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Targeting epigenetic readers 以表观遗传读者为目标
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-09 DOI: 10.1038/s41589-025-02130-9
Catherine A. Musselman, Tatiana G. Kutateladze
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引用次数: 0
Directed evolution of functional intrinsically disordered proteins. 功能性内在无序蛋白的定向进化。
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-09 DOI: 10.1038/s41589-025-02128-3
Yuefeng Ma,Leshan Yang,Yantong Chen,Michael W Chen,Wen Yu,Yifan Dai
Engineering synthetic intrinsically disordered proteins (synIDPs) enables regulation of biomolecular condensation and protein solubility. However, limited understanding of how sequence-dependent interaction cooperativity relates to the fitness impacts of synIDPs on endogenous cellular processes constrains our design capability. Here, to circumvent this design challenge, we present a systematic directed evolution method for the evolution of synIDPs capable of mediating diverse phase behaviors in living cells. The selection methods allow us to evolve a toolbox of synIDPs with distinct phase behaviors and thermoresponsive features in living cells, leading to the evolution of synthetic condensates. The reverse-selection method further allows us to select synIDPs as solubility tags. We demonstrate the applications of the evolved synIDPs in protein circuits to (1) regulate intracellular protein activity and (2) reverse antibiotic resistance. Our systematic evolution and selection strategies provide a versatile platform for developing synIDPs for broad applications in synthetic biology and biotechnology.
工程合成内在无序蛋白(synIDPs)能够调节生物分子缩合和蛋白质溶解度。然而,对序列依赖的相互作用协同性如何与synIDPs对内源性细胞过程的适应度影响相关的理解有限,限制了我们的设计能力。在这里,为了规避这一设计挑战,我们提出了一种系统的定向进化方法,用于能够介导活细胞中不同相行为的synIDPs的进化。这些选择方法使我们能够在活细胞中进化出具有不同相行为和热响应特征的synIDPs工具箱,从而导致合成凝聚物的进化。反向选择方法进一步允许我们选择synIDPs作为溶解度标签。我们展示了进化的synIDPs在蛋白质回路中的应用,以(1)调节细胞内蛋白质活性和(2)逆转抗生素耐药性。我们的系统进化和选择策略为synIDPs的开发提供了一个广泛应用于合成生物学和生物技术的通用平台。
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引用次数: 0
Structural basis for the catalytic mechanism of human lipid phosphate phosphatases. 人脂质磷酸酶催化机制的结构基础。
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-09 DOI: 10.1038/s41589-025-02121-w
Meng Yang,Chunping Sun,Yonglin He,Hongwu Qian
Lipid phosphate phosphatases (LPPs) catalyze the dephosphorylation of a broad range of bioactive lipid phosphates, including lysophosphatidic acid and sphingosine-1-phosphate, playing essential roles in embryonic vasculogenesis, cell differentiation and inflammation. Here we present the cryo-electron microscopic structure of human LPP1 as a tetramer with C4 symmetry. We capture the phosphohistidine intermediate state by using vanadate as a phosphate analog, where vanadate is coordinated by positively charged residues from three conserved motifs (C1, C2 and C3). Structural investigations of LPP1 variants with mutations in two catalytic histidine residues confirm that the histidine in the C2 motif facilitates phosphate bond cleavage. Enzymatic assays validate our structural observations. Additionally, a phosphatidylinositol 4,5-bisphosphate (PIP2) molecule was discovered in the LPP1 structure, underscoring a potential regulatory role for PIP2 in the catalytic activity of LPP1.
脂质磷酸磷酸酶(LPPs)催化多种生物活性脂质磷酸的去磷酸化,包括溶血磷脂酸和鞘氨醇-1-磷酸,在胚胎血管发生、细胞分化和炎症中发挥重要作用。在这里,我们展示了人类LPP1作为C4对称四聚体的低温电镜结构。我们通过使用钒酸盐作为磷酸盐类似物来捕获磷酸组氨酸中间态,其中钒酸盐由来自三个保守基序(C1, C2和C3)的带正电残基配位。对两个催化组氨酸残基突变的LPP1变异的结构研究证实,C2基序中的组氨酸促进了磷酸键的切割。酶分析证实了我们的结构观察。此外,在LPP1结构中发现了磷脂酰肌醇4,5-二磷酸(PIP2)分子,强调了PIP2在LPP1催化活性中的潜在调节作用。
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引用次数: 0
Complex-specific inhibitors for interrogating ATAC histone acetyltransferase complex. ATAC组蛋白乙酰转移酶复合物的复合物特异性抑制剂。
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-09 DOI: 10.1038/s41589-025-02132-7
Sha Liu,Jinzhao Liu,Yinqiao Wu,Xinyi Yao,Xiang Li,Xinyu Dong,Qi Li,Hayden Jit Hei Cheung,Kwan Yuen Wong,Yuanyuan Li,Mu He,Chi-Leung Chiang,Jason Wing Hon Wong,Haitao Li,Weiping Wang,Xin Li,Xiang David Li
Histone acetyltransferases (HATs) modify chromatin to regulate gene expression. Instead of acting alone, HATs function in complexes with other proteins, leading to variations in substrate specificity, genomic localization and cellular function. To understand the complex-dependent roles of HATs, we present a chemical approach to specifically dissociate ATAC (Ada-two-A-containing) HAT complex from chromatin without perturbing other complexes. Rather than targeting the shared HAT enzyme, we developed chemical inhibitors for an ATAC-specific subunit, YEATS2. The most effective inhibitor, LS-170, specifically reduced the chromatin occupancy of the ATAC complex, decreased the ATAC-dependent histone acetylation level and downregulated the expression of ATAC-governed genes, leading to significantly suppressed tumor growth in a lung cancer mouse model. This study not only sheds light on the regulatory roles of the ATAC HAT complex in gene transcription but also provides evidence that the chemical inhibition of the ATAC complex can be a promising therapeutic strategy.
组蛋白乙酰转移酶(HATs)修饰染色质以调节基因表达。HATs不是单独起作用,而是与其他蛋白质复合物一起起作用,从而导致底物特异性、基因组定位和细胞功能的变化。为了了解HAT的复合物依赖作用,我们提出了一种化学方法,可以在不干扰其他复合物的情况下特异性地从染色质上解离ATAC(含ada -two- a) HAT复合物。我们不是针对共享的HAT酶,而是针对atac特异性亚基YEATS2开发了化学抑制剂。在肺癌小鼠模型中,最有效的抑制剂LS-170特异性地降低了ATAC复合物的染色质占用,降低了ATAC依赖的组蛋白乙酰化水平,下调了ATAC控制基因的表达,从而显著抑制了肿瘤的生长。这项研究不仅揭示了ATAC HAT复合物在基因转录中的调节作用,而且提供了化学抑制ATAC复合物可能是一种有前途的治疗策略的证据。
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引用次数: 0
Molecular insight into 5' RNA capping with NpnNs by bacterial RNA polymerase. 细菌RNA聚合酶对NpnNs覆盖5' RNA的分子观察。
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-09 DOI: 10.1038/s41589-025-02134-5
Valentina M Serianni,Jana Škerlová,Anna Knopp Dubánková,Anton Škríba,Hana Šváchová,Tereza Vučková,Anatolij Filimoněnko,Milan Fábry,Pavlína Řezáčová,Tomáš Kouba,Hana Cahova
RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside polyphosphates by RNA polymerase as noncanonical initiating nucleotides. However, how these compounds bind into the active site of RNA polymerase during transcription initiation is unknown. Here, we explored transcription initiation in vitro, using a series of DNA templates in combination with dinucleoside polyphosphates and model RNA polymerase from Thermus thermophilus. We observed that the transcription start site can vary on the basis of the compatibility of the specific template and dinucleoside polyphosphate. Cryo-electron microscopy structures of transcription initiation complexes with dinucleoside polyphosphates revealed that both nucleobase moieties can pair with the DNA template. The first encoded nucleotide pairs in a canonical Watson-Crick manner, whereas the second nucleobase pairs noncanonically in a reverse Watson-Crick manner. Our work provides a structural explanation of how dinucleoside polyphosphates initiate RNA transcription.
最近才在细菌和真核生物中发现了以二核苷多磷酸盖顶的RNA。这种特异性盖顶的可能机制涉及RNA聚合酶作为非规范起始核苷酸直接结合二核苷多磷酸。然而,这些化合物在转录起始过程中如何结合到RNA聚合酶的活性位点尚不清楚。在这里,我们利用一系列DNA模板,结合二核苷多磷酸和来自嗜热热菌的模型RNA聚合酶,探索了体外转录起始。我们观察到转录起始位点可以根据特定模板和二核苷多磷酸的相容性而变化。双核苷多磷酸转录起始复合物的低温电镜结构显示,两个核碱基片段都可以与DNA模板配对。第一个编码的核苷酸以规范的沃森-克里克方式对,而第二个核碱基以非规范的反向沃森-克里克方式对。我们的工作提供了二核苷多磷酸如何启动RNA转录的结构解释。
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引用次数: 0
Complexoform-restricted covalent TRMT112 ligands that allosterically agonize METTL5 变构化METTL5的限制性共价TRMT112配体
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-08 DOI: 10.1038/s41589-025-02099-5
F. Wieland Goetzke, Steffen M. Bernard, Cheng-Wei Ju, Jonathan Pollock, Kristen E. DeMeester, Jacob Gross, Gabriel M. Simon, Chuan He, Bruno Melillo, Benjamin F. Cravatt
Adaptors serve as hubs to regulate diverse protein complexes in cells. This multitude of functions can complicate the study of adaptors, as their genetic disruption may simultaneously impair the activities of several compositionally distinct complexes (or adaptor ‘complexoforms’). Here we describe the chemical proteomic discovery of bicyclopyrrolidine acrylamide stereoprobes that react with C100 of the methyltransferase (MT) adaptor TRMT112 in human cells. Curiously, the stereoprobes showed negligible reactivity with uncomplexed recombinant TRMT112 and we found that this interaction was restored exclusively in the presence of METTL5 but not other MTs. A cocrystal structure revealed stereoprobe binding to a composite pocket proximal to C100 of TRMT112 that is templated by METTL5 and absent in other TRMT112:MT complexes. Structural rearrangements promoted by stereoprobe binding in turn lead to allosteric agonism of METTL5, thus revealing how covalent ligands targeting a pleiotropic adaptor can confer partner-specific functional effects through reactivity with a single complexoform.
接头作为枢纽来调节细胞中不同的蛋白质复合物。这种多种功能可能使接合子的研究复杂化,因为它们的遗传破坏可能同时损害几种组成不同的复合物(或接合子“复杂形式”)的活性。在这里,我们描述了在人类细胞中与甲基转移酶(MT)接头TRMT112的C100反应的双环吡咯烷丙烯酰胺立体探针的化学蛋白质组学发现。奇怪的是,立体探针与未配合的重组TRMT112的反应性可以忽略,我们发现这种相互作用仅在METTL5存在时才恢复,而在其他MT配合物中则没有。共晶结构显示,立体探针与TRMT112 C100附近的复合口袋结合,该口袋由METTL5模板,在其他TRMT112:MT配合物中不存在。立体探针结合促进的结构重排反过来导致METTL5的变构激动作用,从而揭示了针对多效受体的共价配体如何通过与单一络合物的反应性赋予伴侣特异性功能效应。
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引用次数: 0
Membrane editing with proximity labeling reveals regulators of lipid homeostasis 膜编辑与近距离标记揭示调节脂质稳态
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-07 DOI: 10.1038/s41589-025-02104-x
Reika Tei, Xiang-Ling Li, Lin Luan, Jeremy M. Baskin
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引用次数: 0
Rapid evolution of a highly efficient RNA polymerase by homologous recombination 同源重组快速进化高效RNA聚合酶
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-07 DOI: 10.1038/s41589-025-02124-7
Esau L. Medina, Victoria A. Maola, Mohammad Hajjar, Grace K. Ko, Ethan J. Ho, Alexandria R. Horton, Nicholas Chim, John C. Chaput
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引用次数: 0
Engineering metazoan fatty acid synthase to control chain length applied in yeast 工程后生脂肪酸合成酶控制酵母链长
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-07 DOI: 10.1038/s41589-025-02105-w
Damian L. Ludig, Xiaoxin Zhai, Alexander Rittner, Christian Gusenda, Maximilian Heinz, Svenja Berlage, Ning Gao, Adrian J. Jervis, Yongjin J. Zhou, Martin Grininger
Metazoan fatty acid (FA) synthases (mFASs) facilitate the de novo synthesis of C16- and C18-FAs through iterative extensions within the FA cycle and hydrolytic release. Here we re-engineer mFAS to fine-tune the interplay between FA extension and FA hydrolytic release for the targeted production of short- and medium-chain fatty acids. Single amino acid exchanges in the ketosynthase domain can redirect FA product profiles from predominantly C8 (G113W) to C8/C10 (G113F) and C12/C14 (G113M). Integration of a thioreductase domain enables the production of medium-chain fatty aldehydes and alcohols. We apply our approach for controlling chain length in FA biosynthesis to the microbial production of C10- and C12-FAs, translate it into a yeast cell factory and achieve C10/C12-FAs titers of 674 mg l −1 and 67% purity of total free FAs. Our work demonstrates a modular platform for programmable FA synthesis and paves the way toward sustainable bioproduction of valuable oleochemicals.
后生动物脂肪酸(FA)合成酶(mFASs)通过FA循环内的迭代延伸和水解释放促进C16-和C18-FAs的重新合成。在这里,我们重新设计了mFAS,以微调FA延伸和FA水解释放之间的相互作用,以实现短链和中链脂肪酸的目标生产。酮合酶结构域的单氨基酸交换可以将FA产物谱从主要的C8 (G113W)重定向到C8/C10 (G113F)和C12/C14 (G113M)。硫还原酶结构域的整合使中链脂肪醛和醇的生产成为可能。我们将控制FA生物合成链长度的方法应用于微生物生产C10-和C12-FAs,并将其转化为酵母细胞工厂,实现了C10/C12-FAs滴度为674 mg l - 1,总游离FAs纯度为67%。我们的工作展示了一个可编程FA合成的模块化平台,为有价值的油脂化学品的可持续生物生产铺平了道路。
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引用次数: 0
Advances in BRET probes for intracellular target engagement studies BRET探针在细胞内靶接合研究中的进展
IF 14.8 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-06 DOI: 10.1038/s41589-025-02103-y
Jacob L. Capener, Martin P. Schwalm, James D. Vasta, Ani Michaud, Kelly A. Teske, William M. Marsiglia, Kilian V. M. Huber, Arvin C. Dar, Stefan Knapp, Alison D. Axtman, Matthew B. Robers
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引用次数: 0
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Nature chemical biology
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