Communications Biology最新文献

An alternative pattern of head expansion during feeding in cichlids. 在进食过程中头部扩张的另一种模式。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08851-w

Jana De Ridder, Vincent Dujardin, Julia Camacho Garcia, Wilson Sawasawa, Peter Aerts, Hannes Svardal, Sam Van Wassenbergh

引用次数: 0

Structural insights into Cir-mediated killing by the antimicrobial protein Microcin V. 抗微生物蛋白微霉素V介导的cirr杀伤的结构见解。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08846-7

Stavros A Maurakis, Angela C O'Donnell, Istvan Botos, Rodolfo Ghirlando, Bryan W Davies, Susan K Buchanan

{"title":"Structural insights into Cir-mediated killing by the antimicrobial protein Microcin V.","authors":"Stavros A Maurakis, Angela C O'Donnell, Istvan Botos, Rodolfo Ghirlando, Bryan W Davies, Susan K Buchanan","doi":"10.1038/s42003-025-08846-7","DOIUrl":"https://doi.org/10.1038/s42003-025-08846-7","url":null,"abstract":"Drug-resistant bacteria are a global concern. Novel treatments are needed, but are difficult to develop for Gram-negative species due to the need to traverse the outer membrane to reach targets beneath. A promising solution is found in natural antibiotics which bind outer membrane receptors and co-opt them for import. Exploring this mechanism may open avenues for antibiotic development. An underappreciated class of natural antibiotics are microcins - small antimicrobial proteins secreted by certain bacteria during inter-species competition. Microcins bind outer-membrane receptors of prey species for passage into the periplasm. They have potent activity, bind specific targets, and can control pathobiont expansion and colonization. One microcin, MccV, utilizes the E. coli colicin Ia receptor, Cir, for import. Here, we report the first high-resolution structure of the Cir/MccV complex by Cryo-EM, revealing an interaction centered on an electropositive cavity within the Cir extracellular loops. We also report the affinity of MccV for Cir. Lastly, we mutagenized interacting residues and identified key contacts critical to MccV binding, import, and bacteriolysis. Future efforts may help disentangle the mechanisms of microcin killing and will assess relationships between other microcins and their targets to better understand the potential for microcins to be used as antibacterial drugs.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"1449"},"PeriodicalIF":5.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257763","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

Biological sex impacts immune cell proportions and epigenetic profiles in the developing pediatric immune system. 生物性别影响免疫细胞比例和表观遗传谱在发育中的儿童免疫系统。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08844-9

Karlie Edwards, Sarah M Merrill, Chaini Konwar, Marcia S Jude, Beryl C Zhuang, Mandy Meijer, Erick Navarro-Delgado, Julie L MacIsaac, Piush Mandhane, Elinor Simons, Theo J Moraes, Meghan B Azad, Padmaja Subbarao, Mariona Bustamante, Martine Vrijheid, Stuart Turvey, Michael S Kobor

{"title":"Biological sex impacts immune cell proportions and epigenetic profiles in the developing pediatric immune system.","authors":"Karlie Edwards, Sarah M Merrill, Chaini Konwar, Marcia S Jude, Beryl C Zhuang, Mandy Meijer, Erick Navarro-Delgado, Julie L MacIsaac, Piush Mandhane, Elinor Simons, Theo J Moraes, Meghan B Azad, Padmaja Subbarao, Mariona Bustamante, Martine Vrijheid, Stuart Turvey, Michael S Kobor","doi":"10.1038/s42003-025-08844-9","DOIUrl":"https://doi.org/10.1038/s42003-025-08844-9","url":null,"abstract":"Age- and sex-related differences in immune cell compositions and immune outcomes have been identified across the life course, but a comprehensive and nuanced characterization of these changes during the rapid developmental window of early life is lacking. We explore immune associated DNA methylation (DNAm) changes in the context of age and sex leveraging whole blood samples collected at ages one and five from CHILD, a Canadian longitudinal pediatric cohort (n = 760: 356 female and 404 male). DNAm-based computational cell type deconvolution reveals significant changes in all estimated immune cell types across time, with notable sex differences. In addition, we identify distinct DNAm signatures reflecting age- and sex-associated immune profiles in early life. While age-related DNAm changes are relatively limited, sex-associated differences are consistent across this developmental window and partially validate in independent pediatric cohorts. Together, these findings provide insights into early immune system maturation, underscoring the presence of sex differences prior to puberty.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"1447"},"PeriodicalIF":5.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257602","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

Cxcl9^high macrophages recruit circulating Cxcr3+ plasmablasts into kidneys to promote pathogenesis of lupus nephritis mice. 高cxcl9巨噬细胞招募循环中的Cxcr3+质母细胞进入肾脏，促进狼疮性肾炎小鼠的发病。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08852-9

Jing Zhao, Xinlong Bai, Cheng Zhou, Qing Ouyang, Yingjie Zhang, Xiao Zhang, Xumin Zheng, Chaofan Li, Wanjun Shen, Qinggang Li, Guangyan Cai, Xiangmei Chen, Ping Li, Xue-Yuan Bai

{"title":"Cxcl9high macrophages recruit circulating Cxcr3+ plasmablasts into kidneys to promote pathogenesis of lupus nephritis mice.","authors":"Jing Zhao, Xinlong Bai, Cheng Zhou, Qing Ouyang, Yingjie Zhang, Xiao Zhang, Xumin Zheng, Chaofan Li, Wanjun Shen, Qinggang Li, Guangyan Cai, Xiangmei Chen, Ping Li, Xue-Yuan Bai","doi":"10.1038/s42003-025-08852-9","DOIUrl":"https://doi.org/10.1038/s42003-025-08852-9","url":null,"abstract":"Systemic lupus erythematosus (SLE) is an autoimmune disease driven by autoantibody production. Lupus nephritis (LN), a severe SLE complication, is primarily caused by renal autoantibodies. Long-lived plasma cells (LLPCs), the main producers of these autoantibodies, are especially elevated in the kidney of LN patients, particularly in refractory or recurrent cases. However, the cause of increased LLPCs in LN kidneys remains unknown. This study uses an LN mouse model and combines single-cell RNA sequencing with spatial transcriptomics, finding that kidney-resident Cxcl9high macrophages and their secreted chemokine Cxcl9 significantly rise with disease progression. This increase in Cxcl9 attracts Cxcr3+ plasmablasts in peripheral blood into the kidneys, where they differentiate into LLPCs and produce autoantibodies. Based on these findings, this study suggests that Cxcl9high macrophages are the inducing factor causing the increase of LLPCs in LN kidneys and may be a potential therapeutic target for LN.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"1446"},"PeriodicalIF":5.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257647","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

HSPA4 restrains transferrin in dopaminergic neurons to attenuate ferroptosis in a Parkinson's disease model. HSPA4抑制多巴胺能神经元中的转铁蛋白以减轻帕金森病模型中的铁下垂。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08854-7

Tong Gao, Huanhuan Wei, Qianqian Ju, Yongqi Lin, Xiang Yin, Xiaoyu Liu, Jianhong Shen, Qiuhong Ji, Cheng Sun, Lihua Shen

{"title":"HSPA4 restrains transferrin in dopaminergic neurons to attenuate ferroptosis in a Parkinson's disease model.","authors":"Tong Gao, Huanhuan Wei, Qianqian Ju, Yongqi Lin, Xiang Yin, Xiaoyu Liu, Jianhong Shen, Qiuhong Ji, Cheng Sun, Lihua Shen","doi":"10.1038/s42003-025-08854-7","DOIUrl":"https://doi.org/10.1038/s42003-025-08854-7","url":null,"abstract":"Heat shock protein A4 (HSPA4) is a molecular chaperone belonging to the heat shock protein 70 (HSP70) family. This study aims to investigate the antiferroptotic effects of HSPA4 in a Parkinson's disease (PD) model and explore the underlying mechanisms. Here we show that HSPA4 overexpression reduces ferroptosis in erastin-treated SH-SY5Y cells and primary dopaminergic neurons, while HSPA4 knockdown exacerbates ferroptosis. In MPTP-induced PD model mice, HSPA4 rectifies behavioral defects, prevents the loss of dopaminergic neurons, and alleviates ferroptosis. Mechanistically, HSPA4 interacts with transferrin in the cytoplasm and inhibits its export from the cell. Consequently, extracellular iron cannot be transported into cells due to a lack of transferrin, thereby attenuating ferroptosis in dopaminergic neurons and slowing PD progression. By restraining transferrin in dopaminergic neurons, HSPA4 reduces ferroptosis and alleviates parkinsonism in a PD mouse model. Therefore, HSPA4 might present a potential therapeutic target for the development of PD treatments.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"1453"},"PeriodicalIF":5.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257650","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

Tizoxanide associated with anti-virulent activity controls fire blight disease caused by Erwinia amylovora in Malus asiatica. 替替沙尼与抗毒活性相关的防治亚洲海棠白僵病。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08853-8

Yeong Seok Kim, Eom-Jeong Kang, Dohyun Kim, Bomin Kim, Jae Woo Han, Joon-Ho Lee, Sang-Wook Han, Gyung Ja Choi, Hun Kim

{"title":"Tizoxanide associated with anti-virulent activity controls fire blight disease caused by Erwinia amylovora in Malus asiatica.","authors":"Yeong Seok Kim, Eom-Jeong Kang, Dohyun Kim, Bomin Kim, Jae Woo Han, Joon-Ho Lee, Sang-Wook Han, Gyung Ja Choi, Hun Kim","doi":"10.1038/s42003-025-08853-8","DOIUrl":"https://doi.org/10.1038/s42003-025-08853-8","url":null,"abstract":"Erwinia amylovora is a causative pathogen of fire blight disease, affecting apple, pear, and other rosaceous plants. This study aimed to discover new anti-virulence agents to control this plant bacterial disease by preventing its pathogenesis. To this end, 2485 small molecules were screened for targeting the type III secretion system (T3SS) which is a critical virulence factor in E. amylovora. Our screening identified tizoxanide as a potent inhibitor, significantly reducing the promoter activity of hrpA, which encodes the Hrp pilus protein essential for T3SS function. Beyond T3SS inhibition, tizoxanide also exhibited inhibitory effects on other virulence factors by down-regulating genes associated with these functions. Given its broad effects on various virulence factors, we conducted a proteomic analysis of E. amylovora treated with tizoxanide, and the results revealed differentially expressed proteins related to cell metabolism and pathogenesis. In a plant infection model, spray treatment with tizoxanide effectively protected Chinese pearleaf crabapple seedlings against E. amylovora. Furthermore, a synthesized tizoxanide derivative containing an isoxazole moiety further enhanced hrpA promoter inhibition and disease control efficacy compared to the tizoxanide. Taken together, our results highlight the potential of tizoxanide as an anti-virulence agent to prevent plant disease caused by E. amylovora.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"1451"},"PeriodicalIF":5.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257748","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

cryoTIGER: deep-learning based tilt interpolation generator for enhanced reconstruction in cryo electron tomography. cryoTIGER：基于深度学习的倾斜插值生成器，用于增强低温电子断层扫描重建。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08961-5

Tomáš Majtner, Jan Philipp Kreysing, Maarten W Tuijtel, Sergio Cruz-León, Jiasui Liu, Gerhard Hummer, Martin Beck, Beata Turoňová

{"title":"cryoTIGER: deep-learning based tilt interpolation generator for enhanced reconstruction in cryo electron tomography.","authors":"Tomáš Majtner, Jan Philipp Kreysing, Maarten W Tuijtel, Sergio Cruz-León, Jiasui Liu, Gerhard Hummer, Martin Beck, Beata Turoňová","doi":"10.1038/s42003-025-08961-5","DOIUrl":"https://doi.org/10.1038/s42003-025-08961-5","url":null,"abstract":"Cryo-electron tomography enables the visualization of macromolecular complexes within native cellular environments but is limited by incomplete angular sampling and the maximal electron dose that biological specimens can be exposed to. Here, we developed cryoTIGER (Tilt Interpolation Generator for Enhanced Reconstruction), a computational workflow leveraging deep learning-based frame interpolation to generate intermediate tilt images. By interpolating between tilt series projections, cryoTIGER improves angular sampling, leading to enhanced 3D reconstructions, more refined particle localization, and improved segmentation of cellular structures. We evaluated our interpolation workflow on diverse datasets and compared its performance against non-interpolated data. Our results demonstrate that deep learning-based interpolation improves image quality and structural recovery. The presented cryoTIGER framework offers a computational alternative to denser sampling during tilt series acquisition, paving the way for enhanced cryo-ET workflows and advancing structural biology research.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"1443"},"PeriodicalIF":5.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257670","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

Myocardial disarray drives metabolic inefficiency in human cardiomyocytes. 心肌紊乱导致人类心肌细胞代谢效率低下。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08842-x

Charlène Jouve, Andrea Ruiz-Velasco, Erminia Donnarumma, Rémi Le Borgne, Iman Momken, Céline Pereira, Magali Seguret, Eva Vermersch, Elodie Vimont, Ivan Nemazanyy, Luc Bertrand, Timothy Wai, Jean-Marc Verbavatz, Mathias Mericksay, Jean-Sébastien Hulot

{"title":"Myocardial disarray drives metabolic inefficiency in human cardiomyocytes.","authors":"Charlène Jouve, Andrea Ruiz-Velasco, Erminia Donnarumma, Rémi Le Borgne, Iman Momken, Céline Pereira, Magali Seguret, Eva Vermersch, Elodie Vimont, Ivan Nemazanyy, Luc Bertrand, Timothy Wai, Jean-Marc Verbavatz, Mathias Mericksay, Jean-Sébastien Hulot","doi":"10.1038/s42003-025-08842-x","DOIUrl":"https://doi.org/10.1038/s42003-025-08842-x","url":null,"abstract":"Adult cardiomyocytes are embedded within a highly organized myocardial microenvironment that imposes critical geometric cues essential for the alignment and distribution of organelles and the shaping of their unique, rectangular cellular morphology. Despite the association of cardiomyocyte disarray with human heart disease, the functional consequences of this cellular disorganization remain poorly understood. Here, we leveraged micropatterned substrates to promote structural alignment in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), contrasting the effects of mechanical alignment on mitochondrial form and function with hiPSC-CMs cultured under standard unconstrained conditions. Cardiomyocytes cultured under unconstrained conditions exhibited misaligned sarcomeres and a perinuclear mitochondrial distribution while micropatterned hiPSC-CMs developed linear myofibrils and reconfigured sarcomere and mitochondrial organization, which increased mitochondrial respiration without augmenting mitochondrial mass. Notably, micropatterned hiPSC-CMs exhibited an increased number of mitochondria-associated membranes, as determined by proximity ligation assays and transmission electron microscopy, suggesting enhanced interactions between the sarcoplasmic reticulum and mitochondria. Together, these findings demonstrate that mitochondrial-sarcoplasmic architecture and geometry are critical spatial features that ensure bioenergetic efficiency of cardiomyocytes. This work underscores the importance of cellular organization in cardiomyocyte metabolism and function, providing insights into the pathophysiology of cardiac diseases marked by cellular disarray.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"1445"},"PeriodicalIF":5.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257672","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

Systematic over-expression of secondary metabolism transcription factors to reveal the pharmaceutical potential of Aspergillus nidulans. 次生代谢转录因子的系统过表达揭示了细粒曲霉的药用潜力。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08840-z

Shuhui Guo, Lakhansing Pardeshi, Longguang Qin, Chris Y Cheung, Xiaofeng Liu, Lu Fan, Chi Cheng Mok, Chirag Parsania, Zhiqiang Dong, Ben C B Ko, Kaeling Tan, Koon Ho Wong

{"title":"Systematic over-expression of secondary metabolism transcription factors to reveal the pharmaceutical potential of Aspergillus nidulans.","authors":"Shuhui Guo, Lakhansing Pardeshi, Longguang Qin, Chris Y Cheung, Xiaofeng Liu, Lu Fan, Chi Cheng Mok, Chirag Parsania, Zhiqiang Dong, Ben C B Ko, Kaeling Tan, Koon Ho Wong","doi":"10.1038/s42003-025-08840-z","DOIUrl":"https://doi.org/10.1038/s42003-025-08840-z","url":null,"abstract":"Many life-saving drugs are derived from fungal secondary metabolites, and the rich diversity of these metabolites is a gold mine of bioactive compounds for drug discovery. However, the biosynthetic genes for most secondary metabolites remain transcriptionally silent in fungi, posing a significant bottleneck in their discovery. Here, we apply a systematic approach to separately over-express 51 secondary metabolism-related transcription factors using the strong inducible promoter of the xylP gene from Penicillium chrysogenum. Growing the individual secondary metabolism transcription factor over-expression strains under inducible conditions leads to the production of a collection of diverse metabolites with anti-bacterial, anti-fungal and anti-cancer activities. The overall approach and the over-expression system established in this study are broadly-applicable, providing a valuable means to revealing the pharmaceutical potentials of fungi.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"1444"},"PeriodicalIF":5.1,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257712","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

Immediate-early genes Arc and c-Fos show divergent brain-wide expression following contextual fear conditioning. 即时早期基因Arc和c-Fos在情境恐惧条件作用下表现出不同的全脑表达。

IF 5.1 1区生物学

Communications Biology Pub Date : 2025-10-09 DOI: 10.1038/s42003-025-08856-5

Nicholas E Bulthuis, Liliette I Quintana, Michelle Stackmann, Christine A Denny

引用次数: 0