The MAPK p38α is associated with skeletal muscle's development, differentiation and functionality. But, as it is overactive in muscle diseases and aging, it was proposed to be a pivotal promoter of these processes as well. It is not clear how p38α is involved in these disparate activities, in particular whether its chronic activation alone is sufficient to cause them. We established a mouse model designed to study the effects of p38α per se in skeletal muscle. p38α activation is achieved by inducible expression, in muscle, of an intrinsically active variant, p38αD176A+F327S. Two weeks following expression muscle degeneration and necrotic changes were observed, accompanied with elevation of p53, caspase 3 and γH2AX; and, intriguingly, suppression of the p38's substrates MK2 and MK3 and its activator MKK6. At later timepoints the tissue recovered, apoptotic markers disappeared, but MK2, MK3 and MKK6 remained suppressed, perhaps as a response that restrains p38α-mediated damage and allows recovery. Induction of p38αD176A+F327S in young mice (2 months old) caused milder effects, but MK2, MK3 and MKK6 were suppressed. The p38αD176A+F327S effects were associated with altered level of ∼2,000 mRNA molecules. For 1,700 genes the effect was transient and for ∼300 constant. Stress-induced activation of p38α in C2C12 myoblasts was also associated with MK2 downregulation, but with constant elevation of apoptotic markers. Thus, chronic activation of p38α per se in skeletal muscle is sufficient to cause damage reminiscent of aging effects, but cannot impose full-scale and lasting aging phenotype. The tissue recovers while suppressing the p38α pathway.
{"title":"Chronic activation of p38α in skeletal muscle causes necrotic changes, but also abolishes expression of MK2, MK3 and MKK6 and the muscle recovers.","authors":"Nechama Gilad,Ilona Darlyuk-Saadon,Manju Payini Mohanam,David Engelberg","doi":"10.1016/j.jbc.2026.111338","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111338","url":null,"abstract":"The MAPK p38α is associated with skeletal muscle's development, differentiation and functionality. But, as it is overactive in muscle diseases and aging, it was proposed to be a pivotal promoter of these processes as well. It is not clear how p38α is involved in these disparate activities, in particular whether its chronic activation alone is sufficient to cause them. We established a mouse model designed to study the effects of p38α per se in skeletal muscle. p38α activation is achieved by inducible expression, in muscle, of an intrinsically active variant, p38αD176A+F327S. Two weeks following expression muscle degeneration and necrotic changes were observed, accompanied with elevation of p53, caspase 3 and γH2AX; and, intriguingly, suppression of the p38's substrates MK2 and MK3 and its activator MKK6. At later timepoints the tissue recovered, apoptotic markers disappeared, but MK2, MK3 and MKK6 remained suppressed, perhaps as a response that restrains p38α-mediated damage and allows recovery. Induction of p38αD176A+F327S in young mice (2 months old) caused milder effects, but MK2, MK3 and MKK6 were suppressed. The p38αD176A+F327S effects were associated with altered level of ∼2,000 mRNA molecules. For 1,700 genes the effect was transient and for ∼300 constant. Stress-induced activation of p38α in C2C12 myoblasts was also associated with MK2 downregulation, but with constant elevation of apoptotic markers. Thus, chronic activation of p38α per se in skeletal muscle is sufficient to cause damage reminiscent of aging effects, but cannot impose full-scale and lasting aging phenotype. The tissue recovers while suppressing the p38α pathway.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"9 1","pages":"111338"},"PeriodicalIF":4.8,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147368320","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}
Cancer metabolic reprogramming is a driver of tumorigenesis and progression. While extensive research has highlighted the roles of metabolic enzymes and signaling pathways in this process, the mechanisms by which chromatin regulation coordinates the metabolic network at the transcriptional level remain unclear. The SWI/SNF chromatin remodeling complex, a key epigenetic regulator, has recently been shown to modulate multiple tumor metabolic pathways. Metabolic reprogramming induced by mutations in its subunits has garnered increasing attention, but comprehensive reviews on how SWI/SNF-mediated chromatin remodeling governs this process are limited. This paper examines how the SWI/SNF complex regulates metabolic gene transcription by positioning promoters and enhancer regions, guided by transcription factors (TFs), and remodeling nucleosome structures. It further discusses its role in regulating glycolysis, the tricarboxylic acid cycle (TCA), oxidative phosphorylation (OXPHOS), lipid metabolism, and the coupling of carbon-nitrogen metabolism between amino acids and glucose-lipid metabolism. Focusing on subunit mutations such as ARID1A, SMARCA4, and PBRM1, this paper explores their impact on metabolic adaptation, offering insights for identifying therapeutic targets. Based on these findings, a combination intervention strategy targeting the protein levels of glutaminase 1 (GLS1), OXPHOS (complex I), glutamine transport, and glycolysis is proposed. By integrating SWI/SNF complex status and metabolic phenotypes, a therapeutic framework is developed that balances metabolic compensation blockade and enhanced cell death sensitivity, providing a more precise treatment strategy for metabolism-dependent tumors.
{"title":"The SWI/SNF Complex in Tumor Metabolism: Mechanisms and Therapeutic Implications.","authors":"Xuan-Hao Pan,Jian Wang,Jing Su,Rui Zhao,Yu-Fei Gao","doi":"10.1016/j.jbc.2026.111342","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111342","url":null,"abstract":"Cancer metabolic reprogramming is a driver of tumorigenesis and progression. While extensive research has highlighted the roles of metabolic enzymes and signaling pathways in this process, the mechanisms by which chromatin regulation coordinates the metabolic network at the transcriptional level remain unclear. The SWI/SNF chromatin remodeling complex, a key epigenetic regulator, has recently been shown to modulate multiple tumor metabolic pathways. Metabolic reprogramming induced by mutations in its subunits has garnered increasing attention, but comprehensive reviews on how SWI/SNF-mediated chromatin remodeling governs this process are limited. This paper examines how the SWI/SNF complex regulates metabolic gene transcription by positioning promoters and enhancer regions, guided by transcription factors (TFs), and remodeling nucleosome structures. It further discusses its role in regulating glycolysis, the tricarboxylic acid cycle (TCA), oxidative phosphorylation (OXPHOS), lipid metabolism, and the coupling of carbon-nitrogen metabolism between amino acids and glucose-lipid metabolism. Focusing on subunit mutations such as ARID1A, SMARCA4, and PBRM1, this paper explores their impact on metabolic adaptation, offering insights for identifying therapeutic targets. Based on these findings, a combination intervention strategy targeting the protein levels of glutaminase 1 (GLS1), OXPHOS (complex I), glutamine transport, and glycolysis is proposed. By integrating SWI/SNF complex status and metabolic phenotypes, a therapeutic framework is developed that balances metabolic compensation blockade and enhanced cell death sensitivity, providing a more precise treatment strategy for metabolism-dependent tumors.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"19 1","pages":"111342"},"PeriodicalIF":4.8,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147368323","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}
Gastric cancer (GC) is among the most common malignant tumors worldwide. The inhibition of p53 ubiquitination can inhibit the progression of GC. The mechanism through which Plasmolipin (PLLP) regulates p53 ubiquitination in GC remains unclear. In this study, the correlation between PLLP expression and the prognosis of GC was analyzed on the basis of data from the TCGA database, and the expression characteristics of PLLP and p53 were verified by immunohistochemistry. A PLLP overexpression/knockdown GC cell model was constructed, and cell proliferation, apoptosis and invasion were detected by CCK-8, flow cytometry, and Transwell assays. Coimmunoprecipitation (Co-IP) and Western blotting were used to analyze the PLLP-TRIM59-p53 regulatory axis. The antitumor effect of PLLP in vivo was verified by tumor formation experiments in nude mice. CHX tracking assays, Co-IP and ubiquitination analysis were used to determine the effect of PLLP on p53 stability. Combined with bioinformatics prediction and experimental verification, the interaction between PLLP and the E3 ubiquitin ligase TRIM59 and its regulatory effect on the ubiquitination and degradation of p53 were analyzed. Flow cytometry and Transwell assays were used to verify the biological effect of the PLLP-TRIM59-p53 axis. We found that PLLP was downregulated in GC (P<0.05). PLLP interacts with TRIM59, inhibits TRIM59-mediated ubiquitination degradation of p53, and inhibits the progression of GC cells with wild-type p53. PLLP may be used as a potential biomarker for targeted therapy of GC.
{"title":"PLLP inhibits the progression of wild-type p53 gastric cancer by reducing p53 protein ubiquitination by binding to TRIM59.","authors":"Zhenhao Quan,Lin Lin,Feipeng Xu,Caijin Zhou,Renwei Huang,Kaiyu Sun,Haiping Jiang","doi":"10.1016/j.jbc.2026.111341","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111341","url":null,"abstract":"Gastric cancer (GC) is among the most common malignant tumors worldwide. The inhibition of p53 ubiquitination can inhibit the progression of GC. The mechanism through which Plasmolipin (PLLP) regulates p53 ubiquitination in GC remains unclear. In this study, the correlation between PLLP expression and the prognosis of GC was analyzed on the basis of data from the TCGA database, and the expression characteristics of PLLP and p53 were verified by immunohistochemistry. A PLLP overexpression/knockdown GC cell model was constructed, and cell proliferation, apoptosis and invasion were detected by CCK-8, flow cytometry, and Transwell assays. Coimmunoprecipitation (Co-IP) and Western blotting were used to analyze the PLLP-TRIM59-p53 regulatory axis. The antitumor effect of PLLP in vivo was verified by tumor formation experiments in nude mice. CHX tracking assays, Co-IP and ubiquitination analysis were used to determine the effect of PLLP on p53 stability. Combined with bioinformatics prediction and experimental verification, the interaction between PLLP and the E3 ubiquitin ligase TRIM59 and its regulatory effect on the ubiquitination and degradation of p53 were analyzed. Flow cytometry and Transwell assays were used to verify the biological effect of the PLLP-TRIM59-p53 axis. We found that PLLP was downregulated in GC (P<0.05). PLLP interacts with TRIM59, inhibits TRIM59-mediated ubiquitination degradation of p53, and inhibits the progression of GC cells with wild-type p53. PLLP may be used as a potential biomarker for targeted therapy of GC.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"6 1","pages":"111341"},"PeriodicalIF":4.8,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147368324","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}
Pub Date : 2026-03-04DOI: 10.1016/j.jbc.2026.111344
Ruben Rosas,Luisa F Baracaldo-Lancheros,Emily C Dykhuizen,Catherine A Musselman
A fraction of the eukaryotic genome is transcriptionally silenced in the form of facultative heterochromatin, characterized by the histone H3 lysine 27 tri-methyl (H3K27me3) modification. The cell-specific and dynamic nature of H3K27me3-marked chromatin is centrally regulated by the catalytic function of the Polycomb Repressive Complex 2 (PRC2) that deposits it, however the mark can also be removed to activate transcription by the demethylases UTX and JMJD3. An important regulatory mechanism of facultative heterochromatin is the molecular recognition of the H3K27me3 modification by a group of small globular proteins termed readers. Across multiple organisms, the readers of H3K27me3 that have been structurally characterized bound to H3 peptides are restricted to the chromodomain, BAH, Tudor, and the WD40 EED. Here we review the structural diversity of the protein domains that bind to H3K27me3 and highlight the different binding preferences beyond the recognition of the K27me3 moiety. Furthermore, we note recent findings that suggest the nucleosome structure can enhance the specificity of readers for H3K27me3, adding a new layer of regulation. Lastly, we discuss the prevalence of misregulation of H3K27me3 and its cognate proteins in human diseases, and the potential of the latter for therapeutic intervention. Remarkably, almost all the H3K27me3-related proteins are found misregulated in malignances that affect the brain and the nervous system, along with a strong prevalence in cancers of other tissues. Pharmacological efforts to target these pathways include peptide-based inhibitors and small molecules that can block recognition of H3K27me3 by allosteric, complex-disruptive, or degradation-inducing mechanisms of inhibition.
{"title":"Structural landscape of H3K27me3 recognition by protein domains and their potential for inhibition.","authors":"Ruben Rosas,Luisa F Baracaldo-Lancheros,Emily C Dykhuizen,Catherine A Musselman","doi":"10.1016/j.jbc.2026.111344","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111344","url":null,"abstract":"A fraction of the eukaryotic genome is transcriptionally silenced in the form of facultative heterochromatin, characterized by the histone H3 lysine 27 tri-methyl (H3K27me3) modification. The cell-specific and dynamic nature of H3K27me3-marked chromatin is centrally regulated by the catalytic function of the Polycomb Repressive Complex 2 (PRC2) that deposits it, however the mark can also be removed to activate transcription by the demethylases UTX and JMJD3. An important regulatory mechanism of facultative heterochromatin is the molecular recognition of the H3K27me3 modification by a group of small globular proteins termed readers. Across multiple organisms, the readers of H3K27me3 that have been structurally characterized bound to H3 peptides are restricted to the chromodomain, BAH, Tudor, and the WD40 EED. Here we review the structural diversity of the protein domains that bind to H3K27me3 and highlight the different binding preferences beyond the recognition of the K27me3 moiety. Furthermore, we note recent findings that suggest the nucleosome structure can enhance the specificity of readers for H3K27me3, adding a new layer of regulation. Lastly, we discuss the prevalence of misregulation of H3K27me3 and its cognate proteins in human diseases, and the potential of the latter for therapeutic intervention. Remarkably, almost all the H3K27me3-related proteins are found misregulated in malignances that affect the brain and the nervous system, along with a strong prevalence in cancers of other tissues. Pharmacological efforts to target these pathways include peptide-based inhibitors and small molecules that can block recognition of H3K27me3 by allosteric, complex-disruptive, or degradation-inducing mechanisms of inhibition.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"16 1","pages":"111344"},"PeriodicalIF":4.8,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147368352","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}
Immune checkpoint blockade targeting programmed death ligand-1 (PD-L1) has emerged as a cornerstone of cancer immunotherapy, yielding durable responses in subsets of patients across multiple malignancies. However, clinical outcomes remain limited due to incomplete blockade, low tumor immunogenicity, and poor targeting specificity. Here, we report the development of a chondroitin sulfate-modified liposomal formulation (OPCR-Lip) designed to achieve comprehensive PD-L1 blockade while reprogramming the tumor microenvironment to enhance immune activation. OPCR-Lip binds membrane-bound PD-L1, disrupts PD-L1 glycosylation, and inhibits exosomal PD-L1 secretion by damaging the Golgi apparatus, thereby mitigating immunosuppressive signaling. Co-delivery of oxaliplatin (OXA) further promotes immunogenic cell death, enhancing tumor immunogenicity and sustaining anti-tumor immunity in 4T1 breast tumor-bearing mice. The formulation's therapeutic precision was evaluated through circadian rhythm-based dosing, cross-species in vitro validation (canine and human breast cancer cells), and in vivo efficacy across melanoma and lung cancer models. Collectively, this study presents a promising therapeutic platform that augments PD-L1 blockade, broadens its clinical applicability, and improves treatment safety and effectiveness in solid tumors.
{"title":"Targeting the Golgi apparatus enhances PD-L1 blockade and synergizes with oxaliplatin to improve immunotherapy efficacy.","authors":"Haohuan Li,Chao Cui,Chenglu Sun,Ziyu Chen,Dengfeng Gao,Peng Yuan,Shibo Tian,Qin Zhong,Funeng Xu,Xiaoxia Liang,Long Jin,Keren Long,Lu Lu,Juan Deng,Jiaxue Cao,Xiaolan Fan,Fanli Kong,Chengdong Wang,Desheng Li,Zhiyong Qian,Mingzhou Li","doi":"10.1016/j.jbc.2026.111343","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111343","url":null,"abstract":"Immune checkpoint blockade targeting programmed death ligand-1 (PD-L1) has emerged as a cornerstone of cancer immunotherapy, yielding durable responses in subsets of patients across multiple malignancies. However, clinical outcomes remain limited due to incomplete blockade, low tumor immunogenicity, and poor targeting specificity. Here, we report the development of a chondroitin sulfate-modified liposomal formulation (OPCR-Lip) designed to achieve comprehensive PD-L1 blockade while reprogramming the tumor microenvironment to enhance immune activation. OPCR-Lip binds membrane-bound PD-L1, disrupts PD-L1 glycosylation, and inhibits exosomal PD-L1 secretion by damaging the Golgi apparatus, thereby mitigating immunosuppressive signaling. Co-delivery of oxaliplatin (OXA) further promotes immunogenic cell death, enhancing tumor immunogenicity and sustaining anti-tumor immunity in 4T1 breast tumor-bearing mice. The formulation's therapeutic precision was evaluated through circadian rhythm-based dosing, cross-species in vitro validation (canine and human breast cancer cells), and in vivo efficacy across melanoma and lung cancer models. Collectively, this study presents a promising therapeutic platform that augments PD-L1 blockade, broadens its clinical applicability, and improves treatment safety and effectiveness in solid tumors.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"1 1","pages":"111343"},"PeriodicalIF":4.8,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147368326","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}
Pub Date : 2026-03-04DOI: 10.1016/j.jbc.2026.111346
Shiho Takei,Wataru Saburi,Min Yao,Haruhide Mori,Toyoyuki Ose
ATP-binding cassette (ABC) transporters facilitate the translocation of various substrates across biological membranes. In prokaryotic ABC importers, solute binding protein (SBP), which selectively binds to a ligand, is incorporated into the functional complex. Cycloisomaltooligosaccharides (CIs) are produced from α-(1→6)-glucan by CI glucanotransferase, and intracellularly degraded by CI-inducible dextranase. CIs are regarded as incorporated forms; however, their uptake mechanisms have not yet been elucidated. In this study, SBP with a high affinity for CIs from Tepidibacillus decaturensis (TdCIBP) was discovered. TdCIBP showed the highest affinity for cycloisomaltoheptaose, followed by cycloisomaltooctaose and cycloisomaltononaose. TdCIBP also showed binding affinity for linear isomaltooligosaccharides with degree of polymerization ≥3 but preferred longer isomaltooligosaccharides. TdCIBP structures in complex with cycloisomaltooctaose and isomaltoheptaose were determined using X-ray crystallography at 1.6 Å and 1.9 Å resolutions, respectively. Of the modeled five d-glucosyl residues in isomaltoheptaose, the two d-glucosyl residues (the third and fourth residues from the reducing end) were bound to TdCIBP through numerous hydrogen bonding interactions in the same orientation as the corresponding D-glucosyl residues of cycloisomaltooctaose. The other D-glucosyl residues of isomaltoheptaose bind differently to the binding site than the corresponding D-glucosyl residues of cycloisomaltooctaose. As little difference was observed in the amino acid orientation of TdCIBP between the two complexes, cyclic and linear isomaltooligosaccharides were bound to TdCIBP by changing the combination of interacting amino acid residues. The high affinity to CIs and long isomaltooligosaccharides suggests that the ABC transporter cooperating with TdCIBP uptakes these sugars directly, contributing to sugar metabolism and minimizing ATP consumption.
{"title":"Insights into the recognition of cyclic α-(1→6)-glucan by a solute-binding protein of an ABC transporter from Tepidibacillus decaturensis.","authors":"Shiho Takei,Wataru Saburi,Min Yao,Haruhide Mori,Toyoyuki Ose","doi":"10.1016/j.jbc.2026.111346","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111346","url":null,"abstract":"ATP-binding cassette (ABC) transporters facilitate the translocation of various substrates across biological membranes. In prokaryotic ABC importers, solute binding protein (SBP), which selectively binds to a ligand, is incorporated into the functional complex. Cycloisomaltooligosaccharides (CIs) are produced from α-(1→6)-glucan by CI glucanotransferase, and intracellularly degraded by CI-inducible dextranase. CIs are regarded as incorporated forms; however, their uptake mechanisms have not yet been elucidated. In this study, SBP with a high affinity for CIs from Tepidibacillus decaturensis (TdCIBP) was discovered. TdCIBP showed the highest affinity for cycloisomaltoheptaose, followed by cycloisomaltooctaose and cycloisomaltononaose. TdCIBP also showed binding affinity for linear isomaltooligosaccharides with degree of polymerization ≥3 but preferred longer isomaltooligosaccharides. TdCIBP structures in complex with cycloisomaltooctaose and isomaltoheptaose were determined using X-ray crystallography at 1.6 Å and 1.9 Å resolutions, respectively. Of the modeled five d-glucosyl residues in isomaltoheptaose, the two d-glucosyl residues (the third and fourth residues from the reducing end) were bound to TdCIBP through numerous hydrogen bonding interactions in the same orientation as the corresponding D-glucosyl residues of cycloisomaltooctaose. The other D-glucosyl residues of isomaltoheptaose bind differently to the binding site than the corresponding D-glucosyl residues of cycloisomaltooctaose. As little difference was observed in the amino acid orientation of TdCIBP between the two complexes, cyclic and linear isomaltooligosaccharides were bound to TdCIBP by changing the combination of interacting amino acid residues. The high affinity to CIs and long isomaltooligosaccharides suggests that the ABC transporter cooperating with TdCIBP uptakes these sugars directly, contributing to sugar metabolism and minimizing ATP consumption.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"15 1","pages":"111346"},"PeriodicalIF":4.8,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147368325","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}
During DNA replication, the topoisomerases TOP1 and TOP2 resolve topological stress associated with DNA unwinding. Based on their catalytic activities, TOP1 is believed to relieve positive supercoil ahead of the replication fork, while TOP2 primarily removes topological intertwines between sister chromatids behind the replication fork. As the replication fork rotates, these two topoisomerases are considered to function complementarily. While this functional interplay between TOP1 and TOP2 has been well established in yeast, it remains unclear whether a similar genetic interaction exists in vertebrate cells. To investigate this, we generated conditionally TOP1-depleted chicken DT40 cells, a model system amenable to gene editing. Although TOP1 is essential in DT40 cells, its depletion did not affect the replication fork progression. Similarly, treatment with ICRF193, a TOP2 inhibitor, had no impact on DNA replication rates. However, the combination of TOP1 depletion and ICRF193 treatment nearly abolished DNA replication, leading to S phase arrest and rapid apoptosis. Interestingly, treatment of TOP1-depleted cells with etoposide, a TOP2 poison that inhibits DNA re-ligation, did not affect the replication fork progression but instead caused cell cycle arrest in G1/early S phase, suggesting impaired an initiation of DNA replication. These findings demonstrate that TOP1 and TOP2 have complementary roles in both the progression and initiation of DNA replication in vertebrate cells.
{"title":"TOP1 and TOP2 complementarily maintain DNA replication fork progression in vertebrates.","authors":"Koyuki Umemura,Masato Ooka,Miku Sojo,Masayuki Seki,Menghang Xia,Kouji Hirota,Takuya Abe","doi":"10.1016/j.jbc.2026.111339","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111339","url":null,"abstract":"During DNA replication, the topoisomerases TOP1 and TOP2 resolve topological stress associated with DNA unwinding. Based on their catalytic activities, TOP1 is believed to relieve positive supercoil ahead of the replication fork, while TOP2 primarily removes topological intertwines between sister chromatids behind the replication fork. As the replication fork rotates, these two topoisomerases are considered to function complementarily. While this functional interplay between TOP1 and TOP2 has been well established in yeast, it remains unclear whether a similar genetic interaction exists in vertebrate cells. To investigate this, we generated conditionally TOP1-depleted chicken DT40 cells, a model system amenable to gene editing. Although TOP1 is essential in DT40 cells, its depletion did not affect the replication fork progression. Similarly, treatment with ICRF193, a TOP2 inhibitor, had no impact on DNA replication rates. However, the combination of TOP1 depletion and ICRF193 treatment nearly abolished DNA replication, leading to S phase arrest and rapid apoptosis. Interestingly, treatment of TOP1-depleted cells with etoposide, a TOP2 poison that inhibits DNA re-ligation, did not affect the replication fork progression but instead caused cell cycle arrest in G1/early S phase, suggesting impaired an initiation of DNA replication. These findings demonstrate that TOP1 and TOP2 have complementary roles in both the progression and initiation of DNA replication in vertebrate cells.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"62 1","pages":"111339"},"PeriodicalIF":4.8,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147368322","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}
The histone H3-H4 octasome is a nucleosome-like particle in which two DNA gyres are wrapped around each histone (H3-H4)2 tetramer disk, forming a clamshell-like configuration. In the present study, we performed in vitro RNA polymerase II (RNAPII) transcription assays with the H3-H4 octasome and found that RNAPII transcribed the H3-H4 octasome more efficiently than the nucleosome. RNAPII paused at only one position, superhelical location (SHL) -4 in the H3-H4 octasome, in contrast to pausing at the SHL(-5), SHL(-2), and SHL(-1) positions in the nucleosome. Cryo-electron microscopy analysis revealed that two (H3-H4)2 tetramer disks are retained when the RNAPII paused at the SHL(-4) position of the H3-H4 octasome. However, when RNAPII reached the SHL(-0.5) position, five base pairs before the dyad position of the H3-H4 octasome, the proximal (H3-H4)2 tetramer was disassembled but the distal (H3-H4)2 tetramer still remained on the DNA. Therefore, RNAPII efficiently transcribes the H3-H4 octasome by stepwise (H3-H4)2 tetramer disassembly.
{"title":"Structural basis of RNA polymerase II transcription on the histone H3-H4 octasome.","authors":"Cheng-Han Ho, Kayo Nozawa, Masahiro Nishimura, Mayuko Oi, Tomoya Kujirai, Mitsuo Ogasawara, Haruhiko Ehara, Shun-Ichi Sekine, Yoshimasa Takizawa, Hitoshi Kurumizaka","doi":"10.1016/j.jbc.2026.111340","DOIUrl":"10.1016/j.jbc.2026.111340","url":null,"abstract":"<p><p>The histone H3-H4 octasome is a nucleosome-like particle in which two DNA gyres are wrapped around each histone (H3-H4)<sub>2</sub> tetramer disk, forming a clamshell-like configuration. In the present study, we performed in vitro RNA polymerase II (RNAPII) transcription assays with the H3-H4 octasome and found that RNAPII transcribed the H3-H4 octasome more efficiently than the nucleosome. RNAPII paused at only one position, superhelical location (SHL) -4 in the H3-H4 octasome, in contrast to pausing at the SHL(-5), SHL(-2), and SHL(-1) positions in the nucleosome. Cryo-electron microscopy analysis revealed that two (H3-H4)<sub>2</sub> tetramer disks are retained when the RNAPII paused at the SHL(-4) position of the H3-H4 octasome. However, when RNAPII reached the SHL(-0.5) position, five base pairs before the dyad position of the H3-H4 octasome, the proximal (H3-H4)<sub>2</sub> tetramer was disassembled but the distal (H3-H4)<sub>2</sub> tetramer still remained on the DNA. Therefore, RNAPII efficiently transcribes the H3-H4 octasome by stepwise (H3-H4)<sub>2</sub> tetramer disassembly.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"111340"},"PeriodicalIF":4.0,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147369127","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}
The RNA-binding proteins TIAR and TIA1 have been reported to affect beta cell insulin production and viability. The missense E384K TIA1 autosomal dominant mutation is known to cause Welander distal myopathy. The aim of this study was to study the effects of the TIA1 E384K mutation in human insulin-producing EndoC-βH1 cells. The prime editing technique was used to generate EndoC-βH1 cell clones with the homozygous E384K TIA1 mutation. The E384K TIA1 mutation did not affect high glucose + palmitate-induced stress granule formation and cell death. Instead, the mutated cells respired and proliferated faster than wild-type cells. This was paralleled by a higher MYC mRNA and protein level, a profoundly reduced GLP-1 receptor mRNA expression, increased expression of "disallowed" beta cell genes, a proinsulin-to-insulin processing defect, a decreased insulin content and release, a decreased PAX4/ARX mRNA ratio, and an increased glucagon production. The TIA1 mutation reduced MYC mRNA binding to TIA1. Downregulation of MYC mRNA levels normalized insulin/glucagon and PAX4/ARX mRNA ratios. Long-term treatment of TIA1-mutated cells with the GLP-1R agonist liraglutide restored insulin production and reversed beta cell dedifferentiation. It is concluded that the TIA1 E384K mutation, via increased MYC levels and cell proliferation rates, causes beta cell dedifferentiation. Thus, dysfunction of RNA-binding proteins may, at least in certain cases, contribute to the impaired insulin production observed in diabetes. A better understanding of RNA-binding protein-mediated control of beta cell differentiation, and the protective impact of GLP-1 receptor agonism, could facilitate the development of new treatment strategies in diabetes.
{"title":"The Welander TIA1 mutation dedifferentiates insulin-producing cells - reversal by a GLP-1 receptor agonist.","authors":"Tongjian Zhao,Jing Cen,Xuan Wang,Mingyu Yang,Joey Lau,Anders Tengholm,Åke Sjöholm,Nils Welsh","doi":"10.1016/j.jbc.2026.111336","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111336","url":null,"abstract":"The RNA-binding proteins TIAR and TIA1 have been reported to affect beta cell insulin production and viability. The missense E384K TIA1 autosomal dominant mutation is known to cause Welander distal myopathy. The aim of this study was to study the effects of the TIA1 E384K mutation in human insulin-producing EndoC-βH1 cells. The prime editing technique was used to generate EndoC-βH1 cell clones with the homozygous E384K TIA1 mutation. The E384K TIA1 mutation did not affect high glucose + palmitate-induced stress granule formation and cell death. Instead, the mutated cells respired and proliferated faster than wild-type cells. This was paralleled by a higher MYC mRNA and protein level, a profoundly reduced GLP-1 receptor mRNA expression, increased expression of \"disallowed\" beta cell genes, a proinsulin-to-insulin processing defect, a decreased insulin content and release, a decreased PAX4/ARX mRNA ratio, and an increased glucagon production. The TIA1 mutation reduced MYC mRNA binding to TIA1. Downregulation of MYC mRNA levels normalized insulin/glucagon and PAX4/ARX mRNA ratios. Long-term treatment of TIA1-mutated cells with the GLP-1R agonist liraglutide restored insulin production and reversed beta cell dedifferentiation. It is concluded that the TIA1 E384K mutation, via increased MYC levels and cell proliferation rates, causes beta cell dedifferentiation. Thus, dysfunction of RNA-binding proteins may, at least in certain cases, contribute to the impaired insulin production observed in diabetes. A better understanding of RNA-binding protein-mediated control of beta cell differentiation, and the protective impact of GLP-1 receptor agonism, could facilitate the development of new treatment strategies in diabetes.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"4 1","pages":"111336"},"PeriodicalIF":4.8,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147359223","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}
Transfer RNAs (tRNAs) are essential components of the protein synthesis machinery. Their biogenesis is a highly regulated process that involves the incorporation of numerous post-transcriptional chemical modifications, essential for tRNA folding, cellular stability and function. The sequential process by which these modifications are introduced remains poorly characterized. Previous studies have suggested the existence of modification hierarchies, particularly in the anticodon-loop region, but also among tRNA core modifications. Here, aiming to understand the molecular mechanisms by which modifications are incorporated in a bacterial model organism, we employed a combination of NMR spectroscopy and biochemical methods to characterize the maturation process of several E. coli tRNAs. By monitoring tRNA maturation in a time-resolved fashion by NMR, we observed a conserved temporal pattern in the incorporation of the Ψ55, T54, and m7G46 modifications. We also show that Ψ55 stimulates the incorporation of T54 in E. coli tRNAPhe, tRNAVal and tRNAAsp, and stimulates that of m7G46 in tRNAPhe and tRNAAsp. Importantly, we also provide general insights into the impact of modifications on tRNA structural properties, and show that while post-transcriptional modifications generally have a structuring effect that reduces conformational heterogeneities, these effects are tRNA-dependent, with certain tRNAs being more affected than others. These findings provide fundamental insights into the molecular aspects of tRNA maturation in E. coli.
{"title":"Mapping the temporality and structural impacts of modifications in E. coli tRNAs.","authors":"Marcel-Joseph Yared,Carine Chagneau,Pierre Barraud","doi":"10.1016/j.jbc.2026.111337","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111337","url":null,"abstract":"Transfer RNAs (tRNAs) are essential components of the protein synthesis machinery. Their biogenesis is a highly regulated process that involves the incorporation of numerous post-transcriptional chemical modifications, essential for tRNA folding, cellular stability and function. The sequential process by which these modifications are introduced remains poorly characterized. Previous studies have suggested the existence of modification hierarchies, particularly in the anticodon-loop region, but also among tRNA core modifications. Here, aiming to understand the molecular mechanisms by which modifications are incorporated in a bacterial model organism, we employed a combination of NMR spectroscopy and biochemical methods to characterize the maturation process of several E. coli tRNAs. By monitoring tRNA maturation in a time-resolved fashion by NMR, we observed a conserved temporal pattern in the incorporation of the Ψ55, T54, and m7G46 modifications. We also show that Ψ55 stimulates the incorporation of T54 in E. coli tRNAPhe, tRNAVal and tRNAAsp, and stimulates that of m7G46 in tRNAPhe and tRNAAsp. Importantly, we also provide general insights into the impact of modifications on tRNA structural properties, and show that while post-transcriptional modifications generally have a structuring effect that reduces conformational heterogeneities, these effects are tRNA-dependent, with certain tRNAs being more affected than others. These findings provide fundamental insights into the molecular aspects of tRNA maturation in E. coli.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"53 1","pages":"111337"},"PeriodicalIF":4.8,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147359222","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：