E. coli. We find that removal of the long C-terminal α3 and connecting loop 4 (L4) of RelB prevents RelE suppression. Quantitative binding assays of RelE and RelB variants support a reduced affinity upon removal of the RelB C-terminus. Disrupting these interactions between RelB and RelE also led to a significant decrease in transcriptional repression at the relO operator, underscoring the requirement for RelE binding to RelB for optimal repression at DNA repressor elements. Comparison to other structurally homologous TA systems, such as E. coli DinJ-YafQ, reveals key differences in the molecular mechanisms of both toxin suppression and DNA repressor activity highlighting the diversity in TA regulation and function.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"14 1","pages":"110389"},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144335358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sheila C Bonitatibus,Ryan V Pham,Andrew C Weitz,Madeline M Lopéz-Muñoz,Bin Li,William W Metcalf,Satish K Nair,Sean J Elliott
{"title":"The redox landscape of pyruvate:ferredoxin oxidoreductases reveals often conserved Fe-S cluster potentials.","authors":"Sheila C Bonitatibus,Ryan V Pham,Andrew C Weitz,Madeline M Lopéz-Muñoz,Bin Li,William W Metcalf,Satish K Nair,Sean J Elliott","doi":"10.1016/j.jbc.2025.110380","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110380","url":null,"abstract":"Here we investigate the thermodynamic driving force of internal electron transfer (ET) of pyruvate:ferredoxin oxidoreductases (PFORs), by comparing the redox properties of a series of PFORs from Chlorobaculum tepidum (Ct), Magnetococcus marinus (Mm), Methanosarccina acetivorans (Ma), as well as revisiting the single historical precedent, the enzyme from Desulfovibrio africanus. These enzymes require a thiamine pyrophosphate (TPP) cofactor, three [4Fe-4S] clusters, and Coenzyme A (CoA) for activity and are found within anaerobic organisms that utilize the reverse tricarboxylic acid (TCA cycle), or other reductive pathways, performing CO2 reduction and pyruvate synthesis. Yet, PFOR is often invoked as an oxidative enzyme responsible for generating reducing equivalents in the form of the redox carrier ferredoxin. Previous efforts to understand the mechanism of PFOR have relied upon a prior report of the iron-sulfur redox potentials derived from an incomplete redox titration. Here we use direct protein film electrochemistry (PFE) to provide a side-by-comparison of four PFOR enzymes, providing a new assessment of the iron-sulfur cluster redox potentials. As the Ma PFOR is comprised of multiple polypeptides, our investigation of the recombinant PorD sub-unit allows us to construct a model where the revised redox-potentials are mapped to specific iron-sulfur clusters.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"145 1","pages":"110380"},"PeriodicalIF":4.8,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Characterizing the excision of 7,8-dihydro-8-oxoadenine by thymine DNA glycosylase.","authors":"Hardler W Servius, Alexander C Drohat","doi":"10.1016/j.jbc.2025.110363","DOIUrl":"10.1016/j.jbc.2025.110363","url":null,"abstract":"<p><p>Oxidation of DNA yields mutagenic and cytotoxic lesions that threaten genomic integrity, cause cancer and other diseases, and contribute to aging. Oxidative damage is countered by base excision repair, a pathway initiated by DNA glycosylases, which cleave bases through N-glycosyl bond hydrolysis. The major adenine oxidative lesion, 7,8-dihydro-8-oxoadenine (oxoA), is mutagenic in mammalian cells, but repair mechanisms are poorly understood. Thymine DNA glycosylase (TDG) removes T from mutagenic G⋅T mispairs arising through 5-methylcytosine deamination and mediates active DNA demethylation by excising 5-formylcytosine and 5-carboxylcytosine (caC). TDG excises oxoA from G⋅oxoA, A⋅oxoA, or C⋅oxoA pairs with remarkably high activity and from T⋅oxoA pairs with lower activity, comparable to that for established pyrimidine substrates. To further characterize TDG excision of oxoA, single-turnover experiments were collected with varying enzyme concentration, revealing vast differences in catalytic efficiency (k<sub>max</sub>/K<sub>0.5</sub>) among oxoA pairs, reflecting large variances in both substrate affinity (K<sub>0.5</sub>) and maximal activity (k<sub>max</sub>). TDG excision of oxoA depends strongly on the 3' base, as seen for excision of T from G⋅T pairs. Unlike MutY excision of adenine or TDG excision of caC, TDG excision of oxoA is not acid catalyzed, indicating that TDG stabilizes an anionic oxoA leaving group. A conserved TDG residue, H151, strongly promotes oxoA excision, whereas it antagonizes excision of T and uracil. The hydroxyl of Y152 catalyzes excision of oxoA and T, but not uracil, 5-formylcytosine, or caC, whereas its aromatic ring is essential for all substrates. Our results inform the catalytic requirements for enzymatic excision of oxoA from DNA.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"110363"},"PeriodicalIF":4.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Weixiang A Wang, Cheng-I J Ma, Noah Steinfeld, Frederick R Maxfield
{"title":"Itraconazole and posaconazole, inhibitors of NPC1 sterol transport, act as pharmacological chaperones after washout.","authors":"Weixiang A Wang, Cheng-I J Ma, Noah Steinfeld, Frederick R Maxfield","doi":"10.1016/j.jbc.2025.110370","DOIUrl":"10.1016/j.jbc.2025.110370","url":null,"abstract":"<p><p>Niemann-Pick type C (NPC) disease is a rare lysosomal storage disorder primarily caused by mutations in the NPC Cholesterol Transporter 1 (NPC1) gene, resulting in cholesterol and lipid accumulation in late endosomes and lysosomes. While several therapeutic drugs show promise in reducing cholesterol accumulation, none of the current treatments are highly effective. Itraconazole and posaconazole, widely used antifungal drugs, have been shown to stabilize misfolded NPC1 proteins, enabling their escape from endoplasmic reticulum-associated degradation. This chaperone-like property makes them attractive candidates for testing chaperones as possible treatments for NPC disease, but both drugs also inhibit NPC1 function. In this study, we employed a washout approach to reverse the inhibitory effects of these drugs, leveraging the fact that wild-type NPC1 proteins have a half-life of about 42 h. Treating NPC1<sup>I1061T/I1061T</sup> human fibroblasts with itraconazole or posaconazole for 72 h, followed by 24 to 48 h of washout, we observed a significant reduction in lysosomal cholesterol accumulation. A modest rebound was observed 72 h after drug removal, likely due to protein turnover. We also tested a repeated pulsed exposure treatment, in which short drug treatments were followed by extended washout periods. This strategy preserved the functional benefit of NPC1 stabilization while minimizing inhibitory effects. These findings indicate that a washout strategy can enhance the functional benefits of pharmacological chaperones, offering a potential future therapeutic approach for NPC disease.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"110370"},"PeriodicalIF":4.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}