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Structural and Biochemical Insights into the Broad-Spectrum TET Enzyme From Methanocaldococcus jannaschii Reveal the Basis of Substrate Specificity in M42 Aminopeptidases jannaschii甲醇钙球菌广谱TET酶的结构和生化分析揭示了M42氨基肽酶底物特异性的基础。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-02-01 Epub Date: 2025-12-17 DOI: 10.1016/j.jmb.2025.169596
Joaquin Atalah , Hind Basbous , Gregory Effantin , Sylvie Kieffer-Jaquinod , Guy Schoehn , Eric Girard , Bruno Franzetti
{"title":"Structural and Biochemical Insights into the Broad-Spectrum TET Enzyme From Methanocaldococcus jannaschii Reveal the Basis of Substrate Specificity in M42 Aminopeptidases","authors":"Joaquin Atalah ,&nbsp;Hind Basbous ,&nbsp;Gregory Effantin ,&nbsp;Sylvie Kieffer-Jaquinod ,&nbsp;Guy Schoehn ,&nbsp;Eric Girard ,&nbsp;Bruno Franzetti","doi":"10.1016/j.jmb.2025.169596","DOIUrl":"10.1016/j.jmb.2025.169596","url":null,"abstract":"<div><div>TET peptidases of the M42 family are ∼500 kDa hollow dodecameric complexes ubiquitous in prokaryotes. These enzymes act as strict aminopeptidases, catalyzing the removal of N-terminal amino acids from peptides. A common feature of M42 TET aminopeptidases characterized to date is their marked substrate preference for a limited subset of amino acids. Unlike other hyperthermophilic archaea studied so far, the autotrophic archaeon <em>Methanocaldococcus jannaschii</em> possesses only a single gene encoding an M42 peptidase. This enzyme, named MjTET, is the first reported M42 peptidase to exhibit broad amino acid specificity, including activity on aromatic residues. To assess their peptide degradation efficiencies, the catalytic constants of MjTET were compared to those of its close analogs from <em>Pyrococcus horikoshii</em>. The specialized TETs from <em>P. horikoshii</em> displayed higher catalytic efficiencies than the generalist MjTET, likely reflecting the reliance of Thermococcales on peptide fermentation for energy. Additionally, the structure of MjTET was resolved to 3 Å using cryo-EM and compared with the available models of the four <em>P. horikoshii</em> TETs to identify features underlying substrate specificity. This analysis, combined with mutagenesis studies, revealed a previously uncharacterized loop in the catalytic domain that contributes to substrate discrimination. Collectively, these findings show that substrate specificity in TET enzymes arises from a complex interplay of tertiary structure, oligomeric assembly, and electrostatic surface potential.</div></div><div><h3>Importance</h3><div>This study first reported a novel TET peptidase from Methanogenic hyperthermophilic archaea. Its enzymatic properties compared to the specialized TET enzyme characterized so far from heterotrophic archaea suggest a link with autotrophy. It also represents an important step in explaining the structural features guiding substrate specificity.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 3","pages":"Article 169596"},"PeriodicalIF":4.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145792970","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}
引用次数: 0
Influence of Methionine Oxidation on Protein Stability and Association Studied by Free Energy Simulations 用自由能模拟研究了蛋氨酸氧化对蛋白质稳定性和结合体的影响。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-02-01 Epub Date: 2025-12-05 DOI: 10.1016/j.jmb.2025.169576
Tristan Alexander Mauck, Martin Zacharias
{"title":"Influence of Methionine Oxidation on Protein Stability and Association Studied by Free Energy Simulations","authors":"Tristan Alexander Mauck,&nbsp;Martin Zacharias","doi":"10.1016/j.jmb.2025.169576","DOIUrl":"10.1016/j.jmb.2025.169576","url":null,"abstract":"<div><div>Cellular metabolic systems but also the extracellular environment can generate reactive oxygen species that lead to oxidation of methionine (MET) and interfere with protein folding and protein–protein association. The molecular mechanism of how MET oxidation (MEO) influences conformational stability and binding is not well understood. We employ alchemical free energy simulations to systematically study the influence of MET oxidation on protein–protein binding using the tetramerization domain of the tumor suppression protein p53 as a model system. A single MEO in one tetramerisation domain destabilizes the tetramer by ≈1<em>.</em>1–1<em>.</em>8 kcal/mol depending slightly on the MEO diastereomer. The simulations on double and triple oxidations reveal increased destabilization (≈3–7 kcal/mol) and significant cooperative effects depending on the relative position of the oxidized residues. The MET oxidation effects are of similar magnitude for the change in stability of the human prion protein (HPP) that served as a second model system and also agreed with available experimental data. The calculations predict a significant dependence of stability changes on the position of the MEO and also indicate non-additive effects of multiple oxidations which may play a role to protect proteins from oxidative damage and stress. Analysis of the Molecular Dynamics trajectories allowed us to interpret the oxidation effects in molecular detail. The simulation methodology could also serve as a general protocol to analyze single and multiple MET oxidations in other systems and its influence on protein binding and stability.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 3","pages":"Article 169576"},"PeriodicalIF":4.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145699509","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}
引用次数: 0
Transcriptome-wide RNA Stability Across Cancers Reveals Therapeutic Vulnerabilities 转录组范围内的RNA稳定性图谱揭示了癌症的转录后控制和治疗脆弱性。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-02-01 Epub Date: 2025-12-08 DOI: 10.1016/j.jmb.2025.169590
Yang Tong , Yuting Wang , Gerui Liu , Yihu Wei , Xiaoxiao Yang , Jiapei Yuan , Yang Yang , Qiang Zhang
{"title":"Transcriptome-wide RNA Stability Across Cancers Reveals Therapeutic Vulnerabilities","authors":"Yang Tong ,&nbsp;Yuting Wang ,&nbsp;Gerui Liu ,&nbsp;Yihu Wei ,&nbsp;Xiaoxiao Yang ,&nbsp;Jiapei Yuan ,&nbsp;Yang Yang ,&nbsp;Qiang Zhang","doi":"10.1016/j.jmb.2025.169590","DOIUrl":"10.1016/j.jmb.2025.169590","url":null,"abstract":"<div><div>The steady-state abundance of mRNA is governed by the interplay between transcription and degradation, yet the contribution of RNA stability to cancer biology remains incompletely understood. Here, we systematically investigate RNA decay dynamics across 22 cancer types using RNA-seq data from the Cancer Cell Line Encyclopedia. By inferring transcriptome-wide RNA stability profiles, we identify distinct molecular subtypes defined by post-transcriptional regulation. Integrative analyses reveal that RNA-binding proteins (RBPs) and microRNAs (miRNAs), including SNRPA and RBMX, act as key modulators of RNA stability and are essential for cancer cell proliferation and survival. Somatic mutations, particularly those affecting miRNA binding sites, were found to significantly perturb RNA decay, implicating dysregulation of pathways such as nonsense-mediated decay. Furthermore, machine learning models demonstrate that RNA stability profiles predict sensitivity to 24 anticancer drugs, nominating specific RBPs as candidate biomarkers for therapeutic response. Collectively, our findings establish RNA stability as a pivotal layer of gene regulation in cancer, with broad implications for molecular stratification and precision oncology.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 3","pages":"Article 169590"},"PeriodicalIF":4.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145720205","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}
引用次数: 0
Rising Star: A Unified Mechanism of Plant NLR Immune Signaling Rising Star:植物NLR免疫信号的统一机制。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-02-01 Epub Date: 2025-12-12 DOI: 10.1016/j.jmb.2025.169592
Jijie Chai
{"title":"Rising Star: A Unified Mechanism of Plant NLR Immune Signaling","authors":"Jijie Chai","doi":"10.1016/j.jmb.2025.169592","DOIUrl":"10.1016/j.jmb.2025.169592","url":null,"abstract":"<div><div>Jijie Chai earned his Ph.D. in analytical chemistry from the Institute of Materia Medica, Chinese Academy of Medical Sciences, and conducted postdoctoral research at Princeton University. In 2004, he established his independent research group at National Institute of Biological Science (China), focusing on plant immune receptors, particularly nucleotide-binding leucine-rich repeat (NLR) proteins. NLRs are the largest family immune receptors that enable plants to detect a wide array of pathogen effectors and activate effector-triggered immunity (ETI). Despite their recognition diversity, they elicit remarkably conserved immune responses, a mechanistic puzzle for many years. Chai’s team achieved a landmark breakthrough by reconstituting and solving the cryo-EM structure of activated Arabidopsis coiled-coil NLR (CNL) ZAR1, revealing its assembly into a pentameric resistosome. The N-terminal helices of ZAR1 in the resistosome form a funnel-like structure, which was later confirmed as a Ca<sup>2+</sup>-permeable ion channel. These discoveries directly link NLR activation to Ca<sup>2+</sup> influx, a central immune signaling event. Chai’s findings further showed that CNLs form structurally conserved resistosomes with intrinsic Ca2<sup>+</sup>-permeable channel activity. Notably, Chai discovered that TIR-domain NLRs (TNLs) also form resistosomes but function as NADases, producing small-molecule signals that activate downstream helper NLRs. These helper NLRs also assemble into Ca<sup>2+</sup>-conducting resistosomes. Together, these findings establish a unified mechanism in plant immunity, with diverse NLRs converge on resistosome formation that ultimately drives Ca<sup>2+</sup> influx as a central hub of defense activation. This paradigm shift underscores the functional conservation of NLR-mediated immunity across plant species and has fundamentally reshaped the field of plant innate immunity.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 3","pages":"Article 169592"},"PeriodicalIF":4.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145754859","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}
引用次数: 0
MASI2.0: Insights of Microbiota Metabolic Potential from Incorporating Genomic Information on Microbiota-Active Substance Interactions MASI2.0:结合微生物群-活性物质相互作用基因组信息的微生物群代谢潜力的见解。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-02-01 Epub Date: 2025-12-16 DOI: 10.1016/j.jmb.2025.169594
Dongyue Hou , Yuchen Liu , Hanbo Lin , Jiajie Gu , Juncheng Qian , Shaofei Wang , Yuzong Chen , Dianwen Ju , Xian Zeng
{"title":"MASI2.0: Insights of Microbiota Metabolic Potential from Incorporating Genomic Information on Microbiota-Active Substance Interactions","authors":"Dongyue Hou ,&nbsp;Yuchen Liu ,&nbsp;Hanbo Lin ,&nbsp;Jiajie Gu ,&nbsp;Juncheng Qian ,&nbsp;Shaofei Wang ,&nbsp;Yuzong Chen ,&nbsp;Dianwen Ju ,&nbsp;Xian Zeng","doi":"10.1016/j.jmb.2025.169594","DOIUrl":"10.1016/j.jmb.2025.169594","url":null,"abstract":"<div><div>Extensive interactions between microbiota and active substances are health- and disease-relevant. Mechanistic understanding from genomic perspective of these interactions and potential impacts is important for biomedical and pharmaceutical research. However, current data repositories often lack systematic integration from a genomic perspective. Here we describe an update of the MASI microbiota-active substance interactions database. This update includes new data of (1) genomic-derived 166,766 microbiota-drug interactions and 205,505 microbiota-food interactions linked by 415 biosynthetic gene clusters (BGCs), 59 metabolic gene clusters (MGCs), and 7250 genome-scale metabolic network models (GEMs) of ∼1200 microbiota species, and (2) 1848 microbiota-microbiota interaction records mediated by 39 quorum sensing languages, and (3) 46,717 microbiota-disease associations between 640 species and 59 diseases. Overall, this update provides 44,643 interasctions derived from ∼2000 publications and 380,571 genome-derived interactions, covering 1867 microbe species, 1576 therapeutic substances, 357 dietary substances, which is freely accessible at <span><span>https://www.aiddlab.com/MASI2025/index.html</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 3","pages":"Article 169594"},"PeriodicalIF":4.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145779655","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}
引用次数: 0
Cryo-EM of Cardiac AL-224L Amyloid Reveals Shared Structural Motifs and Mutation-induced Differences in λ6 Light Chain Fibrils 心脏AL-224L淀粉样蛋白的冷冻电镜显示了共同的结构基序和突变诱导的λ6轻链原纤维的差异。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-02-01 Epub Date: 2025-12-11 DOI: 10.1016/j.jmb.2025.169591
Chad W. Hicks , Tatiana Prokaeva , Brian Spencer , Shobini Jayaraman , Noorul Huda , Sherry Wong , Hui Chen , Vaishali Sanchorawala , Francesca Lavatelli , Olga Gursky
{"title":"Cryo-EM of Cardiac AL-224L Amyloid Reveals Shared Structural Motifs and Mutation-induced Differences in λ6 Light Chain Fibrils","authors":"Chad W. Hicks ,&nbsp;Tatiana Prokaeva ,&nbsp;Brian Spencer ,&nbsp;Shobini Jayaraman ,&nbsp;Noorul Huda ,&nbsp;Sherry Wong ,&nbsp;Hui Chen ,&nbsp;Vaishali Sanchorawala ,&nbsp;Francesca Lavatelli ,&nbsp;Olga Gursky","doi":"10.1016/j.jmb.2025.169591","DOIUrl":"10.1016/j.jmb.2025.169591","url":null,"abstract":"<div><div>In light chain amyloidosis (AL), aberrant monoclonal antibody light chains (LCs) deposit in vital organs causing organ damage. Each AL patient features a unique LC; previous cryogenic electron microscopy (cryo-EM) studies revealed different amyloid structures in different AL patients. How LC mutations influence amyloid structures remains unclear. We report a cryo-EM structure of cardiac AL-224L amyloid (2.92 Å resolution) from λ6-LC family, which is overrepresented in AL amyloidosis. Comparison with λ6-LC structures from two other patients reveals similarities in amyloid folds, along with major differences caused by specific mutations. Differences in AL-224L include altered C-terminal conformation with an exposed surface forming an apparent ligand-binding site; an enlarged hydrophilic pore with orphan density; and altered steric zipper registry with backbone flipping, which likely represent general adaptive mechanisms in amyloids. The results reveal shared features in λ6-LC amyloid folds and suggest how mutation-induced structural changes influence amyloid-ligand interactions in a patient-specific manner.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 3","pages":"Article 169591"},"PeriodicalIF":4.5,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145751498","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}
引用次数: 0
Functional and Structural Characterization of a Novel Anti-His-tag Antibody, HisMab-1 一种新型抗his标签抗体HisMab-1的功能和结构特征。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-12-03 DOI: 10.1016/j.jmb.2025.169574
Natsuki Hitomi , Satowa Hoshi , Mika K. Kaneko , Ryuichi Kato , Kenji Iwasaki , Junichi Takagi , Yukinari Kato , Ayaka Harada-Hikita , Takao Arimori
{"title":"Functional and Structural Characterization of a Novel Anti-His-tag Antibody, HisMab-1","authors":"Natsuki Hitomi ,&nbsp;Satowa Hoshi ,&nbsp;Mika K. Kaneko ,&nbsp;Ryuichi Kato ,&nbsp;Kenji Iwasaki ,&nbsp;Junichi Takagi ,&nbsp;Yukinari Kato ,&nbsp;Ayaka Harada-Hikita ,&nbsp;Takao Arimori","doi":"10.1016/j.jmb.2025.169574","DOIUrl":"10.1016/j.jmb.2025.169574","url":null,"abstract":"<div><div>The polyhistidine tag (His-tag) is one of the most widely used peptide tags for the purification of recombinant proteins, owing to its compatibility with immobilized metal affinity chromatography. While numerous anti-His-tag antibodies are commercially available, their quantitative affinity data and structural insights are limited. Here, we present a detailed physicochemical and structural characterization of a novel anti-His-tag antibody, HisMab-1. Isothermal titration calorimetry showed that the Fab fragment of HisMab-1 binds to a hexahistidine peptide in an enthalpy-driven manner, with a dissociation constant (<em>K</em><sub>D</sub>) of ∼30 nM at a neutral pH. The crystal structure of the HisMab-1–hexahistidine peptide complex at 2.39-Å resolution revealed that HisMab-1 primarily recognizes the first, second, fourth, and fifth histidine residues of the peptide through multiple interactions, including hydrogen bonding and π–π stacking, which collectively contribute to the high specificity of the antibody. Notably, HisMab-1 also binds to a His-tag embedded within a conformationally constrained β-hairpin loop without reducing affinity, highlighting its structural adaptability. These findings establish HisMab-1 as a high-affinity, high-specificity, structurally validated anti-His-tag antibody with broad potential in diverse protein engineering and structural biology applications.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169574"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145686622","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}
引用次数: 0
Implications of Codon Usage, tRNA Gene Redundancy and tRNA Gene Clustering in Experimental Models of Mistranslation 密码子使用、tRNA基因冗余和tRNA基因聚类在误译实验模型中的意义。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-12-03 DOI: 10.1016/j.jmb.2025.169573
D.W. McDonald , L. Joos , M.L. Duennwald
{"title":"Implications of Codon Usage, tRNA Gene Redundancy and tRNA Gene Clustering in Experimental Models of Mistranslation","authors":"D.W. McDonald ,&nbsp;L. Joos ,&nbsp;M.L. Duennwald","doi":"10.1016/j.jmb.2025.169573","DOIUrl":"10.1016/j.jmb.2025.169573","url":null,"abstract":"<div><div>The genetic code converts information transcribed in messenger-RNA (mRNA) into the amino acid sequences that build proteins. Transfer-RNAs (tRNAs) are the adaptors for this conversion from nucleic acids to proteins as they discriminate mRNA codons via anticodon-codon base pairing and recruit cognate amino acids to the ribosome for faithful protein biosynthesis. Although the genetic code is identical among many common model organisms and humans, there are profound differences in genomic codon usage, tRNA gene redundancy and genomic organization of tRNA genes that may change the accuracy and efficiency by which the genetic code is translated. Furthermore, these factors may influence how organisms tolerate tRNA variants that induce translation errors. Such tRNA variants are common in human populations, yet their contribution to human disease remains mostly unclear. Thus, tRNA variants have been studied in several model organisms and induce different rates of mistranslation and toxicity. To understand why mistranslating tRNA variants affect model organisms differently, we compare codon frequency, tRNA gene abundance and the genomic organization of tRNA genes in these commonly used model organisms (yeast, roundworms, fruit flies, mice and rats) and humans. We describe unique translation biases across model systems that influence tolerance of mistranslating tRNA variants, efficiency of protein biosynthesis, and co-translational protein quality control. Our review serves as a practical resource for researchers studying tRNA biology and the regulation of protein biosynthesis in these model organisms to guide experimental design and data interpretation.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169573"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145686656","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}
引用次数: 0
The Conserved Network of NF-κB Transcriptional Partners From Drosophila to Mammals 从果蝇到哺乳动物NF-κB转录伙伴的保守网络。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-12-03 DOI: 10.1016/j.jmb.2025.169572
Yulia A. Ulianova , Mona Ghassah , Zaur M. Kachaev , Lyubov A. Lebedeva , Yulii V. Shidlovskii
{"title":"The Conserved Network of NF-κB Transcriptional Partners From Drosophila to Mammals","authors":"Yulia A. Ulianova ,&nbsp;Mona Ghassah ,&nbsp;Zaur M. Kachaev ,&nbsp;Lyubov A. Lebedeva ,&nbsp;Yulii V. Shidlovskii","doi":"10.1016/j.jmb.2025.169572","DOIUrl":"10.1016/j.jmb.2025.169572","url":null,"abstract":"<div><div>The nuclear factor κB (NF-κB) pathway governs innate immunity, orchestrating rapid transcriptional responses to infection. While the pathway is often depicted as a linear signaling cascade, NF-κB functions within a complex network of cooperative partnerships with other transcription factors and co-regulators. Here, current data about these NF-κB-centered transcriptional partnerships are described with a focus on the model organism <em>Drosophila melanogaster</em> and a comparative analysis with homologous mammalian factors. We detail how <em>Drosophila melanogaster</em> NF-κB factors (Relish, Dif, and Dorsal) cooperate with each other and other transcription regulators, such as Charon, PARP-1, Akirin, SWI/SNF, Mediator, Stat92E, AP-1, FOXO, Nubbin, Caudal, DEAF1, and GATA family transcription factors, to precisely shape immune specificity and homeostasis. We explore the evolutionary conservation of these mechanisms in mammals, where homologous factors similarly shape NF-κB activity to control inflammatory and antiviral responses. While the core principle of NF-κB cooperativity is ancient, the network has expanded and diversified in mammals, reflecting increased genomic and regulatory complexity. This comparative perspective underscores that the functions of NF-κB are fundamentally defined by its context-dependent partnership network.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169572"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145686676","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}
引用次数: 0
Neutralization Mechanism of a HipA-like Toxin Targeting Isoleucyl-tRNA Synthetase 一种靶向异亮基trna合成酶的hipa样毒素的中和机制。
IF 4.5 2区 生物学
Journal of Molecular Biology Pub Date : 2026-01-15 Epub Date: 2025-11-24 DOI: 10.1016/j.jmb.2025.169563
Si-Ping Zhang , Ying-Jie Song , Yi-Ping Ye , Zi-Rui Ye , Fu-Lin Yang , Bo Niu , Fang-Hui Bai , Chun-Hui Fan , Li-Xin Wan , Miao He , Yong Wang , Rui Bao , Yong-Xing He
{"title":"Neutralization Mechanism of a HipA-like Toxin Targeting Isoleucyl-tRNA Synthetase","authors":"Si-Ping Zhang ,&nbsp;Ying-Jie Song ,&nbsp;Yi-Ping Ye ,&nbsp;Zi-Rui Ye ,&nbsp;Fu-Lin Yang ,&nbsp;Bo Niu ,&nbsp;Fang-Hui Bai ,&nbsp;Chun-Hui Fan ,&nbsp;Li-Xin Wan ,&nbsp;Miao He ,&nbsp;Yong Wang ,&nbsp;Rui Bao ,&nbsp;Yong-Xing He","doi":"10.1016/j.jmb.2025.169563","DOIUrl":"10.1016/j.jmb.2025.169563","url":null,"abstract":"<div><div>The HipA toxin from type II HipBA toxin-antitoxin (TA) system targets and inactivates specific cellular components to inhibit bacterial growth. While the molecular targets and neutralization mechanisms of several HipBA-like systems have been well characterized, their structural and functional diversity remains poorly understood. Here, we investigate a HipBA-like module from <em>Pseudomonas fluorescens</em> (HipBA<sub>Pf</sub>), where the HipB<sub>Pf</sub> antitoxin features a long, disordered C-terminal region in the absence of HipA<sub>Pf</sub>. Using X-ray crystallography, AlphaFold modeling and mutagenesis assays, we show that upon binding to HipA<sub>Pf</sub>, part of this C-terminal region forms two α-helices that are essential for both the interaction with and neutralization of the HipA<sub>Pf</sub> toxin. Importantly, HipB<sub>Pf</sub> binding blocks the ATP binding sites of HipA<sub>Pf</sub>, potentially by inducing a conformational change in the HipA<sub>Pf</sub> N1 subdomain via its C-terminal α6 helix. Finally, we also discovered that HipA<sub>Pf</sub> (clade VI in the “Hip tree”), specifically phosphorylates isoleucyl-tRNA synthetase at Ser604, strongly inhibiting its aminoacylation activity. Collectively, our findings reveal the critical role of the HipB<sub>Pf</sub> C-terminal region in toxin binding and neutralization, while also highlighting the evolutionarily divergent substrate preferences of HipA-like toxins.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"438 2","pages":"Article 169563"},"PeriodicalIF":4.5,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145627185","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}
引用次数: 0
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