Journal of Molecular Biology最新文献_第7页

Targeting DNA Topoisomerase I for the Treatment of Cancer: Past, Present and Future. 靶向DNA拓扑异构酶I治疗癌症：过去，现在和未来。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-21 DOI: 10.1016/j.jmb.2025.169401

Annapoorna Venkatachalam, Scott H Kaufmann

引用次数: 0

Chromatin Binding Regulates Phase Behavior and Morphology of Condensates Formed by Prion-like Domains 染色质结合调节由朊病毒样结构域形成的凝聚物的相行为和形态。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-21 DOI: 10.1016/j.jmb.2025.169398

Anushka Supakar , Richoo B. Davis , Subhadip Biswas , Sean Yang , Davit A. Potoyan , Priya R. Banerjee

{"title":"Chromatin Binding Regulates Phase Behavior and Morphology of Condensates Formed by Prion-like Domains","authors":"Anushka Supakar , Richoo B. Davis , Subhadip Biswas , Sean Yang , Davit A. Potoyan , Priya R. Banerjee","doi":"10.1016/j.jmb.2025.169398","DOIUrl":"10.1016/j.jmb.2025.169398","url":null,"abstract":"<div><div>Many transcription factors (TFs) contain intrinsically disordered regions (IDRs) and are thought to form biomolecular condensates in the cell nucleus. These proteins can be conceptualized as block co-polymers, with the IDRs driving both homotypic and heterotypic protein–protein interactions and the DNA-binding domain (DBD) mediating heterotypic interactions with chromatin. While <em>in vitro</em> studies have predominantly reported micron-scale, spherical condensates in the absence of chromatin, TF condensates in live cells exhibit strikingly different behavior, adopting diverse, nanoscale, often aspherical morphologies and displaying sub-diffusive dynamics. Here, using engineered fusion proteins with tunable IDR-DBD architectures, we show that this distinct phase behavior can arise from TF-chromatin interactions. Specifically, we fused the prion-like domain (PLD) of the SS18 subunit from the mammalian SWI/SNF complex, a domain known to drive homotypic phase separation, to the DBD of the pioneer factor FOXA1. While SS18<sup>PLD</sup> on overexpression forms large, spherical condensates in cells, its fusion with FOXA1<sup>DBD</sup> leads to condensates that re-localize to chromatin, adopt aspherical morphologies, and exhibit chromatin-wetting behavior. Disruption of DBD-chromatin binding shifts condensate morphology toward a mixed or spherical state, implicating chromatin affinity as a key regulator of condensate coarsening and spatial organization. Coarse-grained simulations recapitulate these observations, revealing a finely balanced interplay between PLD-PLD and DBD-DNA interactions that collectively determine condensate dynamics and structure. Together, our findings demonstrate that chromatin binding is a critical modulator of transcriptional condensate behavior in vivo.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169398"},"PeriodicalIF":4.5,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938115","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

Complex Conformational Interplay for Parkin Activation is Revealed by ¹⁹F NMR Spectroscopy. 19F核磁共振揭示了帕金活化的复杂构象相互作用。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-19 DOI: 10.1016/j.jmb.2025.169397

Elizabeth M Connelly, Gary S Shaw

{"title":"Complex Conformational Interplay for Parkin Activation is Revealed by <sup>19</sup>F NMR Spectroscopy.","authors":"Elizabeth M Connelly, Gary S Shaw","doi":"10.1016/j.jmb.2025.169397","DOIUrl":"https://doi.org/10.1016/j.jmb.2025.169397","url":null,"abstract":"<p><p>Parkin is a 52 kDa RING-Between-RING E3 ligase that ubiquitinates proteins at the outer mitochondrial membrane in response to oxidative stress. Part of a neuroprotective pathway, over 100 mutations in the PRKN gene have been associated with Early Onset Parkinson's Disease. To be fully active parkin requires interaction with phosphorylated ubiquitin and phosphorylation of its N-terminal Ubl domain, both dependent on the PINK1 kinase. Along with recruitment of an E2 ∼ Ubiquitin conjugate these events form a ∼90 kDa complex, undergoing a series of conformational changes that regulate transthiolation of ubiquitin from the E2 enzyme to the catalytic domain in parkin (Rcat) prior to substrate labeling. Numerous crystal and NMR structures have captured snapshots of parkin activation and its catalytic mechanism, yet questions surrounding the relative abundance, timing and interplay of parkin conformations remain. Further, most studies use truncated versions of the E3 ligase that may hide details of conformational dependencies. To examine parkin through its activation cycle from inactive (autoinhibited) to E2 ∼ Ubiquitin binding states we incorporated 5-<sup>19</sup>F-tryptophan into the full-length enzyme and used <sup>19</sup>F NMR spectroscopy to identify structural and dynamics changes. Using chemical shift perturbation and T2 analysis, we show that phosphorylation of parkin leads to a population of unbound and bound forms of the phosphorylated Ubl domain and that release of the catalytic Rcat domain is dependent upon E2 ∼ Ub conjugate binding. This study shows the unique abilities of <sup>19</sup>F NMR spectroscopy to provide details of the structural rearrangements required for catalysis for the large E3 ligase parkin.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169397"},"PeriodicalIF":4.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938154","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 C-terminal Domain of SARS-CoV-2 nsp8 is a Molten Globule in the Absence of Binding Partners SARS-CoV-2 nsp8的c端结构域在没有结合伙伴的情况下呈熔融球状。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-19 DOI: 10.1016/j.jmb.2025.169400

Vilius Kurauskas , Marco Tonelli , Robert N. Kirchdoerfer , Katherine Henzler-Wildman

引用次数: 0

TargetPair: A Single Cell-omics Resource of Clinical Trials-derived Therapeutical Target Combinations for Cancer Therapy TargetPair：临床试验衍生的癌症治疗靶标组合的单细胞组学资源

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-19 DOI: 10.1016/j.jmb.2025.169399

Kaicheng Zhou , Xingxiu Li , Yuan Yang , Dongyue Hou , Shuaiqi Wang , Hanbo Lin , Ruining Yin , Dianwen Ju , Xian Zeng , Shaofei Wang

{"title":"TargetPair: A Single Cell-omics Resource of Clinical Trials-derived Therapeutical Target Combinations for Cancer Therapy","authors":"Kaicheng Zhou , Xingxiu Li , Yuan Yang , Dongyue Hou , Shuaiqi Wang , Hanbo Lin , Ruining Yin , Dianwen Ju , Xian Zeng , Shaofei Wang","doi":"10.1016/j.jmb.2025.169399","DOIUrl":"10.1016/j.jmb.2025.169399","url":null,"abstract":"<div><div>The complexity of the tumor microenvironment (TME) makes cancer therapy challenging. Multi-targeting strategies often exhibit superior clinical benefits and dominate ongoing cancer clinical trials. However, existing multi-targeting strategies largely rely on empirical approaches. The rational design of target pairs (TPs) for multi-target cancer therapy development is a high priority but remains a significant challenge, which may benefit from single-cell omics technologies to decode the TME. However, there has been no thorough survey of clinically relevant cancer TPs and their characterization at the single-cell level. Here, we established the TargetPair database to address this gap by manually annotating TPs from drug combinations and multi-targeting drugs whose anti-tumor efficacy has been evaluated, and calculating their omics features at the single-cell level. The TargetPair database provides (1) 60 approved, 1,580 clinical-stage, and 7,424 experimental-stage TPs manually annotated from 3,470 clinical trials and 1,396 publications, and (2) the omics features of TPs (co-expression, distribution, expressed cell fractions, pathways, and single-cell gene networks) from manually curated scRNA-seq datasets derived from 55 pieces of literature (including 3,022,556 single cells, 13 cell types, 16 cancer types, and 588 patients). It can be freely accessed at <span><span>https://www.targetpair.aiddlab.com</span><svg><path></path></svg></span> via several search and browsing modes.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169399"},"PeriodicalIF":4.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144917631","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

Tracing the Origin of the Genetic Code and Thermostability to Dipeptide Sequences in Proteomes. 追踪遗传密码和热稳定性的起源到蛋白质组中的二肽序列。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-14 DOI: 10.1016/j.jmb.2025.169396

Minglei Wang, M Fayez Aziz, Gustavo Caetano-Anollés

{"title":"Tracing the Origin of the Genetic Code and Thermostability to Dipeptide Sequences in Proteomes.","authors":"Minglei Wang, M Fayez Aziz, Gustavo Caetano-Anollés","doi":"10.1016/j.jmb.2025.169396","DOIUrl":"10.1016/j.jmb.2025.169396","url":null,"abstract":"<p><p>The safekeeping of the genetic code has been entrusted to interactions between aminoacyl-tRNA synthetases and their cognate tRNA. In a previous phylogenomic study, chronologies of RNA substructures, protein domains and dipeptide sequences uncovered the early emergence of an 'operational' code in the acceptor arm of tRNA prior to the implementation of the 'standard' genetic code in the anticodon loop of the molecule. This history likely originated in peptide-synthesizing urzymes but was driven by episodes of molecular co-evolution and recruitment that promoted flexibility and protein folding. Here, we show that dipeptide sequences offer deep-time insights into the chronology of code emergence. A phylogeny describing the evolution of the repertoire of 400 canonical dipeptides reconstructed from an analysis of 4.3 billion dipeptide sequences across 1,561 proteomes revealed the overlapping temporal emergence of dipeptides containing Leu, Ser and Tyr, followed by those containing Val, Ile, Met, Lys, Pro, and Ala, all of which supported the operational RNA code. This strengthened a timeline of genetic code entry. The synchronous appearance of dipeptide-antidipeptide sequences along the dipeptide chronology supported an ancestral duality of bidirectional coding operating at the proteome level. Tracing determinants of thermal adaptation showed protein thermostability was a late evolutionary development and bolstered an origin of proteins in the mild environments typical of the Archaean eon. Our study uncovers a hidden evolutionary link between a protein code of dipeptides - arising from the structural demands of emerging proteins - and an early operational code shaped by co-evolution, editing, catalysis and specificity.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169396"},"PeriodicalIF":4.5,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144861993","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

Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues. 小鼠组织中转录延伸灶的组织和动态。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-13 DOI: 10.1016/j.jmb.2025.169395

Chihiro Matsuda, Akane Ichiki, Yuko Sato, Yukino Kudo, Mika Saotome, Chihiro Takayama, Khoa Minh Le, Satoshi Uchino, Ryota Higuchi, Kazuhiko Kawata, Kosuke Tomimatsu, Manabu Ozawa, Masahito Ikawa, Yasuyuki Ohkawa, Yoshihiro Baba, Hiroshi Kimura

{"title":"Organization and Dynamics of Transcription Elongation Foci in Mouse Tissues.","authors":"Chihiro Matsuda, Akane Ichiki, Yuko Sato, Yukino Kudo, Mika Saotome, Chihiro Takayama, Khoa Minh Le, Satoshi Uchino, Ryota Higuchi, Kazuhiko Kawata, Kosuke Tomimatsu, Manabu Ozawa, Masahito Ikawa, Yasuyuki Ohkawa, Yoshihiro Baba, Hiroshi Kimura","doi":"10.1016/j.jmb.2025.169395","DOIUrl":"10.1016/j.jmb.2025.169395","url":null,"abstract":"<p><p>RNA polymerase II (RNAP2) transcribes most genes in eukaryotic nuclei. During the transition from transcription initiation to productive elongation, and throughout the elongation phase, RNAP2 becomes phosphorylated at the Ser2 residue within the heptapeptide repeats of the carboxyl-terminal domain of its largest subunit. Antibodies specific to RNAP2 Ser2 phosphorylation (Ser2ph) have enabled visualization of active transcription sites in fixed cells and tissues. Here, we report the generation and characterization of knock-in mice ubiquitously expressing a fluorescent protein-tagged, modification-specific intracellular antibody (mintbody) targeting RNAP2 Ser2ph. Using these mice, we successfully visualized transcription elongation foci in mouse tissues and characterized their distribution and dynamics across diverse cell types. RNAP2 Ser2ph-mintbody formed hundreds to thousands of nuclear foci, which were excluded from heterochromatin and transcriptionally repressed domains, such as the XY body in pachytene spermatocytes. Quantitative analysis revealed tissue- and cell type-specific variation in both the number and mobility of transcription elongation foci. The mobility of transcription foci was more restricted in differentiated cells compared to differentiating and proliferating cells, likely reflecting a reduced number of actively transcribed genes and more limited open chromatin regions upon differentiation. These findings suggest that the spatial organization and dynamics of transcription elongation are closely associated with cell identity and differentiation status. The RNAP2 Ser2ph-mintbody knock-in mice provide a valuable tool for future studies of transcription organization and dynamics at the tissue level.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169395"},"PeriodicalIF":4.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858693","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 Structure of the Apolipoprotein A-I Monomer Provides Insights Into Its Oligomerisation and Lipid-binding Mechanisms 载脂蛋白A-I单体的结构提供了对其寡聚化和脂质结合机制的见解。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-13 DOI: 10.1016/j.jmb.2025.169394

Hoi In Tou , Zachary Rosenes, Yogesh Khandokar , Courtney O. Zlatic, Riley D. Metcalfe , Yee-Foong Mok, Craig J. Morton , Paul R. Gooley, Michael D.W. Griffin

{"title":"The Structure of the Apolipoprotein A-I Monomer Provides Insights Into Its Oligomerisation and Lipid-binding Mechanisms","authors":"Hoi In Tou , Zachary Rosenes, Yogesh Khandokar , Courtney O. Zlatic, Riley D. Metcalfe , Yee-Foong Mok, Craig J. Morton , Paul R. Gooley, Michael D.W. Griffin","doi":"10.1016/j.jmb.2025.169394","DOIUrl":"10.1016/j.jmb.2025.169394","url":null,"abstract":"<div><div>Apolipoprotein A-I (apoA-I) plays important roles in clearing cholesterol and phospholipids from peripheral tissues, forming high-density lipoprotein (HDL). However, despite this important function, apoA-I has a propensity to form amyloid fibrils implicated in atherosclerosis and hereditary amyloidosis. Historically, structural determination of lipid-free or lipid-poor apoA-I has been difficult. Here, we obtained the crystal structure of the apoA-I monomer in complex with the antigen-binding fragment (Fab) of a monoclonal antibody. The structure reveals that the N-terminal domain (NTD, residues 1–184) of apoA-I is a compact four-helical bundle, whereas the C-terminal domain (CTD, residues 185–243) is unresolved in the structure. Molecular Dynamics (MD) simulations and small-angle X-ray scattering (SAXS) analysis revealed that the apoA-I NTD dimerises by domain-swapping and the dimer is elongated. Methionine (Met) oxidation in apoA-I destabilises both full-length apoA-I (apoA-I<sub>FL</sub>) and C-terminally truncated apoA-I (apoA-I<sub>Δ185–243</sub>), causing dissociation of the domain-swapped dimer and fibril formation. Met oxidation also increased the lipid-binding ability of apoA-I<sub>Δ185–243</sub>, while the amyloidogenic mutation, G26R, did not. Hydrogen-deuterium exchange coupled with nuclear magnetic resonance (HDX-NMR), SAXS, and MD analyses showed that triply Met-oxidised (3MetO) and G26R apoA-I<sub>Δ185–243</sub> are both highly dynamic but remain partially folded. Based on these results, we propose that domain-swapping dimerisation also exists in apoA-I<sub>FL</sub>, with the CTD mediating further oligomerisation. We also propose that lipid-binding is promoted by increased global destabilisation in the protein structure, and/or driven by a specific local conformation that is induced by Met-oxidation but not the G26R mutation.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169394"},"PeriodicalIF":4.5,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858694","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

Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. 用特定同位素标记方案的魔角自旋核磁共振研究精氨酸动力学。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-12 DOI: 10.1016/j.jmb.2025.169379

Darja I Rohden, Federico Napoli, Anna Kapitonova, Ben P Tatman, Roman J Lichtenecker, Paul Schanda

{"title":"Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme.","authors":"Darja I Rohden, Federico Napoli, Anna Kapitonova, Ben P Tatman, Roman J Lichtenecker, Paul Schanda","doi":"10.1016/j.jmb.2025.169379","DOIUrl":"10.1016/j.jmb.2025.169379","url":null,"abstract":"<p><p>The specific introduction of <sup>1</sup>H-<sup>13</sup>C or <sup>1</sup>H-<sup>15</sup>N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a <sup>13</sup>C-<sup>1</sup>H<sub>2</sub> group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected MAS NMR approaches to probe arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169379"},"PeriodicalIF":4.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854185","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

High-resolution Cryo-EM Analysis of the Therapeutic Pseudomonas Phage Pa223 治疗性假单胞菌噬菌体Pa223的高分辨率冷冻电镜分析。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-08-12 DOI: 10.1016/j.jmb.2025.169386

Chun-Feng David Hou , Nathan Bellis , Ravi K Lokareddy , Steven Branston , Johnny Reid , Renae Geier , Angela Soriaga , Lucy Sim , Pierre Kyme , Deborah L. Birx , Sebastien Lemire , Gino Cingolani

{"title":"High-resolution Cryo-EM Analysis of the Therapeutic Pseudomonas Phage Pa223","authors":"Chun-Feng David Hou , Nathan Bellis , Ravi K Lokareddy , Steven Branston , Johnny Reid , Renae Geier , Angela Soriaga , Lucy Sim , Pierre Kyme , Deborah L. Birx , Sebastien Lemire , Gino Cingolani","doi":"10.1016/j.jmb.2025.169386","DOIUrl":"10.1016/j.jmb.2025.169386","url":null,"abstract":"<div><div>Cryogenic electron microscopy (cryo-EM) analysis of bacteriophages is a valuable method for deciphering virus composition and conformational plasticity. In this study, we present a high-resolution structural atlas of the <em>Pseudomonas</em> virus Pa223, a phage from the <em>Bruynoghevirus</em> genus that has recently been used in clinical cocktails for treating cystic fibrosis and non-cystic fibrosis bronchiectasis, as well as for compassionate care. By combining bioinformatics, proteomics, cryo-EM single particle analysis, and localized reconstruction, we annotated and built atomic models for eight structural polypeptide chains that form the icosahedral capsid and noncontractile tail. We discovered that the Pa223 capsid is decorated by a spike protein with a unique triple-β helix fold that has no structural homologs in the database. The Pa223 tail features six trimeric tail fibers extending upward, similar to but shorter than those found in phage T7. Unlike T7, the Pa223 tail is extended by two head-to-tail adaptors and sealed by a trimeric tail needle, similar to P22-like phages. We identified a protein bound around the outer perimeter of the portal protein, positioned similarly to the ejection protein gp72, which was identified in the <em>Pseudomonas</em> phage DEV, a <em>Litunavirus</em> phage, and a member of the reclassified <em>Schitoviridae</em> family. This structural clue led us to identify the Pa223 ejection proteins gp53, gp54, and gp56, which bioinformatically resemble those of phage T7 more closely than <em>Schitoviridae</em>. Thus, Pa223 contains various structural elements similar to those in P22-like, T7-like, and <em>Litunavirus</em> phages, providing a foundation for understanding the evolution of ejection proteins in <em>Bruynogheviruses</em>.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169386"},"PeriodicalIF":4.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854186","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