Journal of Biological Chemistry最新文献

{"title":"Acetylation of microtubule-binding PinX1 orchestrates ribosome biogenesis to nutrient starvation via the RNA polymerase I preinitiation complex.","authors":"Gang Lu,Liqian Yang,Qinxin Zhang,Shiqiang Zhang,Yuqi Xiong,Tong Li,Yanli Zhang,Minghui Liu,Yu Zhang,Jiaxing Wu,Qiaoyou Weng,Xiaoyun Liu,Jiansong Ji,Haiying Wang,Jianyuan Luo","doi":"10.1016/j.jbc.2025.110465","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110465","url":null,"abstract":"Shutdown of ribosome biogenesis is one of the sophisticated strategies for cells to save energy in response to nutrient starvation. However, the mechanism orchestrating ribosome biogenesis with cellular nutrition status remains unclear. Here, we identified a role of PIN2/TRF1-interacting telomerase inhibitor 1 (PinX1) in regulating ribosome biogenesis. PinX1 is highly expressed in colorectal cancers (CRC). Depletion of PinX1 impairs rDNA transcription, compromises ribosome biogenesis and inhibits tumor cells proliferation. Mechanically, associated with UBTF, PinX1 directly binds to RNA polymerase I subunit G (POLR1G) which is required for the assembly of RNA polymerase I preinitiation complex (PIC). Upon nutrient starvation, PinX1 is acetylated at K43, K133, K140, K149, K190, K222, which hinders its binding to POLR1G leading to disassembly of PIC. Collectively, our findings uncover a novel role of PinX1 and its acetylation, fine-tuning nucleolar transcription to stress signaling.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"7 1","pages":"110465"},"PeriodicalIF":4.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144604082","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":"Leber's hereditary optic neuropathy-associated ND1 3733G> C mutation ameliorates the mitochondrial quality control and cellular homeostasis.","authors":"Meiheriayi Yasheng,Yanchun Ji,Yunfan He,Qiuzi Yi,Huanhuan Zhang,Wenqi Shan,Kai Wang,Juanjuan Zhang,Ya Li,Feilong Meng,Minglian Zhang,Jun Qin Mo,Shihui Wei,Min-Xin Guan","doi":"10.1016/j.jbc.2025.110464","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110464","url":null,"abstract":"Leber's hereditary optic neuropathy (LHON) is a paradigm for mitochondrial retinopathy due to mitochondrial DNA (mtDNA) mutations. However, the mechanism underlying LHON-linked mtDNA mutations, especially their impact on mitochondrial and cellular integrity, is not well understood. Recently, the ND1 3733G>C (p.E143Q) mutation was identified in three Chinese pedigrees with suggestively maternal inheritance of LHON. In this study, we investigated the pathogenic mechanism of m.3733G>C mutation using cybrids generated by fusing mtDNA-less ρ0 cells with enucleated cells from a Chinese patient carrying the m.3733G>C mutation and control subject. Molecular dynamics simulations showed that p.E143Q mutation destabilized these interactions between residues E143 and S110/Y114, or between S141 and W290 in the ND1. Its impact of ND1 structure and function was further evidenced by reduced levels of ND1 in mutant cells. The m.3733G>C mutation caused defective assembly and activity of complex I, respiratory deficiency, diminished mitochondrial ATP production, and increased production of mitochondrial ROS in the mutant cybrids carrying the m.3733G>C mutation. These mitochondrial dysfunctions regulated mitochondrial quality control via mitochondrial dynamics and mitophagy. The m.3733G>C mutation-induced dysfunction yielded elevating mitochondrial localization of DRP1, decreasing network connectivity and increasing fission with abnormal morphologies. Furthermore, the m.3733G>C mutation downregulated ubiquitin-dependent mitophagy pathway, evidenced by decreasing the levels of Parkin and Pink, but not ubiquitin-independent mitophagy pathway. The m.3733G>C mutation-induced deficiencies reshaped the cellular homeostasis via impairing autophagy process and promoting intrinsic apoptosis. Our findings provide new insights into pathophysiology of LHON arising from the m.3733G>C mutation-induced mitochondrial dysfunctions and reprograming organellular and cellular homeostasis.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"11 1","pages":"110464"},"PeriodicalIF":4.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144604083","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":"Molecular determinants of nucleic acid recognition by an RNA-targeting ADP-ribosyltransferase toxin.","authors":"Fanyang Lv,Andrea G Alexei,Jake Colautti,Nathan P Bullen,John C Whitney","doi":"10.1016/j.jbc.2025.110463","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110463","url":null,"abstract":"ADP-ribosyltransferases use NAD+ to catalyze ADP-ribosylation reactions that regulate diverse cellular pathways in eukaryotes or function as toxins delivered by bacteria to kill competitor or host cells. Although most characterized ARTs target proteins, we recently identified RhsP2 as an antibacterial ART toxin that modifies the 2'-OH groups of structured RNAs during bacterial competition. However, the molecular basis for RhsP2's unique specificity toward RNA remains poorly understood. Here, we show that RhsP2 is a divergent member of the ART superfamily that recognizes nucleic acid substrates via a positively charged RNA-binding surface adjacent to its catalytic site. Mutations within this surface disrupt both RNA binding and ADP-ribosylation activity, abolishing RhsP2's antibacterial function. We further demonstrate that RhsP2 binds distinct small regulatory RNAs with varying affinities, suggesting that both electrostatic interactions and shape complementarity contribute to RNA target selection. Together, our findings define the molecular determinants of nucleic acid recognition by an unusual RNA-targeting ART toxin.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"22 1","pages":"110463"},"PeriodicalIF":4.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144594403","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":"A bacterial actin with high ATPase activity regulates the polymerization of a partner MreB isoform essential for Spiroplasma swimming motility.","authors":"Daichi Takahashi,Hana Kiyama,Hideaki T Matsubayashi,Ikuko Fujiwara,Makoto Miyata","doi":"10.1016/j.jbc.2025.110462","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110462","url":null,"abstract":"Spiroplasma is a wall-less helical bacterium that is characterized by a unique swimming motility involving five isoforms of the bacterial actin MreBs (SMreB1-5). The functions of SMreBs are unique in the MreB family proteins, as their counterparts in walled-bacteria localize the cell-wall synthesis complex by forming filaments that slowly turn over to maintain the cell shape. In vitro analyses of individual SMreBs provide clues to understand the detailed molecular mechanism of Spiroplasma swimming. However, the purification difficulties have hampered in vitro analyses of one of the SMreBs, SMreB1, which drives the swimming. Here, we isolated soluble SMreB1 of Spiroplasma eriocheiris (SpeMreB1) and evaluated its activity. SpeMreB1 was expressed as a fusion with a solubilization-tag, ProteinS (PrS), which allowed us to purify it in the soluble fraction. SpeMreB1 exhibited the highest phosphate (Pi) release rate and the fold changes of critical concentrations for polymerization across the nucleotide states among the MreB family proteins. SpeMreB1 interacted with polymerized SpeMreB5, another SMreB essential for Spiroplasma swimming. In the AMPPNP- or ADP-bound state, SpeMreB1 decreased the amount of SpeMreB5 filaments, possibly reflecting their disassembly. Regardless of the nucleotide state, SpeMreB1 bound to negatively charged lipids. These results suggest that SpeMreB1 utilizes its highest activity to manage SpeMreB5 filaments underneath the cell membrane to drive Spiroplasma swimming. IMPORTANCE: In most bacterial species, MreB forms stable filaments that are involved in cell-shape maintenance by localizing the bacterial cell-wall synthesis complex. In contrast, five isoforms of MreBs in the pathogenic wall-less helical bacterium Spiroplasma are involved in its unique motility system driven by a kink propagation along the helical cell. Our integrated biochemical assays show that one isoform of MreBs involved in the swimming of a crustacean pathogen S. eriocheiris (SpeMreB1) is exceptionally active in the MreB family proteins and manages the polymerization of another MreB essential for the swimming (SpeMreB5). This study sheds light on an evolutionary mystery how Spiroplasma has adapted static MreB proteins to a dynamic phenomenon like its swimming motility.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"21 1","pages":"110462"},"PeriodicalIF":4.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144594404","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":"Retraction: Induction of Hypoxia-inducible Factor 1 Activity by Muscarinic Acetylcholine Receptor Signaling.","authors":"Kiichi Hirota,Ryo Fukuda,Satoshi Takabuchi,Shinae Kizaka-Kondoh,Takehiko Adachi,Kazuhiko Fukuda,Gregg L Semenza","doi":"10.1016/j.jbc.2025.110218","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110218","url":null,"abstract":"","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"685 1","pages":"110218"},"PeriodicalIF":4.8,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568549","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":"Hypoxia promotes the generation of a versican-rich extracellular matrix by human coronary artery endothelial cells.","authors":"Sara M Jørgensen,Song Huang,Lasse G Lorentzen,Fallen K Y Teoh,Richard Karlsson,John R Harkness,Rebecca L Miller,Michael J Davies,Christine Y Chuang","doi":"10.1016/j.jbc.2025.110459","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110459","url":null,"abstract":"Normal endothelial cell (EC) function is essential for vascular wall homeostasis, whereas dysfunction increases the risk of cardiovascular disease. Low O2 tension (hypoxia) promotes EC dysfunction and the formation of atherosclerotic plaques. Increasing evidence suggests that hypoxia drives extracellular matrix (ECM) remodeling, an established contributing factor in atherosclerosis. However, the effects of hypoxia on ECs and associated ECM proteins are poorly understood. The aim of this study was to investigate whether the culture of human coronary artery ECs under 1% O2 (hypoxia) alters the ECM generated by these cells, and if this affects HCAEC function. Exposure of HCAECs to 1% O2 resulted in a hypoxic response (HIF-1α stabilization), dysfunction (increased oxidant formation and decreased eNOS), and inflammatory activation (increased IL-6 and ICAM-1 expression). Proteomic analysis of HCAECs cultured under 1% and 20% O2 for 7 days revealed many hypoxia-induced changes to extracellular proteins, particularly increased versican, a key ECM proteoglycan. Increased versican expression and deposition was confirmed at the mRNA and protein level, along with its glycosaminoglycan (chondroitin sulfate) chains and particularly 6-O-sulfated species. This versican-rich ECM showed increased hyaluronan binding and decreased cell adhesiveness, but attached cells proliferated at a greater rate. The generation of a versican-rich ECM under 1% O2 provides a link between hypoxia and atherosclerosis, since versican is reported to accumulate in plaques, where it binds and retains low-density lipoproteins and is involved in inflammatory cell recruitment, thereby potentiating low-density lipoprotein modification and the accumulation of lipid-laden (foam) cells.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"106 1","pages":"110459"},"PeriodicalIF":4.8,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578709","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":"Retraction: Nitric Oxide Induces Hypoxia-inducible Factor 1 Activation That Is Dependent on MAPK and Phosphatidylinositol 3-Kinase Signaling.","authors":"Kenji Kasuno, Satoshi Takabuchi, Kazuhiko Fukuda, Shinae Kizaka-Kondoh, Junji Yodoi, Takehiko Adachi, Gregg L Semenza, Kiichi Hirota","doi":"10.1016/j.jbc.2025.110219","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110219","url":null,"abstract":"","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"301 7","pages":"110219"},"PeriodicalIF":4.0,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575504","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":"Repurposing clofazimine as an antibiotic to treat cholera: Identification of cellular and structural targets.","authors":"Ming Yuan,Martín Andrés González Montalvo,Yuyao Hu,Karina Tuz,Oscar X Juárez","doi":"10.1016/j.jbc.2025.110458","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110458","url":null,"abstract":"Vibrio cholerae has shaped the face of human civilization through at least seven pandemic waves. The current wave shows multidrug resistance, has produced enormous human and economic losses, as well as humanitarian crises, and has the potential to collapse the healthcare system of entire countries. Antibiotic resistance in this and other pathogens is an urgent threat that remains unaddressed due to the significant costs to develop new antibiotics. In this work, we have tested several FDA-approved phenazines and phenothiazines, and have identified that clofazimine (Lamprene) shows strong antibiotic effects against V. cholerae cells in culture and in an in vitro infection model, at concentrations well below the clinically-used doses in humans. Our results show that in an animal model, clofazimine is as effective as ampicillin in the treatment of cholerae. In addition, clofazimine shows strong antivirulence properties, almost completely inhibiting cholera toxin production. The characterization of V. cholerae metabolism allowed us to identify that clofazimine's main target in this pathogen is the respiratory complex NQR, an essential enzyme that plays a crucial role in energy metabolism, virulence factor production and multidrug resistance, which is widely distributed among pathogenic bacteria. Biochemical and computational analyses show that the structural target of clofazimine is the catalytically-active ubiquinone-binding site, which is a unique structural motif, not found in any human protein, making it an ideal pharmacologic target. These results show that clofazimine can be repurposed to treat cholera, and open opportunities to develop a novel class of antibiotics that target NQR.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"9 1","pages":"110458"},"PeriodicalIF":4.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568550","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":"The structural characteristics of cellular phospholipid acyl chains required for ABCA1-mediated HDL formation.","authors":"Kohjiro Nagao,Mayu Matsuo,Yoshie Hori,Norihiro Namba,Hiroyuki Saito","doi":"10.1016/j.jbc.2025.110457","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110457","url":null,"abstract":"ATP-binding cassette protein A1 (ABCA1) mediates high-density lipoprotein (HDL) formation by transporting cellular cholesterol and phospholipids to apolipoprotein A-I (apoA-I). Although phospholipids serve as transport substrates for ABCA1 and the membrane constituents surrounding ABCA1, their roles in HDL formation remain unclear. Here, we elucidated the effect of the acyl chain structure of cellular phospholipids on HDL formation, particularly focusing on monounsaturated fatty acid (MUFA)-containing phosphatidylcholine (PC), the predominant phospholipid in most animal cells. PC molecules effluxed to apoA-I had an acyl chain composition similar to cellular PC, both being enriched in MUFA-containing species. Furthermore, manipulating the acyl chain composition of cellular PC by stealoyl-CoA desaturase inhibition or fatty acid supplementation led to similar changes in effluxed PC molecule composition. Thus, ABCA1 can transport various cellular PC molecules, including MUFA-containing species, without apparent preference for their acyl chain structure. Conversely, an appropriate acyl chain composition of cellular phospholipids is required for ABCA1 functional expression. Reducing MUFA content in the cellular phospholipids suppressed ABCA1 expression through two independent mechanisms: first, by inducing an endoplasmic reticulum (ER) stress response that decreases ABCA1 protein production; and second, by causing a folding defect in the ABCA1 protein, leading to immature glycosylation and failure of plasma membrane localization. Excess MUFA supply decreased ABCA1 expression without causing ER stress or defects in glycosylation and localization of ABCA1. Collectively, we revealed the contribution of MUFA-containing PC to HDL formation and identified the structural characteristics of cellular phospholipids required for their transport to apoA-I and functional expression of ABCA1.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"8 1","pages":"110457"},"PeriodicalIF":4.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568580","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":"The GTPase κB-Ras is an essential subunit of the RalGAP tumor suppressor complex.","authors":"René Rasche,Lisa Helene Apken,Sonja Titze,Esther Michalke,Rohit Kumar Singh,Andrea Oeckinghaus,Daniel Kümmel","doi":"10.1016/j.jbc.2025.110460","DOIUrl":"https://doi.org/10.1016/j.jbc.2025.110460","url":null,"abstract":"κB-Ras1 and κB-Ras2 are small GTPases with non-canonical features that act as tumor suppressors downstream of Ras. Via interaction with the RalGAP (GTPase activating protein) complex, they limit activity of Ral GTPases and restrict anchorage-independent proliferation. We here present the crystal structure of κB-Ras1 in complex with the N-terminal domain of RGα2. The structure suggests a mechanism of intrinsic GTP hydrolysis of κB-Ras1 that relies on a scaffolding function of the GTPase rather than on catalytic residues, which we confirm by mutational analysis. The interaction with RGα2 is nucleotide-independent and does not involve κB-Ras1 switch regions, which establishes κB-Ras proteins as a constitutive third subunit of RalGAP complexes. Functional studies demonstrate that κB-Ras proteins are not required for RalGAP catalytic activity in vitro, but for functionality in vivo. We propose that κB-Ras may thus act as regulator of RalGAP localization and thereby control the Ras/Ral signaling pathway.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"48 1","pages":"110460"},"PeriodicalIF":4.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568552","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}