Cell Research最新文献

{"title":"Body–brain axis: orchestrating immune responses","authors":"Leon Hosang, Alexander Flügel, Francesca Odoardi","doi":"10.1038/s41422-024-01004-4","DOIUrl":"10.1038/s41422-024-01004-4","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 11","pages":"757-758"},"PeriodicalIF":28.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01004-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141626192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural basis of tethered agonism and G protein coupling of protease-activated receptors","authors":"Jia Guo, Yun-Li Zhou, Yixin Yang, Shimeng Guo, Erli You, Xin Xie, Yi Jiang, Chunyou Mao, H. Eric Xu, Yan Zhang","doi":"10.1038/s41422-024-00997-2","DOIUrl":"10.1038/s41422-024-00997-2","url":null,"abstract":"Protease-activated receptors (PARs) are a unique group within the G protein-coupled receptor superfamily, orchestrating cellular responses to extracellular proteases via enzymatic cleavage, which triggers intracellular signaling pathways. Protease-activated receptor 1 (PAR1) is a key member of this family and is recognized as a critical pharmacological target for managing thrombotic disorders. In this study, we present cryo-electron microscopy structures of PAR1 in its activated state, induced by its natural tethered agonist (TA), in complex with two distinct downstream proteins, the Gq and Gi heterotrimers, respectively. The TA peptide is positioned within a surface pocket, prompting PAR1 activation through notable conformational shifts. Contrary to the typical receptor activation that involves the outward movement of transmembrane helix 6 (TM6), PAR1 activation is characterized by the simultaneous downward shift of TM6 and TM7, coupled with the rotation of a group of aromatic residues. This results in the displacement of an intracellular anion, creating space for downstream G protein binding. Our findings delineate the TA recognition pattern and highlight a distinct role of the second extracellular loop in forming β-sheets with TA within the PAR family, a feature not observed in other TA-activated receptors. Moreover, the nuanced differences in the interactions between intracellular loops 2/3 and the Gα subunit of different G proteins are crucial for determining the specificity of G protein coupling. These insights contribute to our understanding of the ligand binding and activation mechanisms of PARs, illuminating the basis for PAR1’s versatility in G protein coupling.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 10","pages":"725-734"},"PeriodicalIF":28.1,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00997-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141597399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Perenniality: the tale of three MADS-box genes","authors":"Zheng Li, Ruichen Ma, Rishikesh P. Bhalerao","doi":"10.1038/s41422-024-01001-7","DOIUrl":"10.1038/s41422-024-01001-7","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 11","pages":"753-754"},"PeriodicalIF":28.1,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01001-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141584240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Zero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering","authors":"Peng Cheng, Cong Mao, Jin Tang, Sen Yang, Yu Cheng, Wuke Wang, Qiuxi Gu, Wei Han, Hao Chen, Sihan Li, Yaofeng Chen, Jianglin Zhou, Wuju Li, Aimin Pan, Suwen Zhao, Xingxu Huang, Shiqiang Zhu, Jun Zhang, Wenjie Shu, Shengqi Wang","doi":"10.1038/s41422-024-00989-2","DOIUrl":"10.1038/s41422-024-00989-2","url":null,"abstract":"Mutations in amino acid sequences can provoke changes in protein function. Accurate and unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but remains a fundamental challenge. To resolve this challenge, here we present Protein Mutational Effect Predictor (ProMEP), a general and multiple sequence alignment-free method that enables zero-shot prediction of mutation effects. A multimodal deep representation learning model embedded in ProMEP was developed to comprehensively learn both sequence and structure contexts from ~160 million proteins. ProMEP achieves state-of-the-art performance in mutational effect prediction and accomplishes a tremendous improvement in speed, enabling efficient and intelligent protein engineering. Specifically, ProMEP accurately forecasts mutational consequences on the gene-editing enzymes TnpB and TadA, and successfully guides the development of high-performance gene-editing tools with their engineered variants. The gene-editing efficiency of a 5-site mutant of TnpB reaches up to 74.04% (vs 24.66% for the wild type); and the base editing tool developed on the basis of a TadA 15-site mutant (in addition to the A106V/D108N double mutation that renders deoxyadenosine deaminase activity to TadA) exhibits an A-to-G conversion frequency of up to 77.27% (vs 69.80% for ABE8e, a previous TadA-based adenine base editor) with significantly reduced bystander and off-target effects compared to ABE8e. ProMEP not only showcases superior performance in predicting mutational effects on proteins but also demonstrates a great capability to guide protein engineering. Therefore, ProMEP enables efficient exploration of the gigantic protein space and facilitates practical design of proteins, thereby advancing studies in biomedicine and synthetic biology.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 9","pages":"630-647"},"PeriodicalIF":28.1,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00989-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141537604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bitter taste receptor TAS2R14 activation and G protein assembly by an intracellular agonist","authors":"Lele Tao, Dongxue Wang, Qingning Yuan, Fenghui Zhao, Yu Zhang, Tianyuan Du, Shiyi Shen, H. Eric Xu, Yi Li, Dehua Yang, Jia Duan","doi":"10.1038/s41422-024-00995-4","DOIUrl":"10.1038/s41422-024-00995-4","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 10","pages":"735-738"},"PeriodicalIF":28.1,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141537603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular insights into the inhibition of proton-activated chloride channel by transfer RNA","authors":"Pengliang Chi, Xiang Wang, Jialu Li, Hui Yang, Kaiju Li, Yuqi Zhang, Shiyi Lin, Leiye Yu, Shiqi Liu, Lu Chen, Ruobing Ren, Jianping Wu, Zhuo Huang, Jia Geng, Dong Deng","doi":"10.1038/s41422-024-00993-6","DOIUrl":"10.1038/s41422-024-00993-6","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 10","pages":"743-745"},"PeriodicalIF":28.1,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141462371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Localized, highly efficient secretion of signaling proteins by migrasomes","authors":"Haifeng Jiao, Xiaopeng Li, Ying Li, Yuting Guo, Xiaoyu Hu, Takami Sho, Yiqun Luo, Jinyu Wang, Huizhen Cao, Wanqing Du, Dong Li, Li Yu","doi":"10.1038/s41422-024-00992-7","DOIUrl":"10.1038/s41422-024-00992-7","url":null,"abstract":"Migrasomes, enriched with signaling molecules such as chemokines, cytokines and angiogenic factors, play a pivotal role in the spatially defined delivery of these molecules, influencing critical physiological processes including organ morphogenesis and angiogenesis. The mechanism governing the accumulation of signaling molecules in migrasomes has been elusive. In this study, we show that secretory proteins, including signaling proteins, are transported into migrasomes by secretory carriers via both the constitutive and regulated secretion pathways. During cell migration, a substantial portion of these carriers is redirected to the rear of the cell and actively transported into migrasomes, driven by the actin-dependent motor protein Myosin-5a. Once at the migrasomes, these carriers fuse with the migrasome membrane through SNARE-mediated mechanisms. Inhibiting migrasome formation significantly reduces secretion, suggesting migrasomes as a principal secretion route in migrating cells. Our findings reveal a specialized, highly localized secretion paradigm in migrating cells, conceptually paralleling the targeted neurotransmitter release observed in neuronal systems.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 8","pages":"572-585"},"PeriodicalIF":28.1,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00992-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141448159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ANT2: the first mammalian mitochondrial RNA transport translocon","authors":"Huanhuan Zhu, Weiqiang Lin, Aifu Lin","doi":"10.1038/s41422-024-00994-5","DOIUrl":"10.1038/s41422-024-00994-5","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 8","pages":"535-536"},"PeriodicalIF":28.1,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00994-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141444761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combination therapy of KRAS G12V mRNA vaccine and pembrolizumab: clinical benefit in patients with advanced solid tumors","authors":"Xinjing Wang, Wei Wang, Siyi Zou, Zhiwei Xu, Dan Cao, Shuai Zhang, Minzhi Wei, Qian Zhan, Chenlei Wen, Fanlu Li, Hao Chen, Da Fu, Lingxi Jiang, Ming Zhao, Baiyong Shen","doi":"10.1038/s41422-024-00990-9","DOIUrl":"10.1038/s41422-024-00990-9","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 9","pages":"661-664"},"PeriodicalIF":28.1,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00990-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AMPK targets PDZD8 to trigger carbon source shift from glucose to glutamine","authors":"Mengqi Li, Yu Wang, Xiaoyan Wei, Wei-Feng Cai, Jianfeng Wu, Mingxia Zhu, Yongliang Wang, Yan-Hui Liu, Jinye Xiong, Qi Qu, Yan Chen, Xiao Tian, Luming Yao, Renxiang Xie, Xiaomin Li, Siwei Chen, Xi Huang, Cixiong Zhang, Changchuan Xie, Yaying Wu, Zheni Xu, Baoding Zhang, Bin Jiang, Zhi-Chao Wang, Qinxi Li, Gang Li, Shu-Yong Lin, Li Yu, Hai-Long Piao, Xianming Deng, Jiahuai Han, Chen-Song Zhang, Sheng-Cai Lin","doi":"10.1038/s41422-024-00985-6","DOIUrl":"10.1038/s41422-024-00985-6","url":null,"abstract":"The shift of carbon utilization from primarily glucose to other nutrients is a fundamental metabolic adaptation to cope with decreased blood glucose levels and the consequent decline in glucose oxidation. AMP-activated protein kinase (AMPK) plays crucial roles in this metabolic adaptation. However, the underlying mechanism is not fully understood. Here, we show that PDZ domain containing 8 (PDZD8), which we identify as a new substrate of AMPK activated in low glucose, is required for the low glucose-promoted glutaminolysis. AMPK phosphorylates PDZD8 at threonine 527 (T527) and promotes the interaction of PDZD8 with and activation of glutaminase 1 (GLS1), a rate-limiting enzyme of glutaminolysis. In vivo, the AMPK-PDZD8-GLS1 axis is required for the enhancement of glutaminolysis as tested in the skeletal muscle tissues, which occurs earlier than the increase in fatty acid utilization during fasting. The enhanced glutaminolysis is also observed in macrophages in low glucose or under acute lipopolysaccharide (LPS) treatment. Consistent with a requirement of heightened glutaminolysis, the PDZD8-T527A mutation dampens the secretion of pro-inflammatory cytokines in macrophages in mice treated with LPS. Together, we have revealed an AMPK-PDZD8-GLS1 axis that promotes glutaminolysis ahead of increased fatty acid utilization under glucose shortage.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 10","pages":"683-706"},"PeriodicalIF":28.1,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00985-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}