Pub Date : 2024-09-11DOI: 10.1038/s44318-024-00219-w
Hilda Delgado de la Herran,Denis Vecellio Reane,Yiming Cheng,Máté Katona,Fabian Hosp,Elisa Greotti,Jennifer Wettmarshausen,Maria Patron,Hermine Mohr,Natalia Prudente de Mello,Margarita Chudenkova,Matteo Gorza,Safal Walia,Michael Sheng-Fu Feng,Anja Leimpek,Dirk Mielenz,Natalia S Pellegata,Thomas Langer,György Hajnóczky,Matthias Mann,Marta Murgia,Fabiana Perocchi
The mitochondrial calcium uniporter channel (MCUC) mediates mitochondrial calcium entry, regulating energy metabolism and cell death. Although several MCUC components have been identified, the molecular basis of mitochondrial calcium signaling networks and their remodeling upon changes in uniporter activity have not been assessed. Here, we map the MCUC interactome under resting conditions and upon chronic loss or gain of mitochondrial calcium uptake. We identify 89 high-confidence interactors that link MCUC to several mitochondrial complexes and pathways, half of which are associated with human disease. As a proof-of-concept, we validate the mitochondrial intermembrane space protein EFHD1 as a binding partner of the MCUC subunits MCU, EMRE, and MCUB. We further show a MICU1-dependent inhibitory effect of EFHD1 on calcium uptake. Next, we systematically survey compensatory mechanisms and functional consequences of mitochondrial calcium dyshomeostasis by analyzing the MCU interactome upon EMRE, MCUB, MICU1, or MICU2 knockdown. While silencing EMRE reduces MCU interconnectivity, MCUB loss-of-function leads to a wider interaction network. Our study provides a comprehensive and high-confidence resource to gain insights into players and mechanisms regulating mitochondrial calcium signaling and their relevance in human diseases.
{"title":"Systematic mapping of mitochondrial calcium uniporter channel (MCUC)-mediated calcium signaling networks.","authors":"Hilda Delgado de la Herran,Denis Vecellio Reane,Yiming Cheng,Máté Katona,Fabian Hosp,Elisa Greotti,Jennifer Wettmarshausen,Maria Patron,Hermine Mohr,Natalia Prudente de Mello,Margarita Chudenkova,Matteo Gorza,Safal Walia,Michael Sheng-Fu Feng,Anja Leimpek,Dirk Mielenz,Natalia S Pellegata,Thomas Langer,György Hajnóczky,Matthias Mann,Marta Murgia,Fabiana Perocchi","doi":"10.1038/s44318-024-00219-w","DOIUrl":"https://doi.org/10.1038/s44318-024-00219-w","url":null,"abstract":"The mitochondrial calcium uniporter channel (MCUC) mediates mitochondrial calcium entry, regulating energy metabolism and cell death. Although several MCUC components have been identified, the molecular basis of mitochondrial calcium signaling networks and their remodeling upon changes in uniporter activity have not been assessed. Here, we map the MCUC interactome under resting conditions and upon chronic loss or gain of mitochondrial calcium uptake. We identify 89 high-confidence interactors that link MCUC to several mitochondrial complexes and pathways, half of which are associated with human disease. As a proof-of-concept, we validate the mitochondrial intermembrane space protein EFHD1 as a binding partner of the MCUC subunits MCU, EMRE, and MCUB. We further show a MICU1-dependent inhibitory effect of EFHD1 on calcium uptake. Next, we systematically survey compensatory mechanisms and functional consequences of mitochondrial calcium dyshomeostasis by analyzing the MCU interactome upon EMRE, MCUB, MICU1, or MICU2 knockdown. While silencing EMRE reduces MCU interconnectivity, MCUB loss-of-function leads to a wider interaction network. Our study provides a comprehensive and high-confidence resource to gain insights into players and mechanisms regulating mitochondrial calcium signaling and their relevance in human diseases.","PeriodicalId":501009,"journal":{"name":"The EMBO Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.1038/s44318-024-00220-3
Jia-Wei Shi,Zhen-Zhen Lai,Wen-Jie Zhou,Hui-Li Yang,Tao Zhang,Jian-Song Sun,Jian-Yuan Zhao,Ming-Qing Li
In preparation for a potential pregnancy, the endometrium of the uterus changes into a temporary structure called the decidua. Senescent decidual stromal cells (DSCs) are enriched in the decidua during decidualization, but the underlying mechanisms of this process remain unclear. Here, we performed single-cell RNA transcriptomics on ESCs and DSCs and found that cell senescence during decidualization is accompanied by increased levels of the branched-chain amino acid (BCAA) transporter SLC3A2. Depletion of leucine, one of the branched-chain amino acids, from cultured media decreased senescence, while high leucine diet resulted in increased senescence and high rates of embryo loss in mice. BCAAs induced senescence in DSCs via the p38 MAPK pathway. In contrast, TNFSF14+ decidual natural killer (dNK) cells were found to inhibit DSC senescence by interacting with its ligand TNFRSF14. As in mice fed high-leucine diets, both mice with NK cell depletion and Tnfrsf14-deficient mice with excessive uterine senescence experienced adverse pregnancy outcomes. Further, we found excessive uterine senescence, SLC3A2-mediated BCAA intake, and insufficient TNFRSF14 expression in the decidua of patients with recurrent spontaneous abortion. In summary, this study suggests that dNK cells maintain senescence homeostasis of DSCs via TNFSF14/TNFRSF14, providing a potential therapeutic strategy to prevent DSC senescence-associated spontaneous abortion.
{"title":"TNFSF14+ natural killer cells prevent spontaneous abortion by restricting leucine-mediated decidual stromal cell senescence.","authors":"Jia-Wei Shi,Zhen-Zhen Lai,Wen-Jie Zhou,Hui-Li Yang,Tao Zhang,Jian-Song Sun,Jian-Yuan Zhao,Ming-Qing Li","doi":"10.1038/s44318-024-00220-3","DOIUrl":"https://doi.org/10.1038/s44318-024-00220-3","url":null,"abstract":"In preparation for a potential pregnancy, the endometrium of the uterus changes into a temporary structure called the decidua. Senescent decidual stromal cells (DSCs) are enriched in the decidua during decidualization, but the underlying mechanisms of this process remain unclear. Here, we performed single-cell RNA transcriptomics on ESCs and DSCs and found that cell senescence during decidualization is accompanied by increased levels of the branched-chain amino acid (BCAA) transporter SLC3A2. Depletion of leucine, one of the branched-chain amino acids, from cultured media decreased senescence, while high leucine diet resulted in increased senescence and high rates of embryo loss in mice. BCAAs induced senescence in DSCs via the p38 MAPK pathway. In contrast, TNFSF14+ decidual natural killer (dNK) cells were found to inhibit DSC senescence by interacting with its ligand TNFRSF14. As in mice fed high-leucine diets, both mice with NK cell depletion and Tnfrsf14-deficient mice with excessive uterine senescence experienced adverse pregnancy outcomes. Further, we found excessive uterine senescence, SLC3A2-mediated BCAA intake, and insufficient TNFRSF14 expression in the decidua of patients with recurrent spontaneous abortion. In summary, this study suggests that dNK cells maintain senescence homeostasis of DSCs via TNFSF14/TNFRSF14, providing a potential therapeutic strategy to prevent DSC senescence-associated spontaneous abortion.","PeriodicalId":501009,"journal":{"name":"The EMBO Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, the oxylipin nitrogen signaling factor (NSF) is part of such communication system, which functions to regulate the usage of different nitrogen sources. Yet, the pathways and mechanisms by which NSF acts are poorly understood. Here, we show that NSF physically interacts with the mitochondrial sulfide:quinone oxidoreductase Hmt2 and that it prompts a change from a fermentation- to a respiration-like gene expression program without any change in the carbon source. Our results suggest that NSF activity is not restricted to nitrogen metabolism alone and that it could function as a rheostat to prepare a population of S. pombe cells for an imminent shortage of their preferred nutrients.
微生物进化出了复杂的通讯系统，使群体中的单个细胞能够发送和接收信号，以应对直接环境的变化。在裂殖酵母Schizosaccharomyces pombe中，氧脂素氮信号因子（NSF）就是这种通讯系统的一部分，其功能是调节不同氮源的使用。然而，人们对NSF发挥作用的途径和机制知之甚少。在这里，我们发现 NSF 与线粒体硫化物：醌氧化还原酶 Hmt2 发生了物理作用，并在碳源不变的情况下促使基因表达程序从发酵模式转变为呼吸模式。我们的研究结果表明，NSF 的活性并不局限于氮代谢，它还可以作为一种流变调节器，使 S. pombe 细胞群为即将出现的首选营养物质短缺做好准备。
{"title":"Nitrogen signaling factor triggers a respiration-like gene expression program in fission yeast.","authors":"Shin Ohsawa,Michaela Schwaiger,Vytautas Iesmantavicius,Rio Hashimoto,Hiromitsu Moriyama,Hiroaki Matoba,Go Hirai,Mikiko Sodeoka,Atsushi Hashimoto,Akihisa Matsuyama,Minoru Yoshida,Yoko Yashiroda,Marc Bühler","doi":"10.1038/s44318-024-00224-z","DOIUrl":"https://doi.org/10.1038/s44318-024-00224-z","url":null,"abstract":"Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, the oxylipin nitrogen signaling factor (NSF) is part of such communication system, which functions to regulate the usage of different nitrogen sources. Yet, the pathways and mechanisms by which NSF acts are poorly understood. Here, we show that NSF physically interacts with the mitochondrial sulfide:quinone oxidoreductase Hmt2 and that it prompts a change from a fermentation- to a respiration-like gene expression program without any change in the carbon source. Our results suggest that NSF activity is not restricted to nitrogen metabolism alone and that it could function as a rheostat to prepare a population of S. pombe cells for an imminent shortage of their preferred nutrients.","PeriodicalId":501009,"journal":{"name":"The EMBO Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Phosphorylation is a key post-translational modification regulating protein function and biological outcomes. However, the phosphorylation dynamics orchestrating mammalian oocyte development remains poorly understood. In the present study, we apply high-resolution mass spectrometry-based phosphoproteomics to obtain the first global in vivo quantification of mouse oocyte phosphorylation. Of more than 8000 phosphosites, 75% significantly oscillate and 64% exhibit marked upregulation during meiotic maturation, indicative of the dominant regulatory role. Moreover, we identify numerous novel phosphosites on oocyte proteins and a few highly conserved phosphosites in oocytes from different species. Through functional perturbations, we demonstrate that phosphorylation status of specific sites participates in modulating critical events including metabolism, translation, and RNA processing during meiosis. Finally, we combine inhibitor screening and enzyme-substrate network prediction to discover previously unexplored kinases and phosphatases that are essential for oocyte maturation. In sum, our data define landscape of the oocyte phosphoproteome, enabling in-depth mechanistic insights into developmental control of germ cells.
{"title":"The global phosphorylation landscape of mouse oocytes during meiotic maturation.","authors":"Hongzheng Sun,Longsen Han,Yueshuai Guo,Huiqing An,Bing Wang,Xiangzheng Zhang,Jiashuo Li,Yingtong Jiang,Yue Wang,Guangyi Sun,Shuai Zhu,Shoubin Tang,Juan Ge,Minjian Chen,Xuejiang Guo,Qiang Wang","doi":"10.1038/s44318-024-00222-1","DOIUrl":"https://doi.org/10.1038/s44318-024-00222-1","url":null,"abstract":"Phosphorylation is a key post-translational modification regulating protein function and biological outcomes. However, the phosphorylation dynamics orchestrating mammalian oocyte development remains poorly understood. In the present study, we apply high-resolution mass spectrometry-based phosphoproteomics to obtain the first global in vivo quantification of mouse oocyte phosphorylation. Of more than 8000 phosphosites, 75% significantly oscillate and 64% exhibit marked upregulation during meiotic maturation, indicative of the dominant regulatory role. Moreover, we identify numerous novel phosphosites on oocyte proteins and a few highly conserved phosphosites in oocytes from different species. Through functional perturbations, we demonstrate that phosphorylation status of specific sites participates in modulating critical events including metabolism, translation, and RNA processing during meiosis. Finally, we combine inhibitor screening and enzyme-substrate network prediction to discover previously unexplored kinases and phosphatases that are essential for oocyte maturation. In sum, our data define landscape of the oocyte phosphoproteome, enabling in-depth mechanistic insights into developmental control of germ cells.","PeriodicalId":501009,"journal":{"name":"The EMBO Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Cas3 nuclease is utilized by canonical type I CRISPR-Cas systems for processive target DNA degradation, while a newly identified type I-F CRISPR variant employs an HNH nuclease domain from the natural fusion Cas8-HNH protein for precise target cleavage both in vitro and in human cells. Here, we report multiple cryo-electron microscopy structures of the type I-F Cas8-HNH system at different functional states. The Cas8-HNH Cascade complex adopts an overall G-shaped architecture, with the HNH domain occupying the C-terminal helical bundle domain (HB) of the Cas8 protein in canonical type I systems. The Linker region connecting Cas8-NTD and HNH domains adopts a rigid conformation and interacts with the Cas7.6 subunit, enabling the HNH domain to be in a functional position. The full R-loop formation displaces the HNH domain away from the Cas6 subunit, thus activating the target DNA cleavage. Importantly, our results demonstrate that precise target cleavage is dictated by a C-terminal helix of the HNH domain. Together, our work not only delineates the structural basis for target recognition and activation of the type I-F Cas8-HNH system, but also guides further developments leveraging this system for precise DNA editing.
典型的 I 型 CRISPR-Cas 系统利用 Cas3 核酸酶对目标 DNA 进行过程性降解，而新发现的 I-F 型 CRISPR 变体则利用来自天然融合 Cas8-HNH 蛋白的 HNH 核酸酶结构域，在体外和人体细胞中进行精确的目标切割。在这里，我们报告了 I-F 型 Cas8-HNH 系统在不同功能状态下的多个冷冻电镜结构。Cas8-HNH 级联复合物采用整体 G 型结构，在典型的 I 型系统中，HNH 结构域占据 Cas8 蛋白的 C 端螺旋束结构域（HB）。连接 Cas8-NTD 和 HNH 结构域的 Linker 区域采用刚性构象，并与 Cas7.6 亚基相互作用，使 HNH 结构域处于功能性位置。全 R 环的形成使 HNH 结构域远离 Cas6 亚基，从而激活了目标 DNA 的切割。重要的是，我们的研究结果表明，精确的目标切割是由 HNH 结构域的 C 端螺旋决定的。总之，我们的研究工作不仅阐明了 I-F 型 Cas8-HNH 系统识别和激活靶标的结构基础，还为利用该系统进行精确 DNA 编辑的进一步开发提供了指导。
{"title":"Structural basis for the type I-F Cas8-HNH system.","authors":"Xuzichao Li,Yanan Liu,Jie Han,Lingling Zhang,Zhikun Liu,Lin Wang,Shuqin Zhang,Qian Zhang,Pengyu Fu,Hang Yin,Hongtao Zhu,Heng Zhang","doi":"10.1038/s44318-024-00229-8","DOIUrl":"https://doi.org/10.1038/s44318-024-00229-8","url":null,"abstract":"The Cas3 nuclease is utilized by canonical type I CRISPR-Cas systems for processive target DNA degradation, while a newly identified type I-F CRISPR variant employs an HNH nuclease domain from the natural fusion Cas8-HNH protein for precise target cleavage both in vitro and in human cells. Here, we report multiple cryo-electron microscopy structures of the type I-F Cas8-HNH system at different functional states. The Cas8-HNH Cascade complex adopts an overall G-shaped architecture, with the HNH domain occupying the C-terminal helical bundle domain (HB) of the Cas8 protein in canonical type I systems. The Linker region connecting Cas8-NTD and HNH domains adopts a rigid conformation and interacts with the Cas7.6 subunit, enabling the HNH domain to be in a functional position. The full R-loop formation displaces the HNH domain away from the Cas6 subunit, thus activating the target DNA cleavage. Importantly, our results demonstrate that precise target cleavage is dictated by a C-terminal helix of the HNH domain. Together, our work not only delineates the structural basis for target recognition and activation of the type I-F Cas8-HNH system, but also guides further developments leveraging this system for precise DNA editing.","PeriodicalId":501009,"journal":{"name":"The EMBO Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-19DOI: 10.1038/s44318-023-00017-w
Liyang Du, Qinwei Zhu, Zhonghui Lin
{"title":"Molecular mechanism of allosteric activation of the CRISPR ribonuclease Csm6 by cyclic tetra-adenylate","authors":"Liyang Du, Qinwei Zhu, Zhonghui Lin","doi":"10.1038/s44318-023-00017-w","DOIUrl":"https://doi.org/10.1038/s44318-023-00017-w","url":null,"abstract":"","PeriodicalId":501009,"journal":{"name":"The EMBO Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138961884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-15DOI: 10.1038/s44318-023-00006-z
Jose M Delgado, Logan Wallace Shepard, Sarah W Lamson, Samantha L Liu, Christopher J Shoemaker
{"title":"The ER membrane protein complex restricts mitophagy by controlling BNIP3 turnover","authors":"Jose M Delgado, Logan Wallace Shepard, Sarah W Lamson, Samantha L Liu, Christopher J Shoemaker","doi":"10.1038/s44318-023-00006-z","DOIUrl":"https://doi.org/10.1038/s44318-023-00006-z","url":null,"abstract":"","PeriodicalId":501009,"journal":{"name":"The EMBO Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138996844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-15DOI: 10.1038/s44318-023-00004-1
Joel A. Crossley, W. Allen, Daniel W. Watkins, T. Sabir, S. Radford, Roman Tuma, I. Collinson, Tomas Fessl
{"title":"Dynamic coupling of fast channel gating with slow ATP-turnover underpins protein transport through the Sec translocon","authors":"Joel A. Crossley, W. Allen, Daniel W. Watkins, T. Sabir, S. Radford, Roman Tuma, I. Collinson, Tomas Fessl","doi":"10.1038/s44318-023-00004-1","DOIUrl":"https://doi.org/10.1038/s44318-023-00004-1","url":null,"abstract":"","PeriodicalId":501009,"journal":{"name":"The EMBO Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139000975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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