Pub Date : 2026-03-06DOI: 10.1016/j.jbc.2026.111352
Pavel Simara,Cristina Mazzotti,Gokula Narayanan,Marco Cassani,Stefania Pagliari,Giancarlo Forte
Mechanical signaling has been well documented in certain cell types such as muscle cells, osteoblasts, fibroblasts, and other cells historically defined as mechanocytes for their ability to receive and respond to mechanical stimuli. However, recent data suggest that mechanical signaling is not restricted to given cell types, but it is rather a universal feature of most of the eukaryotic cells that, similarly to extracellular chemical signaling, controls basic metabolic and intracellular signaling processes. Several studies published in recent years provided evidence that mRNA maturation is altered in cells exposed to mechanical stress. These data indicate that the process might be closely related to the three-dimensional (3D) spatial re-organization of RNA-binding proteins. With mounting evidence for the mechanical control of mRNA splicing, this review aims to provide an overview of the available literature and offer a comprehensive vision of this phenomenon that stands out as a fundamental process in cellular biology.
{"title":"Forces That Shape the Transcriptome: Linking Cellular Mechanosensing to mRNA splicing.","authors":"Pavel Simara,Cristina Mazzotti,Gokula Narayanan,Marco Cassani,Stefania Pagliari,Giancarlo Forte","doi":"10.1016/j.jbc.2026.111352","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111352","url":null,"abstract":"Mechanical signaling has been well documented in certain cell types such as muscle cells, osteoblasts, fibroblasts, and other cells historically defined as mechanocytes for their ability to receive and respond to mechanical stimuli. However, recent data suggest that mechanical signaling is not restricted to given cell types, but it is rather a universal feature of most of the eukaryotic cells that, similarly to extracellular chemical signaling, controls basic metabolic and intracellular signaling processes. Several studies published in recent years provided evidence that mRNA maturation is altered in cells exposed to mechanical stress. These data indicate that the process might be closely related to the three-dimensional (3D) spatial re-organization of RNA-binding proteins. With mounting evidence for the mechanical control of mRNA splicing, this review aims to provide an overview of the available literature and offer a comprehensive vision of this phenomenon that stands out as a fundamental process in cellular biology.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"73 1","pages":"111352"},"PeriodicalIF":4.8,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147373845","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 : 2026-03-06DOI: 10.1016/j.jbc.2026.111349
Kenneth J Rodgers
Most organisms rely on 20 DNA-encoded canonical amino acids (AAs) for protein synthesis. However, hundreds of non-canonical amino acids (NCAAs) occur in nature, many of which are plant secondary metabolites. Some NCAAs have been identified as proteinogenic and can mimic canonical AAs in mammalian protein synthesis. The tRNA synthetases responsible for AA recognition have evolved to discriminate against other canonical AAs, but they can activate NCAAs that share close structure similarity with a canonical AA. Some of these proteinogenic NCAAs play a role in plant chemical warfare (allelopathy). When incorporated into proteins, they lead to the production of high levels of non-native proteins, which can negatively impact the health of competing plants or predators. Although the impact of proteinogenic NCAAs on human health is not fully understood, it has generally been attributed to the accumulation of non-native, misfolded proteins in cells, similar to the mechanism of plant allelopathy. More recently, however, the ability of proteinogenic NCAAs to generate immunogenic neoepitopes has been demonstrated in vivo. In this review we summarise emerging experimental evidence supporting NCAA-induced immune responses as a mechanism of NCAA toxicity in humans and its potential as a therapeutic approach for certain cancers.
{"title":"Evidence that non-cognate proteinogenic amino acids generate immunogenic neoepitopes.","authors":"Kenneth J Rodgers","doi":"10.1016/j.jbc.2026.111349","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111349","url":null,"abstract":"Most organisms rely on 20 DNA-encoded canonical amino acids (AAs) for protein synthesis. However, hundreds of non-canonical amino acids (NCAAs) occur in nature, many of which are plant secondary metabolites. Some NCAAs have been identified as proteinogenic and can mimic canonical AAs in mammalian protein synthesis. The tRNA synthetases responsible for AA recognition have evolved to discriminate against other canonical AAs, but they can activate NCAAs that share close structure similarity with a canonical AA. Some of these proteinogenic NCAAs play a role in plant chemical warfare (allelopathy). When incorporated into proteins, they lead to the production of high levels of non-native proteins, which can negatively impact the health of competing plants or predators. Although the impact of proteinogenic NCAAs on human health is not fully understood, it has generally been attributed to the accumulation of non-native, misfolded proteins in cells, similar to the mechanism of plant allelopathy. More recently, however, the ability of proteinogenic NCAAs to generate immunogenic neoepitopes has been demonstrated in vivo. In this review we summarise emerging experimental evidence supporting NCAA-induced immune responses as a mechanism of NCAA toxicity in humans and its potential as a therapeutic approach for certain cancers.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"47 1","pages":"111349"},"PeriodicalIF":4.8,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147373849","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 : 2026-03-06DOI: 10.1016/j.jbc.2026.111355
Emma K Crowley-Dolen,Rafael Junqueira Borges,Paul S Charifson,N Connor Payne,Ramon Guerra de Oliveira,Micael Rodrigues Cunha,Ralph Mazitschek,Katlin B Massirer,Timothy J Mitchison
Vaccinia-related kinase 1 (VRK1) is a promising therapeutic target in gliomas and glioblastomas where VRK2 is silenced by promoter methylation, rendering VRK1 essential for accurate nuclear envelope reassembly following mitosis. Small-molecule ATP-site drug discovery for VRK1 has been hindered by the absence of robust and reproducible biochemical assays. Through virtual screening, we identified previously unreported VRK1-binding scaffolds and validated them in biochemical kinase assays, yielding an 82 nM inhibitor with high selectivity for VRK1 over VRK2. During characterization of this compound, we found that a commonly used commercial time-resolved fluorescence resonance energy transfer (TR-FRET) VRK1 activity assay is dependent on purification tag-mediated VRK1 dimerization. Leveraging the new inhibitor, we developed fluorogenic tool compounds that increase in fluorescence intensity upon binding to the active site of VRK1, and do not require artificial dimerization of VRK1. The top probe exhibits a Kd of 180 nM and is useful for ligand displacement assays using both fluorescence enhancement and TR-FRET readouts. Together, these results introduce new chemical scaffolds for targeting VRK1, define an assay artifact that has complicated VRK1 inhibitor discovery, and deliver fluorogenic tool compounds for high-throughput screening of ATP-site VRK1 inhibitors, enabling future drug discovery efforts against this emerging cancer vulnerability.
{"title":"Structure-Based Discovery of Selective Vaccinia-Related Kinase 1 Inhibitors and Fluorogenic Active-Site Probes.","authors":"Emma K Crowley-Dolen,Rafael Junqueira Borges,Paul S Charifson,N Connor Payne,Ramon Guerra de Oliveira,Micael Rodrigues Cunha,Ralph Mazitschek,Katlin B Massirer,Timothy J Mitchison","doi":"10.1016/j.jbc.2026.111355","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111355","url":null,"abstract":"Vaccinia-related kinase 1 (VRK1) is a promising therapeutic target in gliomas and glioblastomas where VRK2 is silenced by promoter methylation, rendering VRK1 essential for accurate nuclear envelope reassembly following mitosis. Small-molecule ATP-site drug discovery for VRK1 has been hindered by the absence of robust and reproducible biochemical assays. Through virtual screening, we identified previously unreported VRK1-binding scaffolds and validated them in biochemical kinase assays, yielding an 82 nM inhibitor with high selectivity for VRK1 over VRK2. During characterization of this compound, we found that a commonly used commercial time-resolved fluorescence resonance energy transfer (TR-FRET) VRK1 activity assay is dependent on purification tag-mediated VRK1 dimerization. Leveraging the new inhibitor, we developed fluorogenic tool compounds that increase in fluorescence intensity upon binding to the active site of VRK1, and do not require artificial dimerization of VRK1. The top probe exhibits a Kd of 180 nM and is useful for ligand displacement assays using both fluorescence enhancement and TR-FRET readouts. Together, these results introduce new chemical scaffolds for targeting VRK1, define an assay artifact that has complicated VRK1 inhibitor discovery, and deliver fluorogenic tool compounds for high-throughput screening of ATP-site VRK1 inhibitors, enabling future drug discovery efforts against this emerging cancer vulnerability.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"6 1","pages":"111355"},"PeriodicalIF":4.8,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147373841","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 : 2026-03-06DOI: 10.1016/j.jbc.2026.111353
Meenakshi Sharma,Anthony Waterston,Christopher J Randolph,Lauren E Stark,David M Gravano,Michael E Colvin,Eva de Alba
Canonical inflammasome assembly is driven by interactions between sensors and effector procaspase-1, primarily mediated by the adaptor ASC. Homotypic interactions between Death Domains pyrin (PYD) and caspase recruitment and activation domain (CARD) lead to sensor and ASC oligomerization, along with the recruitment of procaspase-1. ASC self-association is essential for inflammasome activation, which initiates inflammatory responses. Therefore, uncontrolled inflammasome activation contributes to chronic inflammatory diseases. ASC-c, an isoform of ASC, acts as a negative regulator of the inflammasome. To better understand ASC-c's regulatory role, we examined its structural properties and interactions with ASC. Our nuclear magnetic resonance data show that ASC-c's CARD is properly folded, whereas the PYD consists of two α-helices instead of the six-helix bundle typical of Death Domains. In addition, a chemical shift perturbation analysis indicates that ASC-c interacts with ASC. We obtained transmission electron micrographs revealing that ASC-c polymerizes into filaments and filament bundles, which display greater heterogeneity than those of ASC based on dynamic light scattering. Overall, our results suggest that ASC-c binding to ASC can have an impact on ASC self-association, thereby affecting inflammasome assembly. Based on these findings, we designed a peptide encompassing the two helices of the ASC-c PYD to target ASC for therapeutic purposes. We demonstrate the interaction between the peptide and ASC by fluorescence anisotropy and show the stability of the complex by molecular dynamics simulations. Finally, cell-based assays measuring inflammasome activation indicate an inhibitory effect of the ASC-c peptide, pointing to its potential use in drug design.
{"title":"The ASC-c isoform as a modulator of inflammasome activation: insights into molecular mechanisms and therapeutic applications.","authors":"Meenakshi Sharma,Anthony Waterston,Christopher J Randolph,Lauren E Stark,David M Gravano,Michael E Colvin,Eva de Alba","doi":"10.1016/j.jbc.2026.111353","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111353","url":null,"abstract":"Canonical inflammasome assembly is driven by interactions between sensors and effector procaspase-1, primarily mediated by the adaptor ASC. Homotypic interactions between Death Domains pyrin (PYD) and caspase recruitment and activation domain (CARD) lead to sensor and ASC oligomerization, along with the recruitment of procaspase-1. ASC self-association is essential for inflammasome activation, which initiates inflammatory responses. Therefore, uncontrolled inflammasome activation contributes to chronic inflammatory diseases. ASC-c, an isoform of ASC, acts as a negative regulator of the inflammasome. To better understand ASC-c's regulatory role, we examined its structural properties and interactions with ASC. Our nuclear magnetic resonance data show that ASC-c's CARD is properly folded, whereas the PYD consists of two α-helices instead of the six-helix bundle typical of Death Domains. In addition, a chemical shift perturbation analysis indicates that ASC-c interacts with ASC. We obtained transmission electron micrographs revealing that ASC-c polymerizes into filaments and filament bundles, which display greater heterogeneity than those of ASC based on dynamic light scattering. Overall, our results suggest that ASC-c binding to ASC can have an impact on ASC self-association, thereby affecting inflammasome assembly. Based on these findings, we designed a peptide encompassing the two helices of the ASC-c PYD to target ASC for therapeutic purposes. We demonstrate the interaction between the peptide and ASC by fluorescence anisotropy and show the stability of the complex by molecular dynamics simulations. Finally, cell-based assays measuring inflammasome activation indicate an inhibitory effect of the ASC-c peptide, pointing to its potential use in drug design.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"6 1","pages":"111353"},"PeriodicalIF":4.8,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147373847","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 : 2026-03-06DOI: 10.1016/j.jbc.2026.111351
Seokjun G Ha,Hyunwoo C Kwon,Jongsun Lee,Hyung-Jun Kim,Seung-Jae V Lee
Aging is a complex biological process characterized by the gradual decline of physiological and molecular functions and increased susceptibility to age-associated diseases. Emerging evidence indicates the role of mRNA quality control mechanisms in the regulation of aging and longevity. This review focuses on the function of mRNA surveillance mechanisms, including nonsense-mediated mRNA decay (NMD), nonstop decay (NSD), and no-go decay (NGD), in aging and age-related diseases. We discuss the critical roles of these pathways in maintaining mRNA quality and preventing the accumulation of aberrant transcripts, which can contribute to aging and age-related disorders. Specifically, we discuss the function of NMD in aging processes and age-related diseases, including cancer and neurodegenerative disorders. We also review the safeguarding roles of NSD and NGD in preventing the accumulation of faulty mRNAs and proteins associated with various diseases. We explore the potential functions of additional mRNA surveillance and the associated signaling pathways, such as ribosome-associated quality control (RQC), in aging and age-related diseases. Understanding the intricate relationship between mRNA surveillance mechanisms and aging may provide key information for developing potential therapeutics that boost these pathways for delaying aging and treating age-related diseases.
{"title":"The function of mRNA quality control in aging and age-related diseases.","authors":"Seokjun G Ha,Hyunwoo C Kwon,Jongsun Lee,Hyung-Jun Kim,Seung-Jae V Lee","doi":"10.1016/j.jbc.2026.111351","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111351","url":null,"abstract":"Aging is a complex biological process characterized by the gradual decline of physiological and molecular functions and increased susceptibility to age-associated diseases. Emerging evidence indicates the role of mRNA quality control mechanisms in the regulation of aging and longevity. This review focuses on the function of mRNA surveillance mechanisms, including nonsense-mediated mRNA decay (NMD), nonstop decay (NSD), and no-go decay (NGD), in aging and age-related diseases. We discuss the critical roles of these pathways in maintaining mRNA quality and preventing the accumulation of aberrant transcripts, which can contribute to aging and age-related disorders. Specifically, we discuss the function of NMD in aging processes and age-related diseases, including cancer and neurodegenerative disorders. We also review the safeguarding roles of NSD and NGD in preventing the accumulation of faulty mRNAs and proteins associated with various diseases. We explore the potential functions of additional mRNA surveillance and the associated signaling pathways, such as ribosome-associated quality control (RQC), in aging and age-related diseases. Understanding the intricate relationship between mRNA surveillance mechanisms and aging may provide key information for developing potential therapeutics that boost these pathways for delaying aging and treating age-related diseases.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"25 1","pages":"111351"},"PeriodicalIF":4.8,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147373842","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 : 2026-03-06DOI: 10.1016/j.jbc.2026.111350
Zahra Nawaz,Trevor Adams,Mariye Erol Demirturk,Fikri Y Avci
The HIV-1 envelope glycoprotein (Env) is essential for viral entry and infection of host cells. Composed of the trimer of the gp120/gp41 heterodimeric glycoproteins, the Env trimer is the primary target for neutralizing antibodies. Extensive research over the past forty years has focused on developing advanced immunogens, specifically recombinant, native-like Env trimers and structure-guided, germline-targeting constructs, to elicit protective antibody responses. The Env trimer is encased by up to 90 N-linked glycosylation sites, whose occupancy effectively shields the underlying protein from immune surveillance. While it is well established that glycosylation of HIV-1 gp120 affects antibody responses in infected individuals and that many broadly neutralizing antibodies (bnAbs) depend on glycan-specific epitopes, the capacity of Env-derived glycopeptides to act as unconventional CD4+ T cell epitopes and shape helper T cell responses remains comparatively underexplored. This review examines the adaptive immune responses triggered by HIV Env, with an emphasis on how Env glycosylation simultaneously constrains B cell recognition and contributes to antigen processing and T cell-mediated immune responses, aiming to lay the groundwork for future vaccine development and to inform strategies that elicit robust and lasting protection against HIV-1 infection.
{"title":"Decoding the Glycan Shield: Immune Recognition and Response to the HIV-1 Envelope Trimer.","authors":"Zahra Nawaz,Trevor Adams,Mariye Erol Demirturk,Fikri Y Avci","doi":"10.1016/j.jbc.2026.111350","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111350","url":null,"abstract":"The HIV-1 envelope glycoprotein (Env) is essential for viral entry and infection of host cells. Composed of the trimer of the gp120/gp41 heterodimeric glycoproteins, the Env trimer is the primary target for neutralizing antibodies. Extensive research over the past forty years has focused on developing advanced immunogens, specifically recombinant, native-like Env trimers and structure-guided, germline-targeting constructs, to elicit protective antibody responses. The Env trimer is encased by up to 90 N-linked glycosylation sites, whose occupancy effectively shields the underlying protein from immune surveillance. While it is well established that glycosylation of HIV-1 gp120 affects antibody responses in infected individuals and that many broadly neutralizing antibodies (bnAbs) depend on glycan-specific epitopes, the capacity of Env-derived glycopeptides to act as unconventional CD4+ T cell epitopes and shape helper T cell responses remains comparatively underexplored. This review examines the adaptive immune responses triggered by HIV Env, with an emphasis on how Env glycosylation simultaneously constrains B cell recognition and contributes to antigen processing and T cell-mediated immune responses, aiming to lay the groundwork for future vaccine development and to inform strategies that elicit robust and lasting protection against HIV-1 infection.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"40 1","pages":"111350"},"PeriodicalIF":4.8,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147373848","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 : 2026-03-06DOI: 10.1016/j.jbc.2026.111348
Dorothy Yanling Zhao,Syed Nabeel-Shah,Zuyao Ni,Shuye Pu,Guoqing Zhong,Frank W Schmitges,Ulrich Braunschweig,Benjamin J Blencowe,Jack F Greenblatt
TDP-43 and FUS are RNA-binding proteins involved in the regulation of diverse RNA processing events and have been strongly implicated in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We have previously demonstrated the role of symmetrical dimethylation (me2s) of a conserved arginine residue (R1810 in human POLR2A) in the C-terminal domain (CTD) of RNA polymerase II (RNAPII), which facilitates the recruitment of the Tudor domain-containing protein SMN to resolve R-loops at transcriptional termination sites. Here, we demonstrate that TDP-43 and FUS contribute to transcription termination through the R1810me2s-SMN pathway. Our data show that TDP-43-and to a lesser extent, FUS-are recruited to chromatin via this pathway, and that disruption of their recruitment leads to defective RNAPII termination. This impairment results in the accumulation of R-loops and elevated DNA damage at gene terminators. Using transcriptome-wide analyses, we further show that TDP-43 RNA-binding sites are highly correlated with regions of R-loop formation. Importantly, we find that the RNA-binding activity of TDP-43 is essential for its role in resolving R-loops and promoting efficient transcription termination. These findings establish a mechanistic link between TDP-43/FUS, R-loop resolution, and transcription termination, providing new insights into how their dysfunction may drive genome instability and contribute to the pathogenesis of ALS and FTD.
{"title":"RNA-Binding Proteins TDP-43 and FUS Promote R-Loop Resolution and Regulate Transcription Termination.","authors":"Dorothy Yanling Zhao,Syed Nabeel-Shah,Zuyao Ni,Shuye Pu,Guoqing Zhong,Frank W Schmitges,Ulrich Braunschweig,Benjamin J Blencowe,Jack F Greenblatt","doi":"10.1016/j.jbc.2026.111348","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111348","url":null,"abstract":"TDP-43 and FUS are RNA-binding proteins involved in the regulation of diverse RNA processing events and have been strongly implicated in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We have previously demonstrated the role of symmetrical dimethylation (me2s) of a conserved arginine residue (R1810 in human POLR2A) in the C-terminal domain (CTD) of RNA polymerase II (RNAPII), which facilitates the recruitment of the Tudor domain-containing protein SMN to resolve R-loops at transcriptional termination sites. Here, we demonstrate that TDP-43 and FUS contribute to transcription termination through the R1810me2s-SMN pathway. Our data show that TDP-43-and to a lesser extent, FUS-are recruited to chromatin via this pathway, and that disruption of their recruitment leads to defective RNAPII termination. This impairment results in the accumulation of R-loops and elevated DNA damage at gene terminators. Using transcriptome-wide analyses, we further show that TDP-43 RNA-binding sites are highly correlated with regions of R-loop formation. Importantly, we find that the RNA-binding activity of TDP-43 is essential for its role in resolving R-loops and promoting efficient transcription termination. These findings establish a mechanistic link between TDP-43/FUS, R-loop resolution, and transcription termination, providing new insights into how their dysfunction may drive genome instability and contribute to the pathogenesis of ALS and FTD.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"75 1","pages":"111348"},"PeriodicalIF":4.8,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147373898","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 : 2026-03-06DOI: 10.1016/j.jbc.2026.111354
Bradley P Clarke, Vadim Pedchenko, Tetyana Pedchenko, Monica Moran, Jacob Edwards, Kyle Vallone, Carl Darris, Gautam Bhave, Patrick Page-McCaw, Julie K Hudson, Sergei P Boudko, Billy G Hudson
Collagen-IV (Col-IV) scaffolds, a primordial basement membrane component, enabled animal multicellularity, evolution and adaptation. These scaffolds provide tensile strength and tether macromolecules, forming supramolecular complexes that interact with cell-surface receptors and influence cell-behavior. Triple-helical Col-IV protomers, composed of three α-chains, with a trimeric globular NC1-domain at the C-terminus, oligomerize forming a NC1-hexamer structure that connects adjoining protomers of Col-IVα121, Col-IVα556-α121, and Col-IVα345 scaffolds. Hexamer formation and stability are driven by the extracellular chloride concentration- "chloride pressure". Hexamer structure is reinforced by six sulfilimine bonds forming covalent crosslinks that weld together trimeric NC1-domains of adjoining protomers. We recently found evidence that sulfilimine bonds, independent of chloride, stabilize the quaternary structure of the Col-IVα345 hexamer of the Col-IVα345 scaffold. Here, we sought to determine whether this function also pertains to the Col-IVα121 scaffold that occurs ubiquitously across the animal kingdom, and whether bromine, a cofactor of peroxidasin in bond formation, are evolutionary conserved. We found that sulfilimine bonds stabilized the quaternary structure of the Col-IVα121 hexamer of bovine, mouse and a basal cnidarian, Nematostella vectensis, and that the mechanism of bond formation mediated by peroxidasin and bromide is evolutionary conserved. Analyses of the crystal structure of the NC1-hexamer revealed that sulfilimine bonds covalently fasten a clasp-motif across the trimer-trimer interface, interlocking the domain-swapping region of neighboring subunits, which reinforces the hexamer quaternary structure imposed by chloride conformational constraints. Collectively, our findings reveal that the sulfilimine-bond reinforcement is a critical event in Col-IV scaffold assembly enabling multicellularity, evolution and adaptation of metazoans, beginning with ancient cnidarians.
胶原- iv （Col-IV）支架是一种原始基底膜成分，使动物具有多细胞性、进化和适应能力。这些支架提供抗拉强度并系住大分子，形成与细胞表面受体相互作用并影响细胞行为的超分子复合物。三螺旋的coli - iv原聚体由三条α-链组成，在c端具有三聚体球形nc1结构域，通过寡聚形成nc1六聚体结构，连接相邻的coli - iv α121、coli - iv α556-α121和coli - iv α345支架原聚体。六聚体的形成和稳定性是由胞外氯浓度——“氯压力”驱动的。六聚体结构由六个亚胺键加强，形成共价交联，将相邻原聚体的三聚体nc1结构域焊接在一起。我们最近发现的证据表明，不依赖于氯化物的亚胺键稳定了coli - iv α345支架的coli - iv α345六聚体的四级结构。在这里，我们试图确定这种功能是否也适用于在动物界普遍存在的Col-IVα121支架，以及溴（过氧化物酶在键形成中的辅助因子）是否具有进化保守性。研究发现，亚砜亚胺键稳定了牛、小鼠和一种基础刺胞动物线虫（Nematostella vectensis） coli - iv α121六聚体的四级结构，并且过氧化物酶和溴化物介导的键形成机制是进化保守的。对nc1 -六聚体晶体结构的分析表明，亚砜亚胺键共价紧固了三聚体-三聚体界面上的一个扣序基序，使相邻亚基的结构交换区互锁，从而增强了六聚体的四元结构。总的来说，我们的研究结果表明，从古老的刺胞动物开始，亚胺键的增强是Col-IV支架组装过程中的一个关键事件，可以使多细胞、进化和适应后生动物。
{"title":"Collagen IV of basement membrane: V. Bromide-mediated sulfilimine bonds interlock the quaternary structure of NC1-hexamer of scaffolds enabling metazoan evolution.","authors":"Bradley P Clarke, Vadim Pedchenko, Tetyana Pedchenko, Monica Moran, Jacob Edwards, Kyle Vallone, Carl Darris, Gautam Bhave, Patrick Page-McCaw, Julie K Hudson, Sergei P Boudko, Billy G Hudson","doi":"10.1016/j.jbc.2026.111354","DOIUrl":"10.1016/j.jbc.2026.111354","url":null,"abstract":"<p><p>Collagen-IV (Col-IV) scaffolds, a primordial basement membrane component, enabled animal multicellularity, evolution and adaptation. These scaffolds provide tensile strength and tether macromolecules, forming supramolecular complexes that interact with cell-surface receptors and influence cell-behavior. Triple-helical Col-IV protomers, composed of three α-chains, with a trimeric globular NC1-domain at the C-terminus, oligomerize forming a NC1-hexamer structure that connects adjoining protomers of Col-IV<sup>α121</sup>, Col-IV<sup>α556-α121</sup>, and Col-IV<sup>α345</sup> scaffolds. Hexamer formation and stability are driven by the extracellular chloride concentration- \"chloride pressure\". Hexamer structure is reinforced by six sulfilimine bonds forming covalent crosslinks that weld together trimeric NC1-domains of adjoining protomers. We recently found evidence that sulfilimine bonds, independent of chloride, stabilize the quaternary structure of the Col-IV<sup>α345</sup> hexamer of the Col-IV<sup>α345</sup> scaffold. Here, we sought to determine whether this function also pertains to the Col-IV<sup>α121</sup> scaffold that occurs ubiquitously across the animal kingdom, and whether bromine, a cofactor of peroxidasin in bond formation, are evolutionary conserved. We found that sulfilimine bonds stabilized the quaternary structure of the Col-IV<sup>α121</sup> hexamer of bovine, mouse and a basal cnidarian, Nematostella vectensis, and that the mechanism of bond formation mediated by peroxidasin and bromide is evolutionary conserved. Analyses of the crystal structure of the NC1-hexamer revealed that sulfilimine bonds covalently fasten a clasp-motif across the trimer-trimer interface, interlocking the domain-swapping region of neighboring subunits, which reinforces the hexamer quaternary structure imposed by chloride conformational constraints. Collectively, our findings reveal that the sulfilimine-bond reinforcement is a critical event in Col-IV scaffold assembly enabling multicellularity, evolution and adaptation of metazoans, beginning with ancient cnidarians.</p>","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":" ","pages":"111354"},"PeriodicalIF":4.0,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147377685","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 : 2026-03-06DOI: 10.1016/j.jbc.2026.111272
Julia Kleetz, Jason C Grigg, Adam A Hassan, Adriana Ibtisam, Janine N Copp, Jennifer Lian, Jie Liu, Lindsay D Eltis
{"title":"Correction: The biosynthesis of N-acyalated tryptazolone in Mycobacterium tuberculosis and related bacteria.","authors":"Julia Kleetz, Jason C Grigg, Adam A Hassan, Adriana Ibtisam, Janine N Copp, Jennifer Lian, Jie Liu, Lindsay D Eltis","doi":"10.1016/j.jbc.2026.111272","DOIUrl":"10.1016/j.jbc.2026.111272","url":null,"abstract":"","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"302 3","pages":"111272"},"PeriodicalIF":4.0,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12992940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147372591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-04DOI: 10.1016/j.jbc.2026.111345
Chunyi Jiang,Xinyi Liu,Hui Li,Yan Lu,Qianqian Cao,Bin Yu,Susu Mao
Metabolic reprogramming is a hallmark of neuronal repair, yet the roles of glucose metabolism-related enzymes remain poorly understood. To investigate their functions, we employed a sciatic nerve injury model, taking advantage the intrinsic regenerative capacity of peripheral neurons. After sciatic nerve crush injury, dorsal root ganglia (DRG) exhibited sustained upregulation of several enzymes in the pentose phosphate pathway (PPP). Notably, glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the PPP, was markedly increased at both RNA and protein levels. Silencing G6PD impaired axon regeneration in vitro and in vivo, whereas its overexpression enhanced regrowth. Interestingly, G6PD overexpression did not alter the NADP+/NADPH ratio, suggesting a non-metabolic role. Using mass spectrometry, co-immunoprecipitation, and Duolink proximity ligation assays, we identified clathrin heavy chain (CLTC) as a specific binding partner of G6PD. Mechanistic analyses further showed that G6PD facilitated neuronal endocytosis through direct interaction with CLTC, thereby promoting axon regeneration. These findings identify G6PD as a molecular link between metabolic reprogramming and membrane trafficking, revealing an unexpected non-metabolic role in neural repair.
{"title":"G6PD facilitates axon regeneration via clathrin-mediated endocytosis.","authors":"Chunyi Jiang,Xinyi Liu,Hui Li,Yan Lu,Qianqian Cao,Bin Yu,Susu Mao","doi":"10.1016/j.jbc.2026.111345","DOIUrl":"https://doi.org/10.1016/j.jbc.2026.111345","url":null,"abstract":"Metabolic reprogramming is a hallmark of neuronal repair, yet the roles of glucose metabolism-related enzymes remain poorly understood. To investigate their functions, we employed a sciatic nerve injury model, taking advantage the intrinsic regenerative capacity of peripheral neurons. After sciatic nerve crush injury, dorsal root ganglia (DRG) exhibited sustained upregulation of several enzymes in the pentose phosphate pathway (PPP). Notably, glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the PPP, was markedly increased at both RNA and protein levels. Silencing G6PD impaired axon regeneration in vitro and in vivo, whereas its overexpression enhanced regrowth. Interestingly, G6PD overexpression did not alter the NADP+/NADPH ratio, suggesting a non-metabolic role. Using mass spectrometry, co-immunoprecipitation, and Duolink proximity ligation assays, we identified clathrin heavy chain (CLTC) as a specific binding partner of G6PD. Mechanistic analyses further showed that G6PD facilitated neuronal endocytosis through direct interaction with CLTC, thereby promoting axon regeneration. These findings identify G6PD as a molecular link between metabolic reprogramming and membrane trafficking, revealing an unexpected non-metabolic role in neural repair.","PeriodicalId":15140,"journal":{"name":"Journal of Biological Chemistry","volume":"1 1","pages":"111345"},"PeriodicalIF":4.8,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147368321","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}
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