CellPub Date : 2025-03-10DOI: 10.1016/j.cell.2025.02.011
Nemanja Vukašinović, Che-Wei Hsu, Marco Marconi, Shaopeng Li, Christopher Zachary, Rachel Shahan, Pablo Szekley, Ziv Aardening, Isabelle Vanhoutte, Qian Ma, Lucrezia Pinto, Pavel Krupař, Nathan German, Jingyuan Zhang, Claire Simon--Vezo, Jessica Perez-Sancho, Pepe Cana Quijada, Qianzi Zhou, Laura R. Lee, Jianghua Cai, Eugenia Russinova
{"title":"Polarity-guided uneven mitotic divisions control brassinosteroid activity in proliferating plant root cells","authors":"Nemanja Vukašinović, Che-Wei Hsu, Marco Marconi, Shaopeng Li, Christopher Zachary, Rachel Shahan, Pablo Szekley, Ziv Aardening, Isabelle Vanhoutte, Qian Ma, Lucrezia Pinto, Pavel Krupař, Nathan German, Jingyuan Zhang, Claire Simon--Vezo, Jessica Perez-Sancho, Pepe Cana Quijada, Qianzi Zhou, Laura R. Lee, Jianghua Cai, Eugenia Russinova","doi":"10.1016/j.cell.2025.02.011","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.011","url":null,"abstract":"Brassinosteroid hormones are positive regulators of plant organ growth, yet their function in proliferating tissues remains unclear. Here, through integrating single-cell RNA sequencing with long-term live-cell imaging of the <em>Arabidopsis</em> root, we reveal that brassinosteroid activity fluctuates throughout the cell cycle, decreasing during mitotic divisions and increasing during the G1 phase. The post-mitotic recovery of brassinosteroid activity is driven by the intrinsic polarity of the mother cell, resulting in one daughter cell with enhanced brassinosteroid signaling, while the other supports brassinosteroid biosynthesis. The coexistence of these distinct daughter cell states during the G1 phase circumvents a negative feedback loop to facilitate brassinosteroid production while signaling increases. Our findings uncover polarity-guided, uneven mitotic divisions in the meristem, which control brassinosteroid hormone activity to ensure optimal root growth.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"38 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582602","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}
CellPub Date : 2025-03-07DOI: 10.1016/j.cell.2025.02.006
Tianxiong Yu, Michaela B.J. Blyton, Milky Abajorga, Birgit S. Koppetsch, Samantha Ho, Bo Xu, Zhongren Hu, Jeremy Luban, Keith Chappell, Zhiping Weng, William E. Theurkauf
{"title":"Evolution of KoRV-A transcriptional silencing in wild koalas","authors":"Tianxiong Yu, Michaela B.J. Blyton, Milky Abajorga, Birgit S. Koppetsch, Samantha Ho, Bo Xu, Zhongren Hu, Jeremy Luban, Keith Chappell, Zhiping Weng, William E. Theurkauf","doi":"10.1016/j.cell.2025.02.006","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.006","url":null,"abstract":"Koala retrovirus-A (KoRV-A) is spreading through wild koalas in a north-to-south wave while transducing the germ line, modifying the inherited genome as it transitions to an endogenous retrovirus. Previously, we found that KoRV-A is expressed in the germ line, but unspliced genomic transcripts are processed into sense-strand PIWI-interacting RNAs (piRNAs), which may provide an initial “innate” form of post-transcriptional silencing. Here, we show that this initial post-transcriptional response is prevalent south of the Brisbane River, whereas KoRV-A expression is suppressed, promoters are methylated, and sense and antisense piRNAs are equally abundant in a subpopulation of animals north of the river. These animals share a KoRV-A provirus in the <em>MAP4K4</em> gene’s 3′ UTR that is spreading through northern koalas and produces hybrid transcripts that are processed into antisense piRNAs, which guide transcriptional silencing. We speculate that this provirus triggers adaptive transcriptional silencing of KoRV-A and is sweeping to fixation.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"2 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569641","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}
CellPub Date : 2025-03-07DOI: 10.1016/j.cell.2025.01.045
Gavin A. Kuziel, Gabriel L. Lozano, Corina Simian, Long Li, John Manion, Emmanuel Stephen-Victor, Talal Chatila, Min Dong, Jing-Ke Weng, Seth Rakoff-Nahoum
{"title":"Functional diversification of dietary plant small molecules by the gut microbiome","authors":"Gavin A. Kuziel, Gabriel L. Lozano, Corina Simian, Long Li, John Manion, Emmanuel Stephen-Victor, Talal Chatila, Min Dong, Jing-Ke Weng, Seth Rakoff-Nahoum","doi":"10.1016/j.cell.2025.01.045","DOIUrl":"https://doi.org/10.1016/j.cell.2025.01.045","url":null,"abstract":"Plants are composed of diverse secondary metabolites (PSMs), which are widely associated with human health. Whether and how the gut microbiome mediates such impacts of PSMs is poorly understood. Here, we show that discrete dietary and medicinal phenolic glycosides, abundant health-associated PSMs, are utilized by distinct members of the human gut microbiome. Within the <em>Bacteroides</em>, the predominant gram-negative bacteria of the Western human gut, we reveal a specialized multi-enzyme system dedicated to the processing of distinct glycosides based on structural differences in phenolic moieties. This <em>Bacteroides</em> metabolic system liberates chemically distinct aglycones with diverse biological functions, such as colonization resistance against the gut pathogen <em>Clostridioides difficile</em> via anti-microbial activation of polydatin to the stilbene resveratrol and intestinal homeostasis via activation of salicin to the immunoregulatory aglycone saligenin. Together, our results demonstrate generation of biological diversity of phenolic aglycone “effector” functions by a distinct gut-microbiome-encoded PSM-processing system.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"17 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569642","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}
CellPub Date : 2025-03-06DOI: 10.1016/j.cell.2025.02.001
Nikhilesh Natraj, Sarah Seko, Reza Abiri, Runfeng Miao, Hongyi Yan, Yasmin Graham, Adelyn Tu-Chan, Edward F. Chang, Karunesh Ganguly
{"title":"Sampling representational plasticity of simple imagined movements across days enables long-term neuroprosthetic control","authors":"Nikhilesh Natraj, Sarah Seko, Reza Abiri, Runfeng Miao, Hongyi Yan, Yasmin Graham, Adelyn Tu-Chan, Edward F. Chang, Karunesh Ganguly","doi":"10.1016/j.cell.2025.02.001","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.001","url":null,"abstract":"The nervous system needs to balance the stability of neural representations with plasticity. It is unclear what the representational stability of simple well-rehearsed actions is, particularly in humans, and their adaptability to new contexts. Using an electrocorticography brain-computer interface (BCI) in tetraplegic participants, we found that the low-dimensional manifold and relative representational distances for a repertoire of simple imagined movements were remarkably stable. The manifold’s absolute location, however, demonstrated constrained day-to-day drift. Strikingly, neural statistics, especially variance, could be flexibly regulated to increase representational distances during BCI control without somatotopic changes. Discernability strengthened with practice and was BCI-specific, demonstrating contextual specificity. Sampling representational plasticity and drift across days subsequently uncovered a meta-representational structure with generalizable decision boundaries for the repertoire; this allowed long-term neuroprosthetic control of a robotic arm and hand for reaching and grasping. Our study offers insights into mesoscale representational statistics that also enable long-term complex neuroprosthetic control.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"16 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560864","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}
CellPub Date : 2025-03-06DOI: 10.1016/j.cell.2024.12.037
Xiang Xiao, Jian Wang, Kang Ding
{"title":"MEER: Extraordinary flourishing ecosystem in the deepest ocean","authors":"Xiang Xiao, Jian Wang, Kang Ding","doi":"10.1016/j.cell.2024.12.037","DOIUrl":"https://doi.org/10.1016/j.cell.2024.12.037","url":null,"abstract":"Here, we introduce the Mariana Trench Environment and Ecology Research (MEER) project, which provides the first systematic view of the ecosystem in the hadal zone.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"31 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560865","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":"Evolution and genetic adaptation of fishes to the deep sea","authors":"Han Xu, Chengchi Fang, Wenjie Xu, Cheng Wang, Yue Song, Chenglong Zhu, Wenyu Fang, Guangyi Fan, Wenqi Lv, Jing Bo, Honghui Zeng, Zhongli Sha, Helu Liu, Hongmei Jing, Hao Liu, Taoshu Wei, Jiwei Li, Lisheng He, Shanya Cai, Xiaoni Gan, Shunping He","doi":"10.1016/j.cell.2025.01.002","DOIUrl":"https://doi.org/10.1016/j.cell.2025.01.002","url":null,"abstract":"The deep sea, especially hadal zones, characterized by high-hydrostatic pressure, low temperatures, and near-total darkness, present some of the most challenging environments for life on Earth. However, teleost fish have successfully colonized these extreme habitats through complex adaptations. We generated genome assemblies of 12 species, including 11 deep-sea fishes. Our findings reconstructed the teleost deep-sea colonization history and revealed the overall impact of the deep-sea environment on fishes. Interestingly, our results question the previously assumed linear correlation between trimethylamine oxide (TMAO) content and depth. By contrast, we observed a convergent aa replacement in the <em>rtf1</em> gene in most deep-sea fishes under 3,000 m, and <em>in vitro</em> experiments suggest that this mutation can influence transcriptional efficiency, which is likely to be advantageous in the deep-sea environment. Moreover, our study underlines the pervasive impact of human activities, as we detected the presence of persistent organic pollutants in species from the Mariana Trench.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"4 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560633","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":"The amphipod genome reveals population dynamics and adaptations to hadal environment","authors":"Haibin Zhang, Shuai Sun, Jun Liu, Qunfei Guo, Liang Meng, Jianwei Chen, Xueyan Xiang, Yang Zhou, Nannan Zhang, Helu Liu, Yalin Liu, Guoyong Yan, Qianyue Ji, Lisheng He, Shanya Cai, Chongyang Cai, Xin Huang, Shiyu Xu, Yunlu Xiao, Yangrui Zhang, Guangyi Fan","doi":"10.1016/j.cell.2025.01.030","DOIUrl":"https://doi.org/10.1016/j.cell.2025.01.030","url":null,"abstract":"The amphipod <em>Hirondellea gigas</em> is a dominant species inhabiting the deepest part of the ocean (∼6,800–11,000 m), but little is known about its genetic adaptation and population dynamics. Here, we present a chromosome-level genome of <em>H. gigas</em>, characterized by a large genome size of 13.92 Gb. Whole-genome sequencing of 510 individuals from the Mariana Trench indicates no population differentiation across depths, suggesting its capacity to tolerate hydrostatic pressure across wide ranges. <em>H. gigas</em> in the West Philippine Basin is genetically divergent from the Mariana and Yap Trenches, suggesting genetic isolation attributed to the geographic separation of hadal features. A drastic reduction in effective population size potentially reflects glacial-interglacial changes. By integrating multi-omics analysis, we propose host-symbiotic microbial interactions may be crucial in the adaptation of <em>H. gigas</em> to the extremely high-pressure and food-limited environment. Our findings provide clues for adaptation to the hadal zone and population genetics.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"53 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560868","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":"Microbial ecosystems and ecological driving forces in the deepest ocean sediments","authors":"Xiang Xiao, Weishu Zhao, Zewei Song, Qi Qi, Bo Wang, Jiahui Zhu, James Lin, Jing Wang, Aoran Hu, Shanshan Huang, Yinzhao Wang, Jianwei Chen, Chao Fang, Qianyue Ji, Nannan Zhang, Liang Meng, Xiaofeng Wei, Chuanxu Chen, Shanya Cai, Shun Chen, Shanshan Liu","doi":"10.1016/j.cell.2024.12.036","DOIUrl":"https://doi.org/10.1016/j.cell.2024.12.036","url":null,"abstract":"Systematic exploration of the hadal zone, Earth’s deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6–11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"16 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560866","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}
CellPub Date : 2025-03-06DOI: 10.1016/j.cell.2025.01.038
Sondra Turjeman, Tommaso Rozera, Eran Elinav, Gianluca Ianiro, Omry Koren
{"title":"From big data and experimental models to clinical trials: Iterative strategies in microbiome research","authors":"Sondra Turjeman, Tommaso Rozera, Eran Elinav, Gianluca Ianiro, Omry Koren","doi":"10.1016/j.cell.2025.01.038","DOIUrl":"https://doi.org/10.1016/j.cell.2025.01.038","url":null,"abstract":"Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging <em>in silico</em>, <em>in vitro</em>, <em>ex vivo</em>, and <em>in vivo</em> studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even “meta-cohort” analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches—such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics—provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream <em>in vitro</em> and <em>in vivo</em> research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"2 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560867","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}
CellPub Date : 2025-03-05DOI: 10.1016/j.cell.2025.02.005
Pamela E. Rios Coronado, Jiayan Zhou, Xiaochen Fan, Daniela Zanetti, Jeffrey A. Naftaly, Pratima Prabala, Azalia M. Martínez Jaimes, Elie N. Farah, Soumya Kundu, Salil S. Deshpande, Ivy Evergreen, Pik Fang Kho, Qixuan Ma, Austin T. Hilliard, Sarah Abramowitz, Saiju Pyarajan, Daniel Dochtermann, Scott M. Damrauer, Kyong-Mi Chang, Themistocles L. Assimes
{"title":"CXCL12 drives natural variation in coronary artery anatomy across diverse populations","authors":"Pamela E. Rios Coronado, Jiayan Zhou, Xiaochen Fan, Daniela Zanetti, Jeffrey A. Naftaly, Pratima Prabala, Azalia M. Martínez Jaimes, Elie N. Farah, Soumya Kundu, Salil S. Deshpande, Ivy Evergreen, Pik Fang Kho, Qixuan Ma, Austin T. Hilliard, Sarah Abramowitz, Saiju Pyarajan, Daniel Dochtermann, Scott M. Damrauer, Kyong-Mi Chang, Themistocles L. Assimes","doi":"10.1016/j.cell.2025.02.005","DOIUrl":"https://doi.org/10.1016/j.cell.2025.02.005","url":null,"abstract":"Coronary arteries have a specific branching pattern crucial for oxygenating heart muscle. Among humans, there is natural variation in coronary anatomy with respect to perfusion of the inferior/posterior left heart, which can branch from either the right arterial tree, the left, or both—a phenotype known as coronary dominance. Using angiographic data for >60,000 US veterans of diverse ancestry, we conducted a genome-wide association study of coronary dominance, revealing moderate heritability and identifying ten significant loci. The strongest association occurred near <em>CXCL12</em> in both European- and African-ancestry cohorts, with downstream analyses implicating effects on <em>CXCL12</em> expression. We show that <em>CXCL12</em> is expressed in human fetal hearts at the time dominance is established. Reducing <em>Cxcl12</em> in mice altered coronary dominance and caused septal arteries to develop away from <em>Cxcl12</em> expression domains. These findings indicate that <em>CXCL12</em> patterns human coronary arteries, paving the way for “medical revascularization” through targeting developmental pathways.","PeriodicalId":9656,"journal":{"name":"Cell","volume":"30 1","pages":""},"PeriodicalIF":64.5,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546572","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}
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