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Closing 2025, and a look ahead 2025年即将结束,展望未来
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-12 DOI: 10.1038/s41594-025-01732-0
We review 2025 and discuss some of the foremost initiatives developed at the journal. We also look back at discoveries we have been proud to publish.
我们回顾了2025年,并讨论了一些在期刊上发展起来的最重要的举措。我们也会回顾我们曾经自豪地发表过的发现。
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引用次数: 0
The aging of the AlphaFold database AlphaFold数据库的老化。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-10 DOI: 10.1038/s41594-025-01725-z
Ifigenia Tsitsa, Anja Conev, Alessia David, Suhail A. Islam, Michael J. E. Sternberg
The AlphaFold database, released in 2022, modeled UniProt sequences from April 2021 and now provides 200 million predicted protein structures. Of the 20,504 full-length predicted human structures, 631 entries conflict with the June 2025 UniProt release. Similar conflicts across species highlight how bioinformatics resources can rapidly age.
AlphaFold数据库于2022年发布,从2021年4月开始模拟UniProt序列,现在提供了2亿个预测的蛋白质结构。在20,504个全长预测的人体结构中,有631个条目与UniProt于2025年6月发布的版本相冲突。跨物种的类似冲突凸显了生物信息学资源是如何迅速老化的。
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引用次数: 0
Author Correction: A small molecule stabilizer rescues the surface expression of nearly all missense variants in a GPCR 作者更正:一种小分子稳定剂挽救了GPCR中几乎所有错义变异的表面表达。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-07 DOI: 10.1038/s41594-025-01734-y
Taylor L. Mighell, Ben Lehner
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引用次数: 0
Gene regulation through exon junction complex modularity 外显子结复杂模块性的基因调控。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-03 DOI: 10.1038/s41594-025-01724-0
Elizabeth T. Abshire, Lynne E. Maquat
The exon junction complex (EJC) begins to assemble on the spliceosome, which deposits EJCs upstream of most exon–exon junctions during pre-messenger RNA (mRNA) splicing. EJCs acquire additional alternative modules that define heterogeneous EJCs during pre-mRNA processing to mRNA in the nucleus and after mRNA export into the cytoplasm. In this Review, we discuss the mechanisms of EJC formation, the many roles of the EJC in pre-mRNA and mRNA regulation and how these roles are influenced by EJC composition. This Review summarizes the various functions of the exon junction complex in RNA splicing and beyond, to influence gene regulation.
外显子连接复合体(EJC)开始在剪接体上组装,在前信使RNA (mRNA)剪接期间,EJC沉积在大多数外显子-外显子连接的上游。EJCs获得额外的替代模块,这些模块定义了在mRNA前加工到细胞核中的mRNA以及mRNA输出到细胞质后的异质EJCs。在这篇综述中,我们讨论了EJC的形成机制,EJC在pre-mRNA和mRNA调控中的许多作用,以及EJC的组成如何影响这些作用。
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引用次数: 0
Editorial Expression of Concern: Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis 编辑关注表达:Munc13 C2B结构域是突触胞外分泌的活性依赖性Ca2+调节剂。
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-03 DOI: 10.1038/s41594-025-01730-2
Ok-Ho Shin, Jun Lu, Jeong-Seop Rhee, Diana R. Tomchick, Zhiping P. Pang, Sonja M. Wojcik, Marcial Camacho-Perez, Nils Brose, Mischa Machius, Josep Rizo, Christian Rosenmund, Thomas C. Südhof
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引用次数: 0
ATG2A–DGAT2 cooperation fuels lipid droplet growth ATG2A-DGAT2协同作用促进脂滴生长
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-11-27 DOI: 10.1038/s41594-025-01720-4
Cells store excess fat in lipid droplets to avoid lipotoxicity and maintain homeostasis. We identified an autophagy-independent role for the autophagy lipid transfer protein ATG2A in helping direct lipids to growing lipid droplets and promoting recruitment of the enzyme DGAT2. This coordination enhances triglyceride storage, protects the endoplasmic reticulum from lipid overload and limits the misrouting of lipids into other metabolic pathways.
细胞将多余的脂肪储存在脂滴中,以避免脂肪中毒并维持体内平衡。我们发现自噬脂质转移蛋白ATG2A在帮助引导脂质生长脂滴和促进DGAT2酶募集方面具有自噬独立作用。这种协调增强了甘油三酯的储存,保护内质网免受脂质过载的影响,并限制了脂质进入其他代谢途径的错误路由。
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引用次数: 0
Expansion of artificial intelligence for genome editing 扩展基因组编辑的人工智能
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-11-20 DOI: 10.1038/s41594-025-01722-2
Heesoo Uhm, Sangsu Bae
Artificial intelligence (AI) is advancing genome editing, from predictive modeling to generative design. Emerging generative AI tools such as RFdiffusion, AlphaFold 3 and ESM now facilitate the de novo design of linkers, inhibitors and enzymes. We highlight work where AI-driven design is used to enhance the precision of mitochondrial cytosine base editors.
人工智能(AI)正在推动基因组编辑,从预测建模到生成设计。新兴的生成式人工智能工具,如RFdiffusion、AlphaFold 3和ESM,现在促进了连接剂、抑制剂和酶的从头设计。我们重点介绍了人工智能驱动设计用于提高线粒体胞嘧啶碱基编辑器精度的工作。
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引用次数: 0
Filament formation and NAD processing by noncanonical human FAM118 sirtuins 非规范人类FAM118 sirtuins的丝形成和NAD加工
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-11-17 DOI: 10.1038/s41594-025-01715-1
Domagoj Baretić, Sophia Missoury, Karishma Patel, Maximilien Martinez, Franck Coste, Kang Zhu, Rebecca Smith, Anna Georgina Kopasz, Yang Lu, Nicolas Bigot, Catherine Chapuis, Romane Riou, Nina Đukić, Stéphane Goffinont, Valentin Pressoir, Sara Patačko, Gyula Timinszky, Marc Delarue, Bertrand Castaing, Dragana Ahel, Andreja Mikoč, Sébastien Huet, Ivan Ahel, Marcin J. Suskiewicz
Sirtuins are an ancient family of enzymes with diverse nicotinamide adenine dinucleotide (NAD)-dependent activities. Here we identify family with sequence similarity 118 member B (FAM118B) and FAM118A—two understudied vertebrate proteins—as vertebrate-specific sirtuins with similarities to bacterial antiphage sirtuins. We show that human FAM118B forms head-to-tail filaments both in vitro and in living human cells, a feature that appears to be conserved in both FAM118B and its paralog FAM118A across vertebrates. While human FAM118B and FAM118A have individually very weak NAD-processing activity in vitro, their interaction leads to markedly increased activity, suggesting a tightly regulated system. The overexpression of wild-type human FAM118B and FAM118A leads to strongly decreased NAD levels in human cells, an effect that is abolished in catalytically dead or filament-deficient mutants. Our study highlights filament formation and NAD processing as conserved mechanisms among immunity-associated sirtuins across evolution. Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that FAM118A/B processing of NAD involves head-to-tail filament formation and a partnership between the two paralogs.
Sirtuins是一个古老的酶家族,具有不同的烟酰胺腺嘌呤二核苷酸(NAD)依赖活性。在这里,我们鉴定了序列相似的家族118成员B (FAM118B)和fam118a -两种未被充分研究的脊椎动物蛋白-作为脊椎动物特异性sirtuins,与细菌抗噬菌体sirtuins相似。我们发现人类FAM118B在体外和活的人类细胞中形成从头到尾的细丝,这一特征似乎在FAM118B及其平行的FAM118A中都是保守的。虽然人类FAM118B和FAM118A在体外单独具有非常弱的nad加工活性,但它们的相互作用导致活性显着增加,表明一个严格调节的系统。野生型人类FAM118B和FAM118A的过度表达导致人类细胞中NAD水平的强烈下降,这种效应在催化死亡或纤维缺陷突变体中被消除。我们的研究强调了丝的形成和NAD加工在整个进化过程中是免疫相关sirtuins的保守机制。
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引用次数: 0
ATG2A-mediated DAG transfer recruits DGAT2 for lipid droplet growth atg2a介导的DAG转移招募DGAT2促进脂滴生长
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-11-17 DOI: 10.1038/s41594-025-01689-0
Helin Elhan, Alicia Damm, Justin L. Korfhage, Daniel Álvarez, Mehdi Zouiouich, Francesca Giordano, Stefano Vanni, Thomas J. Melia, Abdou Rachid Thiam
Lipid droplet (LD) growth mechanisms and the roles of LD-associated lipid transfer proteins remain poorly understood. Here we show that the autophagy lipid transfer protein ATG2A has an anabolic role and promotes LD expansion by transferring diacylglycerol (DAG), triacylglycerol (TAG) and phosphatidic acid, from the endoplasmic reticulum to LDs. In ATG2A deficiency, synthesized lipids are incorporated inefficiently into LDs and assemble new LDs. In addition, DAG O-acyltransferase 2 (DGAT2), which synthesizes TAG and expands LD, fails to relocate to LDs. In vitro, DAG recruits DGAT2 to LDs. These findings support the idea that ATG2A-mediated DAG transfer recruits DGAT2 to LDs, promoting LD expansion. ATG2A alone promotes LD growth by transferring TAG and DAG, but its effectiveness in LD expansion is reduced when DGAT2 is inhibited. This synergistic action with DGAT2 prevents the buildup of nonmembrane lipids within the endoplasmic reticulum and favors TAG synthesis on the LD surface. Elhan et al. show that ATG2A acts with DGAT2, the enzyme producing triacylglycerol (TAG), in lipid droplet growth. By delivering diacylglycerol to lipid droplets, ATG2A not only fuels TAG production but also promotes the recruitment of DGAT2 to droplet surfaces.
脂滴(LD)的生长机制和LD相关的脂质转移蛋白的作用仍然知之甚少。本研究表明,自噬脂质转移蛋白ATG2A具有合成代谢作用,通过将二酰基甘油(DAG)、三酰基甘油(TAG)和磷脂酸从内质网转移到LD,促进LD扩张。在ATG2A缺乏的情况下,合成的脂质不能有效地结合到ld中并组装新的ld。此外,合成TAG并扩展LD的DAG o -酰基转移酶2 (DGAT2)无法迁移到LD上。在体外,DAG将DGAT2招募到ld。这些发现支持了atg2a介导的DAG转移将DGAT2招募到LD,促进LD扩展的观点。单独ATG2A通过转移TAG和DAG促进LD生长,但当DGAT2被抑制时,其对LD扩展的作用降低。这种与DGAT2的协同作用可防止内质网内非膜脂质的积聚,并有利于LD表面TAG的合成。Elhan等人的研究表明,在脂滴生长过程中,ATG2A与生成三酰甘油(TAG)的酶DGAT2共同作用。通过将二酰基甘油输送到脂滴,ATG2A不仅为TAG的产生提供燃料,而且还促进DGAT2在脂滴表面的招募。
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引用次数: 0
Computational design of a high-precision mitochondrial DNA cytosine base editor 高精度线粒体DNA胞嘧啶碱基编辑器的计算设计
IF 10.1 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-11-17 DOI: 10.1038/s41594-025-01714-2
Li Mi, Yu-Xuan Li, Xinchen Lv, Zi-Li Wan, Xu Liu, Kairan Zhang, Huican Li, Yue Yao, Leping Zhang, Zhe Xu, Xingyu Zhuang, Kunqian Ji, Min Jiang, Yangming Wang, Peilong Lu
Bystander editing remains a major limitation of current base editors, hindering their precision and therapeutic potential. Here, we present a de novo protein design strategy that creates a structurally rigid interface between a DNA-binding TALE domain and a cytosine deaminase, forming a unified editing module termed TALE-oriented deaminase (TOD). Cryo-EM analysis of TOD–DNA complexes confirms that this precise spatial architecture tightly restricts the deaminase activity window, thereby minimizing unwanted deamination. To further enhance editing specificity, we develop a split version, termed DdCBE–TOD, which virtually eliminates off-target editing. As a proof of concept, we apply DdCBE–TOD to generate a mitochondrial disease mouse model and to correct a pathogenic mutation associated with MERRF syndrome in patient-derived cells, achieving single-nucleotide precision. This work introduces a generalizable and computationally guided approach for ultra-precise base editing, offering a promising platform for both mechanistic studies and therapeutic correction of single-nucleotide mutations. Mi et al. use de novo protein design to address bystander and off-target editing in base editing, resulting in a highly precise mitochondrial cytosine base editor that is valuable for studying and treating mitochondrial diseases.
旁观者编辑仍然是当前碱基编辑的主要限制,阻碍了它们的准确性和治疗潜力。在这里,我们提出了一种新的蛋白质设计策略,该策略在dna结合的TALE结构域和胞嘧啶脱氨酶之间创建了一个结构刚性的界面,形成了一个统一的编辑模块,称为TALE导向脱氨酶(TOD)。TOD-DNA复合物的低温电镜分析证实,这种精确的空间结构严格限制了脱氨酶的活性窗口,从而最大限度地减少了不必要的脱氨。为了进一步提高编辑的特异性,我们开发了一个分离版本,称为DdCBE-TOD,它实际上消除了脱靶编辑。作为概念的证明,我们应用DdCBE-TOD来生成线粒体疾病小鼠模型,并在患者来源的细胞中纠正与MERRF综合征相关的致病突变,实现单核苷酸精度。这项工作为超精确碱基编辑引入了一种可推广和计算指导的方法,为单核苷酸突变的机制研究和治疗性纠正提供了一个有前途的平台。Mi等人利用从头开始的蛋白质设计来解决碱基编辑中的旁观者编辑和脱靶编辑问题,从而产生了高度精确的线粒体胞嘧啶碱基编辑器,对研究和治疗线粒体疾病具有重要价值。
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Nature Structural & Molecular Biology
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