Journal of Molecular Biology最新文献_第5页

Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly 抗毒素RNA假结在调节毒素活性和毒素-抗毒素RNP复合物组装中的作用

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-11 DOI: 10.1016/j.jmb.2025.169410

Harshita Dutta, Parthasarathy Manikandan , Mahavir Singh

{"title":"Role of Antitoxin RNA Pseudoknot in Regulating Toxin Activity and Toxin-antitoxin RNP Complex Assembly","authors":"Harshita Dutta, Parthasarathy Manikandan , Mahavir Singh","doi":"10.1016/j.jmb.2025.169410","DOIUrl":"10.1016/j.jmb.2025.169410","url":null,"abstract":"<div><div>Toxin-antitoxin (TA) systems are bacterial defense systems that confer survival advantages under stress. TA systems comprise a toxin and an antitoxin gene, usually present as operon on chromosomes or on plasmids in bacteria. In type III ToxIN TA systems toxin gene encodes a protein toxin (ToxN) which is a sequence-specific endoribonuclease and antitoxin gene encodes an RNA antitoxin (ToxI) that neutralizes toxin by forming a closed-cyclic TA RNP complex. In TA assemblies, antitoxin RNA adopts a complex tertiary structure comprising of a central conserved pseudoknot flanked by toxin-binding 5′ and 3′ single-stranded regions. In this study, we have shown that a closed, cyclic assembly of ToxIN RNP complex is required for the complete ToxN inhibition in <em>E. coli.</em> We have probed tertiary contacts within the antitoxin pseudoknot that are essential for toxin inhibition in <em>E. coli</em>. Furthermore, we investigated the impact of several ToxI mutants on antitoxin RNA stability, structure, and TA complex assembly using <em>in vitro</em> biophysical and biochemical experiments. We have shown that ToxI mutants adopt structures different from the functional ToxI repeat. In altered conformations, ToxI mutants were able to bind the toxin but were unable to assemble into closed assemblies, resulting in incomplete inhibition of the toxin. Our findings showed that subtle nucleotide changes in the pseudoknot can disrupt antitoxin-mediated toxin neutralization, emphasizing its role in TA complex assembly.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169410"},"PeriodicalIF":4.5,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045136","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

Recent ¹⁹F NMR Applications to the Study of Membrane Proteins and Protein Complexes. 19F核磁共振在膜蛋白和蛋白复合物研究中的最新应用。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-09 DOI: 10.1016/j.jmb.2025.169434

Philip Drewniak, Celia Yi-Chia Su, Camila Botin Francisco, Robert Scott Prosser

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Phosphomimetic Experiments Do Not Support a Causal Role for TFAM Phosphorylation in mtDNA Elimination in Sperm 拟磷实验不支持TFAM磷酸化在精子mtDNA消除中的因果作用。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-06 DOI: 10.1016/j.jmb.2025.169433

Natalya Kozhukhar , Yidong Bai , Mikhail F. Alexeyev

{"title":"Phosphomimetic Experiments Do Not Support a Causal Role for TFAM Phosphorylation in mtDNA Elimination in Sperm","authors":"Natalya Kozhukhar , Yidong Bai , Mikhail F. Alexeyev","doi":"10.1016/j.jmb.2025.169433","DOIUrl":"10.1016/j.jmb.2025.169433","url":null,"abstract":"<div><div>In sexually reproducing eukaryotes—particularly mammals—mitochondrial DNA (mtDNA) is typically inherited from a single parent, making uniparental mtDNA inheritance a fundamental feature of eukaryotic biology. Recently, it has been suggested that spermatozoa contain no mtDNA because the matrix targeting sequence (MTS) of the mitochondrial transcription factor A (TFAM) becomes phosphorylated, which prevents the mitochondrial import of this protein essential for mtDNA replication. In this study, we used a combination of the GeneSwap technique and phosphomimetic mutations to investigate the impact of TFAM MTS phosphorylation on mtDNA maintenance in cultured cells. TFAM variants carrying phosphomimetic substitutions—S31D, S34D (TFAM-DD), and the double mutants S31D, P32D/S34D, F35D (TFAM-4D)—supported mtDNA maintenance in 143B cells, with their MTSs at least partially processed. This occurred despite the overall negative charge of the MTS in the TFAM-4D variant. Moreover, blocking the MTS processing by a combination of an overall negative charge and a mutation in the arginine residue critical for MTS cleavage did not prevent mtDNA maintenance. These observations led us to conclude that TFAM MTS phosphorylation alone is unlikely to explain mtDNA loss in human sperm during maturation.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169433"},"PeriodicalIF":4.5,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022592","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

Disordered Ferlin C2A–C2B Linkers Bind Membranes and Encode Small Linear Motifs 紊乱的Ferlin C2A-C2B连接体结合膜并编码小线性基序。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-04 DOI: 10.1016/j.jmb.2025.169419

Ethiene Kwok , Patricia Khuu , Erin Huang, Fakhria Saadat, Elijah Urbaitel, Jordan S. Indrawan, Patrick Reardon, Juan Vanegas, Colin P. Johnson

{"title":"Disordered Ferlin C2A–C2B Linkers Bind Membranes and Encode Small Linear Motifs","authors":"Ethiene Kwok , Patricia Khuu , Erin Huang, Fakhria Saadat, Elijah Urbaitel, Jordan S. Indrawan, Patrick Reardon, Juan Vanegas, Colin P. Johnson","doi":"10.1016/j.jmb.2025.169419","DOIUrl":"10.1016/j.jmb.2025.169419","url":null,"abstract":"<div><div>Ferlins are vesicle trafficking proteins composed of folded C2 domains conjugated by linkers which are largely disordered. Although a role for the C2 domains as calcium sensors has been established it remains unclear whether the linkers function beyond acting as passive spacers. We examined the C2A–C2B linker sequences of vertebrate ferlins and found both putative short linear motifs (SLiMs) as well as membrane binding sequences for members of the protein family. Specifically, for otoferlin we identified an arginine-rich region proximal to an AP2 binding dileucine motif which interacts with negatively charged lipid membranes. Further, the linker region dominated the liposome binding properties of a larger recombinant C2A–C2B, two-C2 domain segment of otoferlin, suggesting a dominant role in mediating the membrane binding property of the N-terminus. We also found that alternative splicing of the otoferlin C2A–C2B linker adds an additional membrane binding segment and alters the affinity of membrane binding. Like otoferlin, a recombinant dysferlin linker interacted with liposomes. However, dysferlin encodes for SLiMs not detected in the otoferlin linker and interacted with both SH3- and WW- domain proteins as determined using fluorescence spectroscopy. We conclude that the C2A–C2B linker of vertebrate ferlins serves as a signaling platform by recruiting SLiM-binding partners. Membrane binding “hotspots” encoded in a subset of linkers including otoferlin may serve to localize protein complexes proximal to the cell membrane for activity.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169419"},"PeriodicalIF":4.5,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008009","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

Revisiting a Breathtaking Publication in the History of Molecular Biology 重访分子生物学史上令人惊叹的出版物。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-03 DOI: 10.1016/j.jmb.2025.169415

Richard Losick

引用次数: 0

Periplasmic Serine Protease Prc is Responsible for Amyloid Subunit CsgA Degradation and Proteostasis in Escherichia coli 外质丝氨酸蛋白酶Prc负责大肠杆菌淀粉样蛋白亚基CsgA的降解和蛋白质停滞。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-02 DOI: 10.1016/j.jmb.2025.169418

Shinya Sugimoto , Yurika Terasawa , Naoki Tani , Kunitoshi Yamanaka , Yuki Kinjo

{"title":"Periplasmic Serine Protease Prc is Responsible for Amyloid Subunit CsgA Degradation and Proteostasis in Escherichia coli","authors":"Shinya Sugimoto , Yurika Terasawa , Naoki Tani , Kunitoshi Yamanaka , Yuki Kinjo","doi":"10.1016/j.jmb.2025.169418","DOIUrl":"10.1016/j.jmb.2025.169418","url":null,"abstract":"<div><div><em>Escherichia coli</em> synthesizes curli amyloid fibers extracellularly during biofilm formation and host colonization. The proteostasis network regulates the major curli subunit, CsgA, to prevent intracellular amyloid aggregation, yet the degradation mechanism remains elusive. Here, through a comprehensive investigation employing genetically engineered <em>E. coli</em>, multi-copy-suppressor screening, and biochemical analyses, we identify periplasmic serine protease Prc as a key player in CsgA degradation. Prc directly degrades CsgA through internal cleavage, differing from canonical tail-specific proteases. Although the bacterial HtrA homologs DegP and DegQ exhibit limited CsgA degradation activity <em>in vitro</em> in the presence of the suicide activator YjfN, deletion of these proteases did not affect native CsgA degradation <em>in vivo</em>. Instead, Prc, in coordination with the periplasmic chaperone CsgC, prevents the periplasmic accumulation of CsgA amyloid-like aggregates. Furthermore, impairment of efficient secretion and proteolytic systems leads to reduced <em>csg</em> operon expression mediated by the Rcs and Cpx two-component systems. Our findings reveal a dual-layered strategy employed by <em>E. coli</em> to prevent intracellular accumulation of extracellular amyloids at both protein degradation and transcriptional regulation levels.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169418"},"PeriodicalIF":4.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144999327","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

Assessing In Silico Tools for Accurate Pathogenicity Prediction in CHD Nucleosome Remodelers 评估用于准确预测冠心病核小体重塑者致病性的计算机工具。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-02 DOI: 10.1016/j.jmb.2025.169413

Nazim Rabouhi , Simon Guindon , Emilia Aisha Coleman , H.J. van Heesbeen , Celia M.T. Greenwood , Tianyuan Lu , Philippe M. Campeau

{"title":"Assessing In Silico Tools for Accurate Pathogenicity Prediction in CHD Nucleosome Remodelers","authors":"Nazim Rabouhi , Simon Guindon , Emilia Aisha Coleman , H.J. van Heesbeen , Celia M.T. Greenwood , Tianyuan Lu , Philippe M. Campeau","doi":"10.1016/j.jmb.2025.169413","DOIUrl":"10.1016/j.jmb.2025.169413","url":null,"abstract":"<div><div>Chromodomain Helicase DNA-binding (CHD) proteins compose a family of chromatin remodelers that play crucial roles in DNA repair, gene expression regulation, neural stem cell differentiation and chromatin integrity. Genetic variants in CHD chromatin remodelers are associated with neurodevelopmental disorders with features like autism spectrum disorder and intellectual disability. Consequently, the determination of variant pathogenicity in clinical genetic tests for individuals bearing <em>CHD</em> variants is crucial. In this study, we compared the efficiency of multiple pathogenicity prediction tools, which are valuable resources for the identification and annotation of potentially disease-causing variants, to assess the most accurate <em>in silico</em> tool capable of distinguishing pathogenic <em>CHD</em> variants from benign ones. We have focused specifically on genes that share high structural and functional similarity and are strongly linked to pathogenic mutations. Here, we evaluated a range of pathogenicity prediction tools and compared their output with pathogenicity conclusions reported in the literature and genomic databases. Our findings showed that the top performing tools were BayesDel, ClinPred, AlphaMissense, ESM-1b and SIFT. BayesDel, specifically with its addAF component, was overall the most robust tool for <em>CHD</em> variant pathogenicity prediction. We also suggest incorporating SnpEff’s high-impact variant identification capabilities for the development of a hybrid tool that would enhance the classification of <em>CHD</em> variants. Our study emphasizes the need for continuous evaluation and integration of updated prediction tools, including emerging artificial intelligence (AI) approaches. This research also emphasizes the importance of gathering better clinical and mechanistic data on the deleteriousness of pathogenic variants to improve the accuracy of clinical diagnostics.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169413"},"PeriodicalIF":4.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144999362","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

Configuring the Code: Enhancer-Promoter Arrangement and Transcriptional Regulation. 配置代码：增强子-启动子排列和转录调控。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-02 DOI: 10.1016/j.jmb.2025.169417

Noel Buitrago, J Andres Vidal, Bomyi Lim

{"title":"Configuring the Code: Enhancer-Promoter Arrangement and Transcriptional Regulation.","authors":"Noel Buitrago, J Andres Vidal, Bomyi Lim","doi":"10.1016/j.jmb.2025.169417","DOIUrl":"10.1016/j.jmb.2025.169417","url":null,"abstract":"<p><p>The precise spatial and temporal regulation of gene expression through enhancer-promoter (E-P) interactions represents a fundamental mechanism underlying cellular differentiation and organismal development in multicellular eukaryotes. Despite extensive studies on enhancer-mediated gene regulation, a systematic understanding of how specific E-P configurations affect transcriptional dynamics remains incomplete. Recent advances in live-imaging, single-cell assays, and chromatin conformation capture technologies have enabled unprecedented insights into these dynamic regulatory processes by providing temporal resolution and single-cell specificity that complement traditional population-based approaches. This review examines recent findings on how E-P distance, enhancer orientation and positioning, boundary elements, and multi-way interactions collectively influence gene expression. Key insights include non-linear distance effects on gene expression, enhancer positioning-dependent transcriptional kinetics, context-dependent boundary element function, and synergistic enhancer cooperation that ensures robust developmental programs. Together, these configuration-dependent effects underscore the intricate and dynamic nature of E-P communication in precise transcriptional control across development and evolution.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169417"},"PeriodicalIF":4.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144999318","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 tRNA Editing Complex ADAT2/3 Promotes Cancer Cell Growth and Codon-biased mRNA Translation tRNA编辑复合体ADAT2/3促进癌细胞生长和密码子偏向的mRNA翻译。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-02 DOI: 10.1016/j.jmb.2025.169414

Julia Ramirez-Moya , Titi Rindi Antika , Qi Liu , Xushen Xiong , Raja Ali , Alejandro Gutierrez , Richard I. Gregory

{"title":"The tRNA Editing Complex ADAT2/3 Promotes Cancer Cell Growth and Codon-biased mRNA Translation","authors":"Julia Ramirez-Moya , Titi Rindi Antika , Qi Liu , Xushen Xiong , Raja Ali , Alejandro Gutierrez , Richard I. Gregory","doi":"10.1016/j.jmb.2025.169414","DOIUrl":"10.1016/j.jmb.2025.169414","url":null,"abstract":"<div><div>Transfer RNAs (tRNAs) are subject to various chemical modifications that influence their stability or function. Adenosine to Inosine (A-to-I) editing in the tRNA anticodon at position A34 is an important modification that expands anticodon-codon recognition at the wobble position and is required for normal mRNA translation. The relevance of tRNA editing in cancer remains unexplored. Here we show that the genes encoding the ADAT2/3 deaminase complex, responsible for A-to-I tRNA editing in humans, are commonly amplified and/or overexpressed in several tumor types including liposarcoma (LPS). We find that LPS cell growth and tumorigenicity is dependent on ADAT2/3 tRNA editing activity. Mechanistically, we find decreased tRNA editing upon ADAT2 depletion, defective translation of a subset of mRNAs, and altered protein homeostasis. Thus, ADAT2 promotes oncogenesis and the translation of growth promoting mRNAs that are enriched in NNC codons that lack cognate tRNAs and therefore depend on A-I tRNA editing for decoding and mRNA translation. Our results identify ADAT2/3 as a potential new cancer therapeutic target.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169414"},"PeriodicalIF":4.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144999364","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

Molecular Insights Into the Structure, Function, and Stability of the DNA Polymerase Processivity Factor From Mycobacterium tuberculosis 结核分枝杆菌DNA聚合酶加工因子的结构、功能和稳定性的分子见解。

IF 4.5 2区生物学

Journal of Molecular Biology Pub Date : 2025-09-02 DOI: 10.1016/j.jmb.2025.169416

Meenakshi Mulye, Vikas Jain

{"title":"Molecular Insights Into the Structure, Function, and Stability of the DNA Polymerase Processivity Factor From Mycobacterium tuberculosis","authors":"Meenakshi Mulye, Vikas Jain","doi":"10.1016/j.jmb.2025.169416","DOIUrl":"10.1016/j.jmb.2025.169416","url":null,"abstract":"<div><div>Emergence of drug resistance in <em>Mycobacterium tuberculosis</em> (Mtb) calls for newer drugs and drug targets. Essential proteins such as DNA polymerase (DNAP) processivity factor, also called sliding clamp (DnaN), are indispensable for bacterial survival, and are excellent drug targets. Here, we constructed a <em>dnaN</em>-conditional knockout in <em>Mycobacterium smegmatis</em> (MsmΔ<em>dnaN</em>) and were able to successfully complement it with Mtb DnaN (DnaN<sup>Mtb</sup>). To explore its structure–function–stability relationship, we generated Ala-substituted mutants of the DnaN<sup>Mtb</sup> subunit-subunit interface, and identified R115, F116, and E319 as crucial for MsmΔ<em>dnaN</em> survival in our complementation assay. We used biophysical, biochemical, and <em>in silico</em> molecular dynamics simulation methods to decipher the importance of these residues. We show that mutants exist as dimers, with lesser stability than wildtype. Except F116A, the mutants are largely folded with their CD profiles similar to wildtype. We also assembled and purified Mtb Clamp Loader Complex and used it to assess DNAP processivity function of DnaN<sup>Mtb</sup>. Our <em>in vitro</em> DNA synthesis data show that PolA<sup>Mtb</sup> does not interact with DnaN<sup>Mtb</sup>, whereas <em>E. coli</em> Pol-I Klenow fragment shows enhanced DNA synthesis in presence of DnaN<sup>Mtb</sup>, which was abolished by Griselimycin, an antibiotic that inhibits clamp-DNAP interaction. Interestingly, DnaN<sup>Mtb</sup> mutants that did not complement loss of DnaN in MsmΔ<em>dnaN</em> also did not support enhanced DNA synthesis by Klenow, corroborating our <em>in vivo</em> observation. We suggest that the Mtb clamp subunit-subunit interface is crucial for maintaining structure–function–stability, and thus can be used for the targeted development of small molecule inhibitors and peptidomimetics as potent drugs against tuberculosis.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 21","pages":"Article 169416"},"PeriodicalIF":4.5,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144999332","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