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An Arabidopsis single-nucleus atlas decodes leaf senescence and nutrient allocation
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-11 DOI: 10.1016/j.cell.2025.03.024
Xing Guo, Yichuan Wang, Caiyao Zhao, Cong Tan, Wei Yan, Sunhuan Xiang, Dan Zhang, Hui Zhang, Mengting Zhang, Liujing Yang, Meng Yan, Pingli Xie, Yi Wang, Li Li, Dongming Fang, Xuanmin Guang, Wenwen Shao, Fang Wang, Haoxuan Wang, Sunil Kumar Sahu, Xun Xu
{"title":"An Arabidopsis single-nucleus atlas decodes leaf senescence and nutrient allocation","authors":"Xing Guo, Yichuan Wang, Caiyao Zhao, Cong Tan, Wei Yan, Sunhuan Xiang, Dan Zhang, Hui Zhang, Mengting Zhang, Liujing Yang, Meng Yan, Pingli Xie, Yi Wang, Li Li, Dongming Fang, Xuanmin Guang, Wenwen Shao, Fang Wang, Haoxuan Wang, Sunil Kumar Sahu, Xun Xu","doi":"10.1016/j.cell.2025.03.024","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.024","url":null,"abstract":"With rapid advancements in single-cell RNA sequencing (scRNA-seq) technologies, exploration of the systemic coordination of critical physiological processes has entered a new era. Here, we generated a comprehensive <em>Arabidopsis</em> single-nucleus transcriptomic atlas using over 1 million nuclei from 20 tissues encompassing multiple developmental stages. Our analyses identified cell types that have not been characterized in previous single-protoplast studies and revealed cell-type conservation and specificity across different organs. Through time-resolved sampling, we revealed highly coordinated onset and progression of senescence among the major leaf cell types. We originally formulated two molecular indexes to quantify the aging state of leaf cells at single-cell resolution. Additionally, facilitated by weighted gene co-expression network analysis, we identified hundreds of promising hub genes that may integratively regulate leaf senescence. Inspired by the functional validation of identified hub genes, we built a systemic scenario of carbon and nitrogen allocation among different cell types from source leaves to sink organs.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"108 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143820087","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}
引用次数: 0
Extracellular respiration is a latent energy metabolism in Escherichia coli
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-10 DOI: 10.1016/j.cell.2025.03.016
Biki Bapi Kundu, Jayanth Krishnan, Richard Szubin, Arjun Patel, Bernhard O. Palsson, Daniel C. Zielinski, Caroline M. Ajo-Franklin
{"title":"Extracellular respiration is a latent energy metabolism in Escherichia coli","authors":"Biki Bapi Kundu, Jayanth Krishnan, Richard Szubin, Arjun Patel, Bernhard O. Palsson, Daniel C. Zielinski, Caroline M. Ajo-Franklin","doi":"10.1016/j.cell.2025.03.016","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.016","url":null,"abstract":"Diverse microbes utilize redox shuttles to exchange electrons with their environment through mediated extracellular electron transfer (EET), supporting anaerobic survival. Although mediated EET has been leveraged for bioelectrocatalysis for decades, fundamental questions remain about how these redox shuttles are reduced within cells and their role in cellular bioenergetics. Here, we integrate genome editing, electrochemistry, and systems biology to investigate the mechanism and bioenergetics of mediated EET in <em>Escherichia coli</em>, elusive for over two decades. In the absence of alternative electron sinks, the redox cycling of 2-hydroxy-1,4-naphthoquinone (HNQ) via the cytoplasmic nitroreductases NfsB and NfsA enables <em>E. coli</em> respiration on an extracellular electrode. <em>E. coli</em> also exhibits rapid genetic adaptation in the outer membrane porin OmpC, enhancing HNQ-mediated EET levels coupled to growth. This work demonstrates that <em>E. coli</em> can grow independently of classic electron transport chains and fermentation, unveiling a potentially widespread new type of anaerobic energy metabolism.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"34 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143814058","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}
引用次数: 0
Human proteome distribution atlas for tissue-specific plasma proteome dynamics
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-08 DOI: 10.1016/j.cell.2025.03.013
Erik Malmström, Lars Malmström, Simon Hauri, Tirthankar Mohanty, Aaron Scott, Christofer Karlsson, Carlos Gueto-Tettay, Emma Åhrman, Shahab Nozohoor, Bobby Tingstedt, Sara Regner, Peter Elfving, Leif Bjermer, Andreas Forsvall, Alexander Doyle, Mattias Magnusson, Ingrid Hedenfalk, Päivi Kannisto, Christian Brandt, Emma Nilsson, Johan Malmström
{"title":"Human proteome distribution atlas for tissue-specific plasma proteome dynamics","authors":"Erik Malmström, Lars Malmström, Simon Hauri, Tirthankar Mohanty, Aaron Scott, Christofer Karlsson, Carlos Gueto-Tettay, Emma Åhrman, Shahab Nozohoor, Bobby Tingstedt, Sara Regner, Peter Elfving, Leif Bjermer, Andreas Forsvall, Alexander Doyle, Mattias Magnusson, Ingrid Hedenfalk, Päivi Kannisto, Christian Brandt, Emma Nilsson, Johan Malmström","doi":"10.1016/j.cell.2025.03.013","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.013","url":null,"abstract":"The plasma proteome is maintained by the influx and efflux of proteins from surrounding organs and cells. To quantify the extent to which different organs and cells impact the plasma proteome in healthy and diseased conditions, we developed a mass-spectrometry-based proteomics strategy to infer the tissue origin of proteins detected in human plasma. We first constructed an extensive human proteome atlas from 18 vascularized organs and the 8 most abundant cell types in blood. The atlas was interfaced with previous RNA and protein atlases to objectively define proteome-wide protein-organ associations to infer the origin and enable the reproducible quantification of organ-specific proteins in plasma. We demonstrate that the resource can determine disease-specific quantitative changes of organ-enriched protein panels in six separate patient cohorts, including sepsis, pancreatitis, and myocardial injury. The strategy can be extended to other diseases to advance our understanding of the processes contributing to plasma proteome dynamics.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"21 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143797999","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}
引用次数: 0
Autoimmune mechanisms elucidated through muscle acetylcholine receptor structures
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-08 DOI: 10.1016/j.cell.2025.03.004
Huanhuan Li, Minh C. Pham, Jinfeng Teng, Kevin C. O’Connor, Colleen M. Noviello, Ryan E. Hibbs
{"title":"Autoimmune mechanisms elucidated through muscle acetylcholine receptor structures","authors":"Huanhuan Li, Minh C. Pham, Jinfeng Teng, Kevin C. O’Connor, Colleen M. Noviello, Ryan E. Hibbs","doi":"10.1016/j.cell.2025.03.004","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.004","url":null,"abstract":"Skeletal muscle contraction is triggered by acetylcholine (ACh) binding to its ionotropic receptors (AChRs) at neuromuscular junctions. In myasthenia gravis (MG), autoantibodies target AChRs, disrupting neurotransmission and causing muscle weakness. While treatments exist, variable patient responses suggest pathogenic heterogeneity. Progress in understanding the molecular basis of MG has been limited by the absence of structures of intact human muscle AChRs. Here, we present high-resolution cryoelectron microscopy (cryo-EM) structures of the human adult AChR in different functional states. Using six MG patient-derived monoclonal antibodies, we mapped distinct epitopes involved in diverse pathogenic mechanisms, including receptor blockade, internalization, and complement activation. Electrophysiological and binding assays revealed how these autoantibodies directly inhibit AChR channel activation. These findings provide critical insights into MG immunopathogenesis, uncovering unrecognized antibody epitope diversity and modes of receptor inhibition, and provide a framework for developing personalized therapies targeting antibody-mediated autoimmune disorders.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"32 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143798001","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}
引用次数: 0
Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-08 DOI: 10.1016/j.cell.2025.03.012
Xuelong Mi, Alex Bo-Yuan Chen, Daniela Duarte, Erin Carey, Charlotte R. Taylor, Philipp N. Braaker, Mark Bright, Rafael G. Almeida, Jing-Xuan Lim, Virginia M.S. Ruetten, Yizhi Wang, Mengfan Wang, Weizhan Zhang, Wei Zheng, Michael E. Reitman, Yongkang Huang, Xiaoyu Wang, Lei Li, HanFei Deng, Song-Hai Shi, Guoqiang Yu
{"title":"Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals","authors":"Xuelong Mi, Alex Bo-Yuan Chen, Daniela Duarte, Erin Carey, Charlotte R. Taylor, Philipp N. Braaker, Mark Bright, Rafael G. Almeida, Jing-Xuan Lim, Virginia M.S. Ruetten, Yizhi Wang, Mengfan Wang, Weizhan Zhang, Wei Zheng, Michael E. Reitman, Yongkang Huang, Xiaoyu Wang, Lei Li, HanFei Deng, Song-Hai Shi, Guoqiang Yu","doi":"10.1016/j.cell.2025.03.012","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.012","url":null,"abstract":"Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce activity quantification and analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine-learning techniques. It decomposes complex live-imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, microscopy techniques, and imaging approaches. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, as well as distinct sensorimotor signal propagation patterns in the mouse spinal cord.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"28 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143798000","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}
引用次数: 0
Quiescent cell re-entry is limited by macroautophagy-induced lysosomal damage
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-08 DOI: 10.1016/j.cell.2025.03.009
Andrew Murley, Ann Catherine Popovici, Xiwen Sophie Hu, Anina Lund, Kevin Wickham, Jenni Durieux, Larry Joe, Etai Koronyo, Hanlin Zhang, Naomi R. Genuth, Andrew Dillin
{"title":"Quiescent cell re-entry is limited by macroautophagy-induced lysosomal damage","authors":"Andrew Murley, Ann Catherine Popovici, Xiwen Sophie Hu, Anina Lund, Kevin Wickham, Jenni Durieux, Larry Joe, Etai Koronyo, Hanlin Zhang, Naomi R. Genuth, Andrew Dillin","doi":"10.1016/j.cell.2025.03.009","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.009","url":null,"abstract":"To maintain tissue homeostasis, many cells reside in a quiescent state until prompted to divide. The reactivation of quiescent cells is perturbed with aging and may underlie declining tissue homeostasis and resiliency. The unfolded protein response regulators IRE-1 and XBP-1 are required for the reactivation of quiescent cells in developmentally L1-arrested <em>C. elegans</em>. Utilizing a forward genetic screen in <em>C. elegans</em>, we discovered that macroautophagy targets protein aggregates to lysosomes in quiescent cells, leading to lysosome damage. Genetic inhibition of macroautophagy and stimulation of lysosomes via the overexpression of HLH-30 (TFEB/TFE3) synergistically reduces lysosome damage. Damaged lysosomes require IRE-1/XBP-1 for their repair following prolonged L1 arrest. Protein aggregates are also targeted to lysosomes by macroautophagy in quiescent cultured mammalian cells and are associated with lysosome damage. Thus, lysosome damage is a hallmark of quiescent cells, and limiting lysosome damage by restraining macroautophagy can stimulate their reactivation.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"183 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143798003","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}
引用次数: 0
Peripheral nervous system microglia-like cells regulate neuronal soma size throughout evolution
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-07 DOI: 10.1016/j.cell.2025.02.007
Zhisheng Wu, Yiheng Wang, Wei-wei Chen, Hua Sun, Xiaoyan Chen, Xiaobo Li, Zeshuai Wang, Weizheng Liang, Shuang-Yin Wang, Xuemei Luan, Yijiang Li, Shangjin Huang, Yuteng Liang, Jiaqi Zhang, Zhou-Feng Chen, Guanlin Wang, Yun Gao, Yanan Liu, Jun Wang, Zhen Liu, Hanjie Li
{"title":"Peripheral nervous system microglia-like cells regulate neuronal soma size throughout evolution","authors":"Zhisheng Wu, Yiheng Wang, Wei-wei Chen, Hua Sun, Xiaoyan Chen, Xiaobo Li, Zeshuai Wang, Weizheng Liang, Shuang-Yin Wang, Xuemei Luan, Yijiang Li, Shangjin Huang, Yuteng Liang, Jiaqi Zhang, Zhou-Feng Chen, Guanlin Wang, Yun Gao, Yanan Liu, Jun Wang, Zhen Liu, Hanjie Li","doi":"10.1016/j.cell.2025.02.007","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.007","url":null,"abstract":"Microglia, essential in the central nervous system (CNS), were historically considered absent from the peripheral nervous system (PNS). Here, we show a PNS-resident macrophage population that shares transcriptomic and epigenetic profiles as well as an ontogenetic trajectory with CNS microglia. This population (termed PNS microglia-like cells) enwraps the neuronal soma inside the satellite glial cell envelope, preferentially associates with larger neurons during PNS development, and is required for neuronal functions by regulating soma enlargement and axon growth. A phylogenetic survey of 24 vertebrates revealed an early origin of PNS microglia-like cells, whose presence is correlated with neuronal soma size (and body size) rather than evolutionary distance. Consistent with their requirement for soma enlargement, PNS microglia-like cells are maintained in vertebrates with large peripheral neuronal soma but absent when neurons evolve to have smaller soma. Our study thus reveals a PNS counterpart of CNS microglia that regulates neuronal soma size during both evolution and ontogeny.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"183 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789766","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}
引用次数: 0
Brain-wide mapping of immune receptors uncovers a neuromodulatory role of IL-17E and the receptor IL-17RB
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-07 DOI: 10.1016/j.cell.2025.03.006
Yunjin Lee, Tomoe Ishikawa, Hyeseung Lee, Byeongjun Lee, Changhyeon Ryu, Irene Davila Mejia, Minjin Kim, Guangqing Lu, Yujin Hong, Mengyang Feng, Hyeyoon Shin, Sylvain Meloche, Richard M. Locksley, Ekaterina Koltsova, Sergei I. Grivennikov, Myriam Heiman, Gloria B. Choi, Jun R. Huh
{"title":"Brain-wide mapping of immune receptors uncovers a neuromodulatory role of IL-17E and the receptor IL-17RB","authors":"Yunjin Lee, Tomoe Ishikawa, Hyeseung Lee, Byeongjun Lee, Changhyeon Ryu, Irene Davila Mejia, Minjin Kim, Guangqing Lu, Yujin Hong, Mengyang Feng, Hyeyoon Shin, Sylvain Meloche, Richard M. Locksley, Ekaterina Koltsova, Sergei I. Grivennikov, Myriam Heiman, Gloria B. Choi, Jun R. Huh","doi":"10.1016/j.cell.2025.03.006","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.006","url":null,"abstract":"Cytokines interact with their receptor complexes to orchestrate diverse processes—from immune responses to behavioral modulation. Interleukin-17A (IL-17A) mediates protective immune responses by binding to IL-17 receptor A (IL-17RA) and IL-17RC subunits. IL-17A also modulates social interaction, yet the role of cytokine receptors in this process and their expression in the brain remains poorly characterized. Here, we mapped the brain-region-specific expression of all major IL-17R subunits and found that in addition to IL-17RA, IL-17RB—but not IL-17RC—plays a role in social behaviors through its expression in the cortex. We further showed that IL-17E, expressed in cortical neurons, enhances social interaction by acting on IL-17RA- and IL-17RB-expressing neurons. These findings highlight an IL-17 circuit within the cortex that modulates social behaviors. Thus, characterizing spatially restricted cytokine receptor expression can be leveraged to elucidate how cytokines function as critical messengers mediating neuroimmune interactions to shape animal behaviors.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"20 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789991","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}
引用次数: 0
Inflammatory and anti-inflammatory cytokines bidirectionally modulate amygdala circuits regulating anxiety
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-07 DOI: 10.1016/j.cell.2025.03.005
Byeongjun Lee, Jeong-Tae Kwon, Yire Jeong, Hannah Caris, Dongsun Oh, Mengyang Feng, Irene Davila Mejia, Xiaoying Zhang, Tomoe Ishikawa, Brianna R. Watson, Jeffrey R. Moffitt, Kwanghun Chung, Jun R. Huh, Gloria B. Choi
{"title":"Inflammatory and anti-inflammatory cytokines bidirectionally modulate amygdala circuits regulating anxiety","authors":"Byeongjun Lee, Jeong-Tae Kwon, Yire Jeong, Hannah Caris, Dongsun Oh, Mengyang Feng, Irene Davila Mejia, Xiaoying Zhang, Tomoe Ishikawa, Brianna R. Watson, Jeffrey R. Moffitt, Kwanghun Chung, Jun R. Huh, Gloria B. Choi","doi":"10.1016/j.cell.2025.03.005","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.005","url":null,"abstract":"Patients with autoimmune or infectious diseases can develop persistent mood alterations after inflammatory episodes. Peripheral immune molecules, like cytokines, can influence behavioral and internal states, yet their impact on the function of specific neural circuits in the brain remains unclear. Here, we show that cytokines act as neuromodulators to regulate anxiety by engaging receptor-expressing neurons in the basolateral amygdala (BLA). Heightened interleukin-17A (IL-17A) and IL-17C levels, paradoxically induced from treatment with anti-IL-17 receptor A (IL-17RA) antibodies, promote anxiogenic behaviors by increasing the excitability of IL-17RA/RE-expressing BLA neurons. Conversely, the anti-inflammatory IL-10, acting on the same population of BLA neurons via its receptor, exerts opposite effects on neuronal excitability and behavior. These findings reveal that inflammatory and anti-inflammatory cytokines bidirectionally modulate anxiety by engaging their respective receptors in the same BLA population. Our results highlight the role of cytokine signaling in shaping internal states through direct modulation of specific neural substrates.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"37 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789810","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}
引用次数: 0
Conserved genetic basis for microbial colonization of the gut
IF 64.5 1区 生物学
Cell Pub Date : 2025-04-04 DOI: 10.1016/j.cell.2025.03.010
Menghan Liu, Sydney B. Blattman, Mai Takahashi, Nandan Mandayam, Wenyan Jiang, Panos Oikonomou, Sohail F. Tavazoie, Saeed Tavazoie
{"title":"Conserved genetic basis for microbial colonization of the gut","authors":"Menghan Liu, Sydney B. Blattman, Mai Takahashi, Nandan Mandayam, Wenyan Jiang, Panos Oikonomou, Sohail F. Tavazoie, Saeed Tavazoie","doi":"10.1016/j.cell.2025.03.010","DOIUrl":"https://doi.org/10.1016/j.cell.2025.03.010","url":null,"abstract":"Despite the fundamental importance of gut microbes, the genetic basis of their colonization remains largely unexplored. Here, by applying cross-species genotype-habitat association at the tree-of-life scale, we identify conserved microbial gene modules associated with gut colonization. Across thousands of species, we discovered 79 taxonomically diverse putative colonization factors organized into operonic and non-operonic modules. They include previously characterized colonization pathways such as autoinducer-2 biosynthesis and novel processes including tRNA modification and translation. <em>In vivo</em> functional validation revealed YigZ (IMPACT family) and tRNA hydroxylation protein-P (TrhP) are required for <em>E. coli</em> intestinal colonization. Overexpressing YigZ alone is sufficient to enhance colonization of the poorly colonizing MG1655 <em>E. coli</em> by &gt;100-fold. Moreover, natural allelic variations in YigZ impact inter-strain colonization efficiency. Our findings highlight the power of large-scale comparative genomics in revealing the genetic basis of microbial adaptations. These broadly conserved colonization factors may prove critical for understanding gastrointestinal (GI) dysbiosis and developing therapeutics.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"18 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143775930","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}
引用次数: 0
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