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Coordination of force-generating actin-based modules stabilizes and remodels membranes in vivo. 以肌动蛋白为基础的发力模块的协调可稳定和重塑体内膜。
IF 7.4 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-11-04 Epub Date: 2024-08-22 DOI: 10.1083/jcb.202401091
Marco Heydecker, Akiko Shitara, Desu Chen, Duy T Tran, Andrius Masedunskas, Muhibullah S Tora, Seham Ebrahim, Mark A Appaduray, Jorge Luis Galeano Niño, Abhishek Bhardwaj, Kedar Narayan, Edna C Hardeman, Peter W Gunning, Roberto Weigert

Membrane remodeling drives a broad spectrum of cellular functions, and it is regulated through mechanical forces exerted on the membrane by cytoplasmic complexes. Here, we investigate how actin filaments dynamically tune their structure to control the active transfer of membranes between cellular compartments with distinct compositions and biophysical properties. Using intravital subcellular microscopy in live rodents we show that a lattice composed of linear filaments stabilizes the granule membrane after fusion with the plasma membrane and a network of branched filaments linked to the membranes by Ezrin, a regulator of membrane tension, initiates and drives to completion the integration step. Our results highlight how the actin cytoskeleton tunes its structure to adapt to dynamic changes in the biophysical properties of membranes.

膜重塑驱动着广泛的细胞功能,它通过细胞质复合物对膜施加的机械力进行调节。在这里,我们研究了肌动蛋白丝如何动态调整其结构,以控制具有不同成分和生物物理特性的细胞成分之间膜的主动转移。通过在活体啮齿动物体内进行亚细胞内显微镜观察,我们发现由线性丝组成的晶格在颗粒膜与质膜融合后起到稳定作用,而由膜张力调节因子 Ezrin 连接到膜上的分支丝网络则启动并推动完成整合步骤。我们的研究结果突显了肌动蛋白细胞骨架如何调整其结构以适应膜的生物物理特性的动态变化。
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引用次数: 0
Unbiased MD simulations identify lipid binding sites in lipid transfer proteins. 无偏差 MD 模拟确定脂质转移蛋白中的脂质结合位点。
IF 7.4 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-11-04 Epub Date: 2024-08-06 DOI: 10.1083/jcb.202312055
Sriraksha Srinivasan, Daniel Álvarez, Arun T John Peter, Stefano Vanni

The characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to understand their molecular mechanism. However, several structures of LTPs, and notably those proposed to act as bridges between membranes, do not provide the precise location of their endogenous lipid ligands. To address this limitation, computational approaches are a powerful alternative methodology, but they are often limited by the high flexibility of lipid substrates. Here, we develop a protocol based on unbiased coarse-grain molecular dynamics simulations in which lipids placed away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the lipid entry pathway. We apply this approach to characterize lipid binding to bridge LTPs of the Vps13-Atg2 family, for which the lipid localization inside the protein is currently unknown. Overall, our work paves the way to determine binding pockets and entry pathways for several LTPs in an inexpensive, fast, and accurate manner.

要了解脂质转移蛋白(LTPs)的分子机理,就必须确定其与脂质结合的特性。然而,一些 LTPs 的结构,尤其是那些被认为在膜之间起桥梁作用的 LTPs,并没有提供其内源性脂质配体的精确位置。为了解决这一限制,计算方法是一种强大的替代方法,但它们往往受到脂质底物高度灵活性的限制。在这里,我们开发了一种基于无偏粗粒度分子动力学模拟的方案,在这种模拟中,远离蛋白质的脂质可以自发地与 LTP 结合。这种方法能准确确定 LTPs 中的结合口袋,并为脂质进入途径提供一个工作假设。我们运用这种方法描述了脂质与 Vps13-Atg2 家族桥 LTPs 结合的特征,目前还不知道脂质在蛋白质内部的定位。总之,我们的工作为以廉价、快速和准确的方式确定几种 LTPs 的结合口袋和进入途径铺平了道路。
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引用次数: 0
INPP4B promotes PDAC aggressiveness via PIKfyve and TRPML-1-mediated lysosomal exocytosis. INPP4B通过PIKfyve和TRPML-1介导的溶酶体外渗促进PDAC的侵袭性。
IF 7.4 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-11-04 Epub Date: 2024-08-09 DOI: 10.1083/jcb.202401012
Golam T Saffi, Lydia To, Nicholas Kleine, Ché M P Melo, Keyue Chen, Gizem Genc, K C Daniel Lee, Jonathan Tak-Sum Chow, Gun Ho Jang, Steven Gallinger, Roberto J Botelho, Leonardo Salmena

Aggressive solid malignancies, including pancreatic ductal adenocarcinoma (PDAC), can exploit lysosomal exocytosis to modify the tumor microenvironment, enhance motility, and promote invasiveness. However, the molecular pathways through which lysosomal functions are co-opted in malignant cells remain poorly understood. In this study, we demonstrate that inositol polyphosphate 4-phosphatase, Type II (INPP4B) overexpression in PDAC is associated with PDAC progression. We show that INPP4B overexpression promotes peripheral dispersion and exocytosis of lysosomes resulting in increased migratory and invasive potential of PDAC cells. Mechanistically, INPP4B overexpression drives the generation of PtdIns(3,5)P2 on lysosomes in a PIKfyve-dependent manner, which directs TRPML-1 to trigger the release of calcium ions (Ca2+). Our findings offer a molecular understanding of the prognostic significance of INPP4B overexpression in PDAC through the discovery of a novel oncogenic signaling axis that orchestrates migratory and invasive properties of PDAC via the regulation of lysosomal phosphoinositide homeostasis.

包括胰腺导管腺癌(PDAC)在内的侵袭性实体恶性肿瘤可利用溶酶体外泌来改变肿瘤微环境、增强运动性和促进侵袭性。然而,人们对溶酶体功能在恶性细胞中的分子途径仍然知之甚少。在这项研究中,我们证明了肌醇多磷酸4-磷酸酶II型(INPP4B)在PDAC中的过表达与PDAC的进展有关。我们发现,INPP4B 的过表达会促进溶酶体的外周弥散和外排,从而导致 PDAC 细胞的迁移和侵袭潜力增加。从机理上讲,INPP4B 过表达以 PIKfyve 依赖性方式驱动溶酶体上 PtdIns(3,5)P2 的生成,从而引导 TRPML-1 触发钙离子(Ca2+)的释放。我们的研究发现了一个新的致癌信号轴,它通过调节溶酶体磷酸肌醇的平衡来协调 PDAC 的迁移和侵袭特性,从而从分子角度理解了 INPP4B 过表达在 PDAC 中的预后意义。
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引用次数: 0
Near millimolar concentration of nucleosomes in mitotic chromosomes from late prometaphase into anaphase. 从有丝分裂后期到无丝分裂期,有丝分裂染色体中的核小体浓度接近毫摩尔。
IF 7.4 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-11-04 Epub Date: 2024-08-26 DOI: 10.1083/jcb.202403165
Fernanda Cisneros-Soberanis, Eva L Simpson, Alison J Beckett, Nina Pucekova, Samuel Corless, Natalia Y Kochanova, Ian A Prior, Daniel G Booth, William C Earnshaw

Chromosome compaction is a key feature of mitosis and critical for accurate chromosome segregation. However, a precise quantitative analysis of chromosome geometry during mitotic progression is lacking. Here, we use volume electron microscopy to map, with nanometer precision, chromosomes from prometaphase through telophase in human RPE1 cells. During prometaphase, chromosomes acquire a smoother surface, their arms shorten, and the primary centromeric constriction is formed. The chromatin is progressively compacted, ultimately reaching a remarkable nucleosome concentration of over 750 µM in late prometaphase that remains relatively constant during metaphase and early anaphase. Surprisingly, chromosomes then increase their volume in late anaphase prior to deposition of the nuclear envelope. The plateau of total chromosome volume from late prometaphase through early anaphase described here is consistent with proposals that the final stages of chromatin condensation in mitosis involve a limit density, such as might be expected for a process involving phase separation.

染色体压实是有丝分裂的一个关键特征,也是染色体准确分离的关键。然而,目前还缺乏对有丝分裂过程中染色体几何形状的精确定量分析。在这里,我们使用体电子显微镜以纳米级精度绘制了人类 RPE1 细胞从有丝分裂后期到端期的染色体图谱。在端粒期,染色体表面变得更加光滑,染色体臂缩短,并形成初级中心粒收缩。染色质逐渐压缩,最终在原核后期达到超过 750 µM 的显著核小体浓度,并在分裂后期和无核初期保持相对稳定。令人惊讶的是,染色体在核包膜沉积之前的无丝分裂后期体积会增大。这里描述的染色体总体积从有丝分裂后期到无丝分裂初期的高原现象,与有丝分裂中染色质凝聚的最后阶段涉及极限密度的建议是一致的,如涉及相分离的过程所预期的那样。
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引用次数: 0
CYRI controls epidermal wound closure and cohesion of invasive border cell cluster in Drosophila. CYRI控制果蝇表皮伤口闭合和侵入性边界细胞簇的内聚。
IF 7.8 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-10-25 DOI: 10.1083/jcb.202310153
Marvin Rötte,Mila Y Höhne,Dennis Klug,Kirsten Ramlow,Caroline Zedler,Franziska Lehne,Meike Schneider,Maik C Bischoff,Sven Bogdan
Cell motility is crucial for many biological processes including morphogenesis, wound healing, and cancer invasion. The WAVE regulatory complex (WRC) is a central Arp2/3 regulator driving cell motility downstream of activation by Rac GTPase. CYFIP-related Rac1 interactor (CYRI) proteins are thought to compete with WRC for interaction with Rac1 in a feedback loop regulating lamellipodia dynamics. However, the physiological role of CYRI proteins in vivo in healthy tissues is unclear. Here, we used Drosophila as a model system to study CYRI function at the cellular and organismal levels. We found that CYRI is not only a potent WRC regulator in single macrophages that controls lamellipodial spreading but also identified CYRI as a molecular brake on the Rac-WRC-Arp2/3 pathway to slow down epidermal wound healing. In addition, we found that CYRI limits invasive border cell migration by controlling cluster cohesion and migration. Thus, our data highlight CYRI as an important regulator of cellular and epithelial tissue dynamics conserved across species.
细胞运动对形态发生、伤口愈合和癌症侵袭等许多生物过程至关重要。WAVE 调节复合体(WRC)是一个中心 Arp2/3 调节器,在 Rac GTPase 激活的下游驱动细胞运动。CYFIP相关Rac1互作因子(CYRI)蛋白被认为在调节片层动态的反馈环中与WRC竞争与Rac1的互作。然而,CYRI 蛋白在体内健康组织中的生理作用尚不清楚。在这里,我们以果蝇为模型系统,研究 CYRI 在细胞和机体水平上的功能。我们发现,CYRI 不仅在单个巨噬细胞中是一种强效的 WRC 调节器,可控制薄片扩散,而且还发现 CYRI 是 Rac-WRC-Arp2/3 通路的分子制动器,可减缓表皮伤口愈合。此外,我们还发现,CYRI 通过控制集群的凝聚和迁移,限制了侵袭性边界细胞的迁移。因此,我们的数据突出表明,CYRI 是细胞和上皮组织动态的重要调节因子,在不同物种之间是一致的。
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引用次数: 0
Distinct roles of two homologous kinesins in mammalian motile cilia. 哺乳动物运动纤毛中两种同源驱动蛋白的不同作用
IF 7.8 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-10-24 DOI: 10.1083/jcb.202409214
Kaiming Xu,Ming Li,Guangshuo Ou
How do the two kinesin-9 members Kif6 and Kif9 function in mammalian cilia? Ou and colleagues discuss new work from Fang et al. (https://doi.org/10.1083/jcb.202312060) showing that Kif6 is an active motor while Kif9 serves as a stationary regulator, both of which are essential for cilia motility.
驱动蛋白-9 的两个成员 Kif6 和 Kif9 在哺乳动物纤毛中是如何发挥作用的?欧文及其同事讨论了方等人(https://doi.org/10.1083/jcb.202312060)的新研究,该研究显示 Kif6 是一种主动马达,而 Kif9 则是一种静止调节器,两者对纤毛运动都至关重要。
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引用次数: 0
CryoVesNet: A dedicated framework for synaptic vesicle segmentation in cryo-electron tomograms. CryoVesNet:用于低温电子断层扫描图中突触小泡分割的专用框架。
IF 7.8 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-10-24 DOI: 10.1083/jcb.202402169
Amin Khosrozadeh,Raphaela Seeger,Guillaume Witz,Julika Radecke,Jakob B Sørensen,Benoît Zuber
Cryo-electron tomography (cryo-ET) has the potential to reveal cell structure down to atomic resolution. Nevertheless, cellular cryo-ET data is highly complex, requiring image segmentation for visualization and quantification of subcellular structures. Due to noise and anisotropic resolution in cryo-ET data, automatic segmentation based on classical computer vision approaches usually does not perform satisfactorily. Communication between neurons relies on neurotransmitter-filled synaptic vesicle (SV) exocytosis. Cryo-ET study of the spatial organization of SVs and their interconnections allows a better understanding of the mechanisms of exocytosis regulation. Accurate SV segmentation is a prerequisite to obtaining a faithful connectivity representation. Hundreds of SVs are present in a synapse, and their manual segmentation is a bottleneck. We addressed this by designing a workflow consisting of a convolutional network followed by post-processing steps. Alongside, we provide an interactive tool for accurately segmenting spherical vesicles. Our pipeline can in principle segment spherical vesicles in any cell type as well as extracellular and in vitro spherical vesicles.
低温电子断层扫描(cryo-ET)可揭示低至原子分辨率的细胞结构。然而,细胞低温电子扫描数据非常复杂,需要进行图像分割,以实现亚细胞结构的可视化和量化。由于低温电子显微镜数据中存在噪声和各向异性的分辨率,基于经典计算机视觉方法的自动分割通常无法达到令人满意的效果。神经元之间的通信依赖于充满神经递质的突触囊泡 (SV) 外渗。通过低温电子显微镜研究 SV 的空间组织及其相互连接,可以更好地了解外吞调节机制。准确的 SV 分割是获得忠实连接表征的先决条件。突触中存在数以百计的 SV,人工分割是一个瓶颈。为了解决这个问题,我们设计了一个由卷积网络和后处理步骤组成的工作流程。同时,我们还提供了一种交互式工具,用于准确分割球形囊泡。原则上,我们的工作流程可以分割任何细胞类型的球形囊泡以及细胞外和体外球形囊泡。
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引用次数: 0
Rapid turnover of CTLA4 is associated with a complex architecture of reversible ubiquitylation. CTLA4 的快速更替与可逆泛素化的复杂结构有关。
IF 7.8 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-10-15 DOI: 10.1083/jcb.202312141
Pei Yee Tey,Almut Dufner,Klaus-Peter Knobeloch,Jonathan N Pruneda,Michael J Clague,Sylvie Urbé
The immune checkpoint regulator CTLA4 is an unusually short-lived membrane protein. Here, we show that its lysosomal degradation is dependent on ubiquitylation at lysine residues 203 and 213. Inhibition of the v-ATPase partially restores CTLA4 levels following cycloheximide treatment, but also reveals a fraction that is secreted in exosomes. The endosomal deubiquitylase, USP8, interacts with CTLA4, and its loss enhances CTLA4 ubiquitylation in cancer cells, mouse CD4+ T cells, and cancer cell-derived exosomes. Depletion of the USP8 adapter protein, HD-PTP, but not ESCRT-0 recapitulates this cellular phenotype but shows distinct properties vis-à-vis exosome incorporation. Re-expression of wild-type USP8, but neither a catalytically inactive nor a localization-compromised ΔMIT domain mutant can rescue delayed degradation of CTLA4 or counteract its accumulation in clustered endosomes. UbiCRest analysis of CTLA4-associated ubiquitin chain linkages identifies a complex mixture of conventional Lys63- and more unusual Lys27- and Lys29-linked polyubiquitin chains that may underly the rapidity of protein turnover.
免疫检查点调节因子 CTLA4 是一种异常短命的膜蛋白。在这里,我们发现它的溶酶体降解依赖于赖氨酸残基 203 和 213 的泛素化。在环己亚胺处理后,抑制 v-ATP 酶可部分恢复 CTLA4 的水平,但同时也发现了外泌体中分泌的部分 CTLA4。内体去泛素化酶 USP8 与 CTLA4 相互作用,失去 USP8 会增强 CTLA4 在癌细胞、小鼠 CD4+ T 细胞和癌细胞衍生的外泌体中的泛素化。USP8适配蛋白HD-PTP而非ESCRT-0的缺失再现了这种细胞表型,但在外泌体结合方面显示出不同的特性。重新表达野生型 USP8(但催化不活跃或定位受损的 ΔMIT 结构域突变体)不能挽救 CTLA4 的延迟降解,也不能抵消其在聚类内体中的积累。对与 CTLA4 相关的泛素链连接进行的 UbiCRest 分析发现,传统的 Lys63 与更不寻常的 Lys27 和 Lys29 连接的多泛素链形成了复杂的混合物,这可能是蛋白质快速周转的基础。
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引用次数: 0
Making lipids very unhappy to discover how they bind to proteins. 让脂质变得非常不开心,以发现它们是如何与蛋白质结合的。
IF 7.8 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-10-15 DOI: 10.1083/jcb.202410022
Christopher Stefan,Roberto Covino
Membrane lipid composition is maintained by conserved lipid transfer proteins, but computational approaches to study their lipid-binding mechanisms are limiting. Srinivasan et al. (https://doi.org/10.1083/jcb.202312055) develop a clever molecular dynamics simulations assay to accurately model lipid-binding poses in lipid transfer proteins.
膜脂组成由保守的脂质转移蛋白维持,但研究其脂质结合机制的计算方法却受到限制。Srinivasan 等人(https://doi.org/10.1083/jcb.202312055)开发了一种巧妙的分子动力学模拟测定法,以准确模拟脂质转移蛋白的脂质结合姿势。
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引用次数: 0
MONITTR allows real-time imaging of transcription and endogenous proteins in C. elegans. MONITTR 可对秀丽隐杆线虫的转录和内源蛋白进行实时成像。
IF 7.8 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-10-14 DOI: 10.1083/jcb.202403198
Xiaofan Liu,Zhi Chang,Pingping Sun,Beibei Cao,Yuzhi Wang,Jie Fang,Yechun Pei,Baohui Chen,Wei Zou
Maximizing cell survival under stress requires rapid and transient adjustments of RNA and protein synthesis. However, capturing these dynamic changes at both single-cell level and across an organism has been challenging. Here, we developed a system named MONITTR (MS2-embedded mCherry-based monitoring of transcription) for real-time simultaneous measurement of nascent transcripts and endogenous protein levels in C. elegans. Utilizing this system, we monitored the transcriptional bursting of fasting-induced genes and found that the epidermis responds to fasting by modulating the proportion of actively transcribing nuclei and transcriptional kinetics of individual alleles. Additionally, our findings revealed the essential roles of the transcription factors NHR-49 and HLH-30 in governing the transcriptional kinetics of fasting-induced genes under fasting. Furthermore, we tracked transcriptional dynamics during heat-shock response and ER unfolded protein response and observed rapid changes in the level of nascent transcripts under stress conditions. Collectively, our study provides a foundation for quantitatively investigating how animals spatiotemporally modulate transcription in various physiological and pathological conditions.
要在压力下最大限度地提高细胞存活率,就必须快速、瞬时地调整 RNA 和蛋白质的合成。然而,在单细胞水平和整个生物体内捕捉这些动态变化一直是个挑战。在这里,我们开发了一种名为 MONITTR(MS2-嵌入式 mCherry 转录监测)的系统,用于实时同步测量秀丽隐杆线虫的新生转录本和内源蛋白质水平。利用该系统,我们监测了禁食诱导基因的转录突变,发现表皮通过调节活跃转录核的比例和单个等位基因的转录动力学对禁食做出反应。此外,我们的研究结果还揭示了转录因子NHR-49和HLH-30在管理禁食诱导基因转录动力学中的重要作用。此外,我们还追踪了热休克反应和ER未折叠蛋白反应期间的转录动态,观察到新生转录本水平在应激条件下的快速变化。总之,我们的研究为定量研究动物在各种生理和病理条件下如何时空调节转录提供了基础。
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引用次数: 0
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Journal of Cell Biology
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