Proceedings of the National Academy of Sciences of the United States of America最新文献

{"title":"A minimal complex of KHNYN and zinc-finger antiviral protein binds and degrades single-stranded RNA","authors":"Zoe C. Yeoh, Jennifer L. Meagher, Chia-Yu Kang, Paul D. Bieniasz, Janet L. Smith, Melanie D. Ohi","doi":"10.1073/pnas.2415048121","DOIUrl":"https://doi.org/10.1073/pnas.2415048121","url":null,"abstract":"Detecting viral infection is a key role of the innate immune system. The genomes of some RNA viruses have a high CpG dinucleotide content relative to most vertebrate cell RNAs, making CpGs a molecular marker of infection. The human zinc-finger antiviral protein (ZAP) recognizes CpG, mediates clearance of the foreign CpG-rich RNA, and causes attenuation of CpG-rich RNA viruses. While ZAP binds RNA, it lacks enzymatic activity that might be responsible for RNA degradation and thus requires interacting cofactors for its function. One of these cofactors, KHNYN, has a predicted nuclease domain. Using biochemical approaches, we found that the KHNYN NYN domain is a single-stranded RNA ribonuclease that does not have sequence specificity and digests RNA with or without CpG dinucleotides equivalently in vitro. We show that unlike most KH domains, the KHNYN KH domain does not bind RNA. Indeed, a crystal structure of the KH region revealed a double-KH domain with a negatively charged surface that accounts for the lack of RNA binding. Rather, the KHNYN C-terminal domain (CTD) interacts with the ZAP RNA-binding domain (RBD) to provide target RNA specificity. We define a minimal complex composed of the ZAP RBD and the KHNYN NYN-CTD and use a fluorescence polarization assay to propose a model for how this complex interacts with a CpG dinucleotide-containing RNA. In the context of the cell, this module would represent the minimum ZAP and KHNYN domains required for CpG-recognition and ribonuclease activity essential for attenuation of viruses with clusters of CpG dinucleotides.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"48 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Some coral reef communities may degrade and change but persist.","authors":"Nancy Knowlton","doi":"10.1073/pnas.2422158121","DOIUrl":"https://doi.org/10.1073/pnas.2422158121","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2422158121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142802081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Low-temperature gas-phase formation of cyclopentadiene and its role in the formation of aromatics in the interstellar medium.","authors":"Zhenghai Yang, Iakov A Medvedkov, Shane J Goettl, Anatoliy A Nikolayev, Alexander M Mebel, Xiaohu Li, Ralf I Kaiser","doi":"10.1073/pnas.2409933121","DOIUrl":"https://doi.org/10.1073/pnas.2409933121","url":null,"abstract":"<p><p>The cyclopentadiene (C₅H₆) molecule has emerged as a molecular building block of nonplanar polycyclic aromatic hydrocarbons (PAHs) and carbonaceous nanostructures such as corannulene (C₂₀H₁₀), nanobowls (C₄₀H₁₀), and fullerenes (C₆₀) in deep space. However, the underlying elementary gas-phase processes synthesizing cyclopentadiene from acyclic hydrocarbon precursors have remained elusive. Here, by merging crossed molecular beam experiments with rate coefficient calculations and comprehensive astrochemical modeling, we afford persuasive testimony on an unconventional low-temperature cyclization pathway to cyclopentadiene from acyclic precursors through the reaction of the simplest diatomic organic radical-methylidyne (CH)-with 1,3-butadiene (C₄H₆) representing main route to cyclopentadiene observed in TaurusMolecular Cloud. This facile route provides potential solution for the incorporation of the cyclopentadiene moiety in complex aromatic systems via bottom-up molecular mass growth processes and offers an entry point to the low-temperature chemistry in deep space leading eventually to nonplanar PAHs in our carbonaceous Universe.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2409933121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting DTX2/UFD1-mediated FTO degradation to regulate antitumor immunity.","authors":"Yan-Hong Cui, Jiangbo Wei, Hao Fan, Wenlong Li, Lijie Zhao, Emma Wilkinson, Jack Peterson, Lishi Xie, Zhongyu Zou, Seungwon Yang, Mark A Applebaum, Justin Kline, Jing Chen, Chuan He, Yu-Ying He","doi":"10.1073/pnas.2407910121","DOIUrl":"https://doi.org/10.1073/pnas.2407910121","url":null,"abstract":"<p><p>Here, we show that vitamin E succinate (VES) acts as a degrader for the m⁶A RNA demethylase fat mass and obesity-associated protein (FTO), thus suppressing tumor growth and resistance to immunotherapy. FTO is ubiquitinated by its E3 ligase DTX2, followed by UFD1 recruitment and subsequent degradation in the proteasome. VES binds to FTO and DTX2, leading to enhanced FTO-DTX2 interaction, FTO ubiquitination, and degradation in FTO-dependent tumor cells. VES suppressed tumor growth and enhanced antitumor immunity and response to immunotherapy in vivo in mouse models. Genetic FTO knockdown or VES treatment increased m⁶A methylation in the LIF (Leukemia Inhibitory Factor) gene and decreased LIF mRNA decay, and thus sensitized melanoma cells to T cell-mediated cytotoxicity. Taken together, our findings reveal the underlying molecular mechanism for FTO protein degradation and identify a dietary degrader for FTO that inhibits tumor growth and overcomes immunotherapy resistance.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2407910121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distinct modulation of calcium-activated chloride channel TMEM16A by drug-binding sites.","authors":"Jae Won Roh, Heon Yung Gee, Brian Wainger, Woo Kyung Kim, Wook Lee, Joo Hyun Nam","doi":"10.1073/pnas.2314011121","DOIUrl":"https://doi.org/10.1073/pnas.2314011121","url":null,"abstract":"<p><p>TMEM16A is a calcium-activated chloride channel with significant role in epithelial fluid secretion, sensory transduction, and smooth muscle contraction. Several TMEM16A inhibitors have been identified; however, their binding sites and inhibitory mechanisms remain unclear. Using magnolol and honokiol, the two regioisomeric inhibitors, as chemical probes, we have identified a drug-binding site distinct from the pore region, in TMEM16A, which is described here. With electrophysiology, unbiased molecular docking and clustering, molecular dynamics simulations, and experimental validation with mutant cycle analysis, we show that magnolol and honokiol utilize different drug-binding sites, pore and nonpore pockets. The pore blocker utilizes amino acids crucial for chloride passage, whereas the nonpore blocker allosterically modulates the pore residues to hinder ion permeation. Among 17 inhibitors tested, 11 were pore blockers and 6 were nonpore blockers, indicating the importance of this nonpore pocket. Our study provides insights into drug-binding mechanism in TMEM16A together with a rationale for future drug development.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2314011121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Informing public health protection under new patterns of wildfire smoke.","authors":"Jason D Sacks","doi":"10.1073/pnas.2418529121","DOIUrl":"https://doi.org/10.1073/pnas.2418529121","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2418529121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142802061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-range <i>Atoh1</i> enhancers maintain competency for hair cell regeneration in the inner ear.","authors":"Tuo Shi, Yeeun Kim, Juan Llamas, Xizi Wang, Peter Fabian, Thomas P Lozito, Neil Segil, Ksenia Gnedeva, J Gage Crump","doi":"10.1073/pnas.2418098121","DOIUrl":"10.1073/pnas.2418098121","url":null,"abstract":"<p><p>During tissue regeneration, lineage-related cells can switch their fate to replace missing cells. This cell plasticity is particularly prominent in more regenerative vertebrates such as zebrafish, yet the molecular basis by which cells transdifferentiate into another cell type upon injury remains unclear. Here, we investigate the epigenetic basis of regenerative transdifferentiation in the inner ear, where supporting cells (SCs) generate mechanosensory hair cells (HCs) upon damage. By comparing the chromatin landscapes in regenerative zebrafish and green anole lizards versus nonregenerative mice, we identified a class of enhancers that function in progenitors to generate HCs and then are selectively maintained in SCs of regenerative vertebrates to regenerate HCs. In particular, we uncovered a syntenic class of long-range enhancers for <i>Atoh1</i>, a master transcription factor for HC differentiation. In the absence of injury, these enhancers maintain accessibility in SCs through adulthood but are prevented from driving zebrafish <i>atoh1a</i> expression through Notch repression. Deletion of these enhancers not only impaired <i>atoh1a</i> expression and HC formation during development but also blocked the ability of SCs to transdifferentiate into HCs during regeneration. Moreover, defects were specific to the inner ear versus the lateral line, revealing distinct mechanisms of regeneration in these mechanosensory organs. These findings reveal a class of regenerative enhancer that maintains competency of inner ear SCs to upregulate <i>atoh1a</i> and transdifferentiate into HCs upon damage. We propose that the continued accessibility of developmental enhancers for one cell fate in lineage-related cells may be a common theme underlying adult cell plasticity in regenerative vertebrates.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2418098121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Excimer formation in zinc-phthalocyanine revealed using ultrafast electron diffraction.","authors":"Sebastian Hammer, Tristan L Britt, Laurenz Kremeyer, Maximilian Rödel, David Cai, Jens Pflaum, Bradley J Siwick","doi":"10.1073/pnas.2411975121","DOIUrl":"https://doi.org/10.1073/pnas.2411975121","url":null,"abstract":"<p><p>The formation of excited dimer states, so called excimers, is an important phenomenon in many organic molecular semiconductor solid state aggregates. In contrast to Frenkel exciton-polarons, an excimer is long-lived and energetically low-lying due to stabilization resulting from a substantial reorganization of the intermolecular geometry. Here, we show that ultrafast electron diffraction can follow the dynamics of solid-state excimer formation in polycrystalline thin films of a molecular semiconductor, revealing both the key reaction modes and the eventual structure of the emitting state. We study the prototypical organic semiconductor zinc-phthalocyanine (ZnPc) in its crystallographic <i>α</i>-phase as a model excimeric system. We show that the excimer forms in a two-step process starting with a fast dimerization (approx. 0.4 ps) followed by a subsequent slow shear-twist motion (14 ps) leading to an alignment of the <i>π</i>-systems of the involved monomers. This structural distortion persists well beyond 300 ps. Furthermore, we show that while the same excimer geometry is present in partially fluorinated derivatives of ZnPc, the formation kinematics slow down with increasing level of fluorination.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2411975121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142801698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrocalcium coupling in brain capillaries: Rapidly traveling electrical signals ignite local calcium signals.","authors":"Amreen Mughal, Grant W Hennig, Thomas Heppner, Nikolaos M Tsoukias, David Hill-Eubanks, Mark T Nelson","doi":"10.1073/pnas.2415047121","DOIUrl":"https://doi.org/10.1073/pnas.2415047121","url":null,"abstract":"<p><p>The routing of blood flow throughout the brain vasculature is precisely controlled by mechanisms that serve to maintain a fine balance between local neuronal demands and vascular supply of nutrients. We recently identified two capillary endothelial cell (cEC)-based mechanisms that control cerebral blood flow in vivo: 1) electrical signaling, mediated by extracellular K⁺-dependent activation of strong inward rectifying K⁺ (Kir2.1) channels, which are steeply activated by hyperpolarization and thus are capable of cell-to-cell propagation, and 2) calcium (Ca²⁺) signaling, which reflects release of Ca²⁺ via the inositol 1,4,5-trisphosphate receptor (IP₃R)-a target of G_q-protein-coupled receptor signaling. Notably, Ca²⁺ signals were restricted to the cell in which they were initiated. Unexpectedly, we found that these two mechanisms, which were presumed to operate in distinct spatiotemporal realms, are linked such that Kir2.1-dependent hyperpolarization induces increases in the electrical driving force for Ca²⁺ entry into cECs through resident TRPV4 channels. This process, termed electrocalcium (E-Ca) coupling, enhances IP₃R-mediated Ca²⁺ release via a Ca²⁺-induced Ca²⁺-release mechanism, and allows focally induced hyperpolarization, including that initiated by ATP-dependent K⁺ (K_ATP) channels, to travel cell-to-cell via activation of Kir2.1 channels in adjacent cells, providing a mechanism for the \"pseudopropagation\" of Ca²⁺ signals. Computational modeling supported the basic features of E-Ca coupling and provided insight into the intracellular processes involved. Collectively, these data provide strong support for the concept of E-Ca coupling and provide a mechanism for the spatiotemporal integration of diverse signaling pathways in the control of cerebral blood flow.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2415047121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Activation of the proton-sensing GPCR, GPR65 on fibroblast-like synoviocytes contributes to inflammatory joint pain.","authors":"Luke A Pattison, Rebecca H Rickman, Helen Hilton, Maya Dannawi, Susanne N Wijesinghe, Graham Ladds, Li V Yang, Simon W Jones, Ewan St John Smith","doi":"10.1073/pnas.2410653121","DOIUrl":"https://doi.org/10.1073/pnas.2410653121","url":null,"abstract":"<p><p>Inflammation is associated with localized acidosis, however, attributing physiological and pathological roles to proton-sensitive receptors is challenging due to their diversity and widespread expression. Here, agonists of the proton-sensing GPCR, GPR65, were systematically characterized. The synthetic agonist BTB09089 (BTB) recapitulated many proton-induced signaling events and demonstrated selectivity for GPR65. BTB was used to show that GPR65 activation on fibroblast-like synoviocytes (FLS), cells that line synovial joints, results in the secretion of proinflammatory mediators capable of recruiting immune cells and sensitizing sensory neurons. Intra-articular injection of BTB resulted in GPR65-dependent sensitization of knee-innervating neurons and nocifensive behaviors in mice. Stimulation of GPR65 on human FLS also triggered the release of inflammatory mediators and synovial fluid samples from human osteoarthritis patients were shown to activate GPR65. These results suggest a role of GPR65 in mediating cell-cell interactions that drive inflammatory joint pain in both mice and humans.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"121 51","pages":"e2410653121"},"PeriodicalIF":9.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}