Pub Date : 2025-11-14DOI: 10.1007/s44154-025-00264-3
Xueer Du, Lamei Wang, Yanfei Dai, Jing Lu, Hongrui Li, Dangdang Wang, Jun Zhang, Chuanjiang Cai, Shimin Liu, Junhu Yao, Jianguo Wang, Yangchun Cao
To elucidate the molecular mechanisms by which choline regulates hepatic lipid metabolism under negative energy balance conditions, we established non-esterified fatty acid (NEFA)-induced hepatic steatosis models in both calf primary hepatocytes and human LO2 hepatocytes. Choline supplementation significantly reduced intracellular triglyceride accumulation and cytotoxicity induced by NEFA exposure. Transcriptomic profiling identified glycine N-methyltransferase (GNMT) as a key differentially expressed gene. Subsequent experiments confirmed that choline upregulated GNMT expression at both the mRNA and protein levels in a concentration-dependent manner. Knockdown of GNMT reversed the beneficial effects of choline on genes related to lipid synthesis (FAS, ACC), fatty acid oxidation (CPT1), lipoprotein assembly (ApoB100, MTTP), and bile acid metabolism (CYP7A1, CYP27A1, BSEP). Furthermore, inhibition of AMP-activated protein kinase (AMPK) reduced GNMT protein expression and elevated Myc, a negative transcriptional regulator of GNMT, suggesting that choline may regulate GNMT through the AMPK/Myc axis. Collectively, our findings demonstrate that choline alleviates NEFA-induced lipid accumulation and hepatocellular damage by modulating lipid and bile acid metabolism through GNMT, with the AMPK/Myc/GNMT signaling axis playing a pivotal regulatory role. These results provide mechanistic insights into the hepatic protective effects of choline and suggest GNMT as a potential therapeutic target for metabolic disorders in dairy cows and beyond.
{"title":"Choline attenuates NEFA-induced hepatic steatosis via GNMT regulation in hepatocytes.","authors":"Xueer Du, Lamei Wang, Yanfei Dai, Jing Lu, Hongrui Li, Dangdang Wang, Jun Zhang, Chuanjiang Cai, Shimin Liu, Junhu Yao, Jianguo Wang, Yangchun Cao","doi":"10.1007/s44154-025-00264-3","DOIUrl":"10.1007/s44154-025-00264-3","url":null,"abstract":"<p><p>To elucidate the molecular mechanisms by which choline regulates hepatic lipid metabolism under negative energy balance conditions, we established non-esterified fatty acid (NEFA)-induced hepatic steatosis models in both calf primary hepatocytes and human LO2 hepatocytes. Choline supplementation significantly reduced intracellular triglyceride accumulation and cytotoxicity induced by NEFA exposure. Transcriptomic profiling identified glycine N-methyltransferase (GNMT) as a key differentially expressed gene. Subsequent experiments confirmed that choline upregulated GNMT expression at both the mRNA and protein levels in a concentration-dependent manner. Knockdown of GNMT reversed the beneficial effects of choline on genes related to lipid synthesis (FAS, ACC), fatty acid oxidation (CPT1), lipoprotein assembly (ApoB100, MTTP), and bile acid metabolism (CYP7A1, CYP27A1, BSEP). Furthermore, inhibition of AMP-activated protein kinase (AMPK) reduced GNMT protein expression and elevated Myc, a negative transcriptional regulator of GNMT, suggesting that choline may regulate GNMT through the AMPK/Myc axis. Collectively, our findings demonstrate that choline alleviates NEFA-induced lipid accumulation and hepatocellular damage by modulating lipid and bile acid metabolism through GNMT, with the AMPK/Myc/GNMT signaling axis playing a pivotal regulatory role. These results provide mechanistic insights into the hepatic protective effects of choline and suggest GNMT as a potential therapeutic target for metabolic disorders in dairy cows and beyond.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"70"},"PeriodicalIF":5.8,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12615869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145515192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-14DOI: 10.1007/s44154-025-00262-5
Ying Zhou, Zhuo Yang, Jiaxue Li, Xuemei Xia, Wei Yuan, Chen Li, Wenxiu Qiu, Li Liu, Liu Duan
Mosses play a crucial role in environmental protection, ecological preservation, and horticulture. While the effects of nanomaterials on angiosperms have been widely studied, their impact on bryophytes remains underexplored. In this study, we investigated the effects of mesoporous silica nanoparticles (MSNs) and virus-like mesoporous silica nanoparticles (VMSNs) on the model moss species Physcomitrium patens (P. patens). Our results revealed that MSNs, with an average size of approximately 123 nm, are nontoxic to P. patens and enhance its salt tolerance. The expression of key genes involved in stress responses were significantly induced in MSN-treated plants under salt stress, including peroxidase (POX), L-ascorbate oxidase (L-AO), alternative oxidase (AOX), and calcium-dependent protein kinase (CPK). MSN treatment reduced the accumulation of H2O2 and O2·-, increased Ca2+ signaling, and modulated reactive oxygen species (ROS) homeostasis, collectively improving moss tolerance to salt stress. MSNs were observed on the cell surface, in intercellular space, and within the cytosol and vesicles. They were transported bidirectionally between rhizoids and apical leaves. This study provides novel insights into the distribution, transport, and functional mechanisms of MSNs in mosses, offering a valuable foundation for the application of nanomaterials in plant stress biology and ecological management of bryophytes.
{"title":"Nontoxic mesoporous silica nanoparticles protect Physcomitrium patens against salt stress.","authors":"Ying Zhou, Zhuo Yang, Jiaxue Li, Xuemei Xia, Wei Yuan, Chen Li, Wenxiu Qiu, Li Liu, Liu Duan","doi":"10.1007/s44154-025-00262-5","DOIUrl":"10.1007/s44154-025-00262-5","url":null,"abstract":"<p><p>Mosses play a crucial role in environmental protection, ecological preservation, and horticulture. While the effects of nanomaterials on angiosperms have been widely studied, their impact on bryophytes remains underexplored. In this study, we investigated the effects of mesoporous silica nanoparticles (MSNs) and virus-like mesoporous silica nanoparticles (VMSNs) on the model moss species Physcomitrium patens (P. patens). Our results revealed that MSNs, with an average size of approximately 123 nm, are nontoxic to P. patens and enhance its salt tolerance. The expression of key genes involved in stress responses were significantly induced in MSN-treated plants under salt stress, including peroxidase (POX), L-ascorbate oxidase (L-AO), alternative oxidase (AOX), and calcium-dependent protein kinase (CPK). MSN treatment reduced the accumulation of H<sub>2</sub>O<sub>2</sub> and O<sub>2</sub><sup>·-</sup>, increased Ca<sup>2+</sup> signaling, and modulated reactive oxygen species (ROS) homeostasis, collectively improving moss tolerance to salt stress. MSNs were observed on the cell surface, in intercellular space, and within the cytosol and vesicles. They were transported bidirectionally between rhizoids and apical leaves. This study provides novel insights into the distribution, transport, and functional mechanisms of MSNs in mosses, offering a valuable foundation for the application of nanomaterials in plant stress biology and ecological management of bryophytes.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"69"},"PeriodicalIF":5.8,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12615889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145515159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Desert plants have evolved remarkable adaptations to survive in arid environments, where water scarcity and extreme temperatures pose significant challenges to life. The desert moss Syntrichia caninervis stands out as an exemplary model of extreme desiccation tolerance (DT), offering invaluable insights into plant adaptation to water deficit. This study presents a comprehensive multi-omics analysis of S. caninervis during controlled dehydration and rehydration process, integrating transcriptomic, proteomic, and metabolomic data to elucidate the molecular mechanisms underlying its remarkable resilience. Our findings reveal a sophisticated, multilayered response characterized by extensive transcriptional reprogramming (3,153 differentially expressed genes), dynamic proteome remodeling (873 differentially expressed proteins), and strategic metabolic reconfiguration (185 differentially abundant metabolites). Key adaptations include the coordinated downregulation of photosynthetic processes, upregulation of stress-responsive genes and proteins, accumulation of protective metabolites, and enhancement of antioxidant systems. Notably, we observed significant temporal asynchrony between transcript and protein levels, underscoring the complexity of post-transcriptional regulation in stress responses. The core mechanisms of S. caninervis DT comprises cellular protection and metabolic dormancy during dehydration, followed by efficient repair and recovery processes upon rehydration. These findings not only advance our understanding of plant evolution and adaptation to extreme environments but also identify potential targets for enhancing drought tolerance in crops and exploring plant survival under extreme environment. By deciphering the molecular basis of extreme DT, this research opens new avenues for addressing agricultural challenges in water-limited environments and expands our knowledge of plant life's adaptability to harsh terrestrial.
{"title":"Exploring the mechanisms of desert plant adaptation to arid climates: a multi-omics analysis of dehydration and rehydration responses in Syntrichia caninervis.","authors":"Qilin Yang, Huan Zhang, Fangliu Yin, Haron Salih, RuiRui Yang, Bei Gao, Xiaoshuang Li, Daoyuan Zhang","doi":"10.1007/s44154-025-00241-w","DOIUrl":"10.1007/s44154-025-00241-w","url":null,"abstract":"<p><p>Desert plants have evolved remarkable adaptations to survive in arid environments, where water scarcity and extreme temperatures pose significant challenges to life. The desert moss Syntrichia caninervis stands out as an exemplary model of extreme desiccation tolerance (DT), offering invaluable insights into plant adaptation to water deficit. This study presents a comprehensive multi-omics analysis of S. caninervis during controlled dehydration and rehydration process, integrating transcriptomic, proteomic, and metabolomic data to elucidate the molecular mechanisms underlying its remarkable resilience. Our findings reveal a sophisticated, multilayered response characterized by extensive transcriptional reprogramming (3,153 differentially expressed genes), dynamic proteome remodeling (873 differentially expressed proteins), and strategic metabolic reconfiguration (185 differentially abundant metabolites). Key adaptations include the coordinated downregulation of photosynthetic processes, upregulation of stress-responsive genes and proteins, accumulation of protective metabolites, and enhancement of antioxidant systems. Notably, we observed significant temporal asynchrony between transcript and protein levels, underscoring the complexity of post-transcriptional regulation in stress responses. The core mechanisms of S. caninervis DT comprises cellular protection and metabolic dormancy during dehydration, followed by efficient repair and recovery processes upon rehydration. These findings not only advance our understanding of plant evolution and adaptation to extreme environments but also identify potential targets for enhancing drought tolerance in crops and exploring plant survival under extreme environment. By deciphering the molecular basis of extreme DT, this research opens new avenues for addressing agricultural challenges in water-limited environments and expands our knowledge of plant life's adaptability to harsh terrestrial.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"68"},"PeriodicalIF":5.8,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12583356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145440365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Clothianidin, a widely used neonicotinoid pesticide, poses potential ecological risks to aquatic ecosystems due to its unique mode of action and widespread environmental dispersal. This study investigates the toxic effects of clothianidin on Penaeus vannamei at different concentrations over 28 days. High concentrations of clothianidin significantly affected shrimp physiology, as evidenced by changes in survival rate and weight gain. Markers of oxidative stress, including decreased respiratory burst, reduced glutathione levels, and diminished antioxidant enzyme activities, indicated that clothianidin triggered oxidative stress responses in shrimp. Additionally, changes in lactate dehydrogenase, succinate dehydrogenase, and isocitrate dehydrogenase activities suggested disruptions in energy metabolism in the hepatopancreas. Analysis of the nervous system revealed significant disturbances in neural signaling, reflected by altered levels of acetylcholine, acetylcholinesterase, and dopamine. Transcriptomic analysis highlighted significant changes in gene expression and metabolic processes in the nervous system. This study demonstrates that clothianidin disrupts oxidative balance, energy metabolism, and neural signaling, affecting the growth of P. vannamei and providing valuable insights into its biochemical and transcriptomic toxicity in aquatic environments.
{"title":"Impact of clothianidin exposure on the growth, metabolism, and neurological function of Penaeus vannamei.","authors":"Zhi Luo, Zhen-Fei Li, Zhi-Yu Lin, Zhen-Qiang Fu, Feng-Lu Han, Er-Chao Li","doi":"10.1007/s44154-025-00259-0","DOIUrl":"10.1007/s44154-025-00259-0","url":null,"abstract":"<p><p>Clothianidin, a widely used neonicotinoid pesticide, poses potential ecological risks to aquatic ecosystems due to its unique mode of action and widespread environmental dispersal. This study investigates the toxic effects of clothianidin on Penaeus vannamei at different concentrations over 28 days. High concentrations of clothianidin significantly affected shrimp physiology, as evidenced by changes in survival rate and weight gain. Markers of oxidative stress, including decreased respiratory burst, reduced glutathione levels, and diminished antioxidant enzyme activities, indicated that clothianidin triggered oxidative stress responses in shrimp. Additionally, changes in lactate dehydrogenase, succinate dehydrogenase, and isocitrate dehydrogenase activities suggested disruptions in energy metabolism in the hepatopancreas. Analysis of the nervous system revealed significant disturbances in neural signaling, reflected by altered levels of acetylcholine, acetylcholinesterase, and dopamine. Transcriptomic analysis highlighted significant changes in gene expression and metabolic processes in the nervous system. This study demonstrates that clothianidin disrupts oxidative balance, energy metabolism, and neural signaling, affecting the growth of P. vannamei and providing valuable insights into its biochemical and transcriptomic toxicity in aquatic environments.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"67"},"PeriodicalIF":5.8,"publicationDate":"2025-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12579615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145426592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plants are continuously exposed to environmental abiotic and biotic stressors that can significantly impact their growth, development, productivity, and lifespan. However, plants have developed exceptionally complex signaling pathways that enable their ability to sense, transduce, and respond to these diverse stress stimuli. Salicylates (SA) and jasmonates (JA) are two key phytohormones that significantly influence plant adaptation to environmental and biotic stressors, pivotal in enhancing stress resilience. The interaction and crosstalk between SA and JA signaling cascades are essential for orchestrating appropriate physiological and biochemical responses to biotic (e.g., pathogen attack, herbivory) and abiotic (e.g., oxidative stress, drought, temperature extremes, UV radiation, salinity, heavy metal toxicity) stresses. Salicylates are primarily recognized for being involved in systemic acquired resistance (SAR) against biotic stressors like pathogens. Conversely, jasmonates are well-documented in their function in defenses aimed at herbivorous insects and in mitigating the outcomes of abiotic conditions such as salinity and drought. However, the crosstalk between SAs and JAs is complex, involving both synergistic and antagonistic interactions that finely tune the natural defensive mechanism of the plant toward both biotic and abiotic stresses. This comprehensive review summarizes the most recent research on how SA and JA biosynthesis, signaling, and interactions govern diverse stress adaptive mechanisms in plants. It covers emerging evidence on the importance of SA-JA crosstalk in regulating physiological, biochemical, and molecular adaptations to combined biotic and abiotic stresses.
{"title":"Linking the interaction of Salicylates and Jasmonates for stress resilience in plants.","authors":"Ekta Pandey, Rinkee Kumari, Shahla Faizan, Saurabh Pandey","doi":"10.1007/s44154-025-00250-9","DOIUrl":"10.1007/s44154-025-00250-9","url":null,"abstract":"<p><p>Plants are continuously exposed to environmental abiotic and biotic stressors that can significantly impact their growth, development, productivity, and lifespan. However, plants have developed exceptionally complex signaling pathways that enable their ability to sense, transduce, and respond to these diverse stress stimuli. Salicylates (SA) and jasmonates (JA) are two key phytohormones that significantly influence plant adaptation to environmental and biotic stressors, pivotal in enhancing stress resilience. The interaction and crosstalk between SA and JA signaling cascades are essential for orchestrating appropriate physiological and biochemical responses to biotic (e.g., pathogen attack, herbivory) and abiotic (e.g., oxidative stress, drought, temperature extremes, UV radiation, salinity, heavy metal toxicity) stresses. Salicylates are primarily recognized for being involved in systemic acquired resistance (SAR) against biotic stressors like pathogens. Conversely, jasmonates are well-documented in their function in defenses aimed at herbivorous insects and in mitigating the outcomes of abiotic conditions such as salinity and drought. However, the crosstalk between SAs and JAs is complex, involving both synergistic and antagonistic interactions that finely tune the natural defensive mechanism of the plant toward both biotic and abiotic stresses. This comprehensive review summarizes the most recent research on how SA and JA biosynthesis, signaling, and interactions govern diverse stress adaptive mechanisms in plants. It covers emerging evidence on the importance of SA-JA crosstalk in regulating physiological, biochemical, and molecular adaptations to combined biotic and abiotic stresses.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"64"},"PeriodicalIF":5.8,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12569331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145395909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Exosomes as bilayer membranous vesicles are abundant in seminal plasma and mediate intercellular communication by transferring active biomolecules. Numerous studies have revealed the involvement of exosomes in regulating various biological properties of spermatozoa. However, the beneficial roles of seminal plasma exosomes in maintaining spermatozoon motility and mitochondrial function during liquid storage have not yet been unexplored in goat. In this study, the reduction of ATP content in goat spermatozoa was detected along with the decrease in spermatozoon motility under liquid storage, and the level of oxidative phosphorylation was also decreased. The interaction of exosomes and spermatozoon mitochondria was observed using high pressure freezing/freeze-substitution in combination with transmission electron microscope. Seminal plasma exosomes of goat were isolated and used to incubate with spermatozoa, and the binding and fusing of exosomes with spermatozoa was further validated. Furthermore, the addition of seminal plasma exosomes exhibited an increase in motility and oxidative phosphorylation in liquid-stored spermatozoa. Several mitochondrial functional parameters, including mitochondrial membrane potential, the levels of mitochondrial ROS and intracellular Ca2+, and the copy number and integrity of mitochondrial DNA, were also improved in spermatozoa after incubating with exosomes. Notably, the level of TFAM protein was increased in exosome-treated spermatozoa, indicating that the enhanced proteins may be delivered by exosomes to spermatozoa. These results suggest that seminal plasma exosomes could improve spermatozoon motility and mitochondrial function by regulating oxidative phosphorylation, which would provide insights into the understanding of protective roles of exosomes in goat spermatozoa during liquid storage.
{"title":"Seminal plasma exosomes improve the motility and mitochondrial function of goat spermatozoa during liquid storage by regulating oxidative phosphorylation.","authors":"Tengfei Liu, Mengmei Zhang, Xinkang Li, Xinyan Zhao, Yongjie Wu, Hong Chen","doi":"10.1007/s44154-025-00253-6","DOIUrl":"10.1007/s44154-025-00253-6","url":null,"abstract":"<p><p>Exosomes as bilayer membranous vesicles are abundant in seminal plasma and mediate intercellular communication by transferring active biomolecules. Numerous studies have revealed the involvement of exosomes in regulating various biological properties of spermatozoa. However, the beneficial roles of seminal plasma exosomes in maintaining spermatozoon motility and mitochondrial function during liquid storage have not yet been unexplored in goat. In this study, the reduction of ATP content in goat spermatozoa was detected along with the decrease in spermatozoon motility under liquid storage, and the level of oxidative phosphorylation was also decreased. The interaction of exosomes and spermatozoon mitochondria was observed using high pressure freezing/freeze-substitution in combination with transmission electron microscope. Seminal plasma exosomes of goat were isolated and used to incubate with spermatozoa, and the binding and fusing of exosomes with spermatozoa was further validated. Furthermore, the addition of seminal plasma exosomes exhibited an increase in motility and oxidative phosphorylation in liquid-stored spermatozoa. Several mitochondrial functional parameters, including mitochondrial membrane potential, the levels of mitochondrial ROS and intracellular Ca<sup>2+</sup>, and the copy number and integrity of mitochondrial DNA, were also improved in spermatozoa after incubating with exosomes. Notably, the level of TFAM protein was increased in exosome-treated spermatozoa, indicating that the enhanced proteins may be delivered by exosomes to spermatozoa. These results suggest that seminal plasma exosomes could improve spermatozoon motility and mitochondrial function by regulating oxidative phosphorylation, which would provide insights into the understanding of protective roles of exosomes in goat spermatozoa during liquid storage.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"65"},"PeriodicalIF":5.8,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12569307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145395851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-28DOI: 10.1007/s44154-025-00260-7
Sadegh Balotf, Richard Wilson, Roghayeh Hemmati, Mahsa Eshaghi, Calum Wilson, Luis A J Mur
Understanding plant-pathogen interactions requires a systems-level perspective that single-omics approaches, such as genomics, transcriptomics, proteomics, or metabolomics alone, often fail to provide. While these methods are informative, they are limited in their ability to capture the complexity of the dynamic molecular interactions between host and pathogen. Multi-omics strategies offer a powerful solution by integrating complementary data types, enabling a more comprehensive view of the molecular networks and pathways involved in disease progression and defence. Although technological advances have made omics analyses more accessible and affordable, their integration remains underutilised in plant science. This review highlights the limitations of single-omics studies in dissecting plant-pathogen interactions and emphasises the value of multi-omics approaches. We discuss available computational tools for data integration and visualisation, outline current challenges, including data heterogeneity, normalisation issues, and computational demands, and explore future directions such as the exploitation of artificial intelligence-based approaches and single-cell omics. We conclude that the increasing accessibility and affordability of omics analysis means that multi-omics strategies are now indispensable tools to investigate complex biological processes such as plant-pathogen interactions.
{"title":"Plant-pathogen interactions: making the case for multi-omics analysis of complex pathosystems.","authors":"Sadegh Balotf, Richard Wilson, Roghayeh Hemmati, Mahsa Eshaghi, Calum Wilson, Luis A J Mur","doi":"10.1007/s44154-025-00260-7","DOIUrl":"10.1007/s44154-025-00260-7","url":null,"abstract":"<p><p>Understanding plant-pathogen interactions requires a systems-level perspective that single-omics approaches, such as genomics, transcriptomics, proteomics, or metabolomics alone, often fail to provide. While these methods are informative, they are limited in their ability to capture the complexity of the dynamic molecular interactions between host and pathogen. Multi-omics strategies offer a powerful solution by integrating complementary data types, enabling a more comprehensive view of the molecular networks and pathways involved in disease progression and defence. Although technological advances have made omics analyses more accessible and affordable, their integration remains underutilised in plant science. This review highlights the limitations of single-omics studies in dissecting plant-pathogen interactions and emphasises the value of multi-omics approaches. We discuss available computational tools for data integration and visualisation, outline current challenges, including data heterogeneity, normalisation issues, and computational demands, and explore future directions such as the exploitation of artificial intelligence-based approaches and single-cell omics. We conclude that the increasing accessibility and affordability of omics analysis means that multi-omics strategies are now indispensable tools to investigate complex biological processes such as plant-pathogen interactions.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"66"},"PeriodicalIF":5.8,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12569278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145395903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Asian soybean rust, caused by Phakopsora pachyrhizi, is a devastating fungal disease threatening global soybean production, particularly in tropical regions where chemical control is increasingly unsustainable. This study employed cutting-edge 4D-DIA proteomics to investigate molecular defense mechanisms in resistant (SX6907) and susceptible (Tianlong 1) soybean cultivars during early infection (12 hpi and 3 dpi). We identified 12,852 proteins, with 1,510 differentially expressed proteins (DEPs) revealing genotype-specific responses. Resistant plants exhibited sustained upregulation of immune receptors (CRKs, LRR-RLKs), MAPK signaling components, and cell wall reinforcement proteins (peroxidases, XTHs), alongside dynamic modulation of calcium signaling and ROS homeostasis. These patterns suggest key pathways enriched in resistance may include phenylpropanoid biosynthesis, isoflavonoid production, and ER stress responses, while susceptible plants showed suppression of photosynthesis and defense pathways. Weighted Protein Co-expression Network Analysis(WPCNA) highlighted co-expression modules linked to resistance, potentially including NLR-mediated effector-triggered immunity. Crucially, DIR proteins and organelle-specific defense hubs (e.g., chloroplasts, nuclei) were implicated in rust resistance. Validation by qPCR confirmed concordance for 84% of tested DEPs. Our findings provide a protein-level blueprint of soybean rust resistance, identifying candidate targets for marker-assisted breeding and genetic engineering to develop durable resistant varieties, reducing reliance on fungicides.
{"title":"Temporal proteomic profiling via 4D-DIA reveals early defense mechanisms and core resistance determinants in soybean against Phakopsora pachyrhizi.","authors":"Zihua Lu, Cong Han, Chao Li, Kelin Deng, Zhihui Shan, Shuilian Chen, Hongli Yang, Yuanxiao Yang, Zhonglu Yang, Hongwei Wang, Haifeng Chen, Qingnan Hao","doi":"10.1007/s44154-025-00268-z","DOIUrl":"10.1007/s44154-025-00268-z","url":null,"abstract":"<p><p>Asian soybean rust, caused by Phakopsora pachyrhizi, is a devastating fungal disease threatening global soybean production, particularly in tropical regions where chemical control is increasingly unsustainable. This study employed cutting-edge 4D-DIA proteomics to investigate molecular defense mechanisms in resistant (SX6907) and susceptible (Tianlong 1) soybean cultivars during early infection (12 hpi and 3 dpi). We identified 12,852 proteins, with 1,510 differentially expressed proteins (DEPs) revealing genotype-specific responses. Resistant plants exhibited sustained upregulation of immune receptors (CRKs, LRR-RLKs), MAPK signaling components, and cell wall reinforcement proteins (peroxidases, XTHs), alongside dynamic modulation of calcium signaling and ROS homeostasis. These patterns suggest key pathways enriched in resistance may include phenylpropanoid biosynthesis, isoflavonoid production, and ER stress responses, while susceptible plants showed suppression of photosynthesis and defense pathways. Weighted Protein Co-expression Network Analysis(WPCNA) highlighted co-expression modules linked to resistance, potentially including NLR-mediated effector-triggered immunity. Crucially, DIR proteins and organelle-specific defense hubs (e.g., chloroplasts, nuclei) were implicated in rust resistance. Validation by qPCR confirmed concordance for 84% of tested DEPs. Our findings provide a protein-level blueprint of soybean rust resistance, identifying candidate targets for marker-assisted breeding and genetic engineering to develop durable resistant varieties, reducing reliance on fungicides.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"63"},"PeriodicalIF":5.8,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12559523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145380128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gayal (Bos frontalis) an endangered bovine species inhabitingChina, India, Bangladesh, Myanmar and Bhutan, has a mysterious evolutionary origin. Shaped by natural selection, its unique traits make it a valuable genetic resource; however, its populations are rapidly declining. In this study, comprehensive whole-genome resequencing of fifty-eight samples of Gayal from China, India, Myanmar and Bangladesh was performed. We identified over 44 million SNPs across four Gayal populations. Nucleotide diversity analysis revealed variations in genetic diversity, with the lowest occurring in India and the highest occurring in China. Phylogenetic tree analysis revealed three distinct clades representing China, India and Bangladesh-Myanmar, which were further confirmed by principal component and admixture analyses. The genetic exchanges between Gayal and other bovine species indicate limited influence from domestic cattle in both the Chinese and Bangladeshi Gayal populations. Mitochondrial DNA sequences and a phylogenetic tree highlighted the unique mitochondrial genome of Gayal. Genome-wide selection signals pinpointed candidate genes linked to mitochondrial function, immunity, musculoskeletal development, reproduction and growth performance. Distinct haplotype patterns emerged for the CCDC157, KIAA0753 and MTFP1 genes in the Chinese and Bangladesh-Myanmar Gayal populations, indicating artificial selection in the Chinese population. KEGG pathway and gene ontology enrichment analyses provided insights into processes related to neurodevelopment, cardiac function, tissue growth, immunity and metabolism. In summary, our study enhances our understanding of Gayal genetics, population structure and selection signals across four countries. This knowledge is crucial for conserving this endangered species amid its rapid decline.
{"title":"Evaluation of genetic diversity and selection signals in gayal populations across four countries through whole-genome resequencing.","authors":"Xin Liu, Qiaoxian Li, Jianyong Liu, Zulfiqar Ahmed, Jicai Zhang, Zhe Wang, Ankui Wang, Ningbo Chen, Yongzhen Huang, Gang Ren, Hong Chen, Chuzhao Lei, Bizhi Huang","doi":"10.1007/s44154-025-00252-7","DOIUrl":"10.1007/s44154-025-00252-7","url":null,"abstract":"<p><p>Gayal (Bos frontalis) an endangered bovine species inhabitingChina, India, Bangladesh, Myanmar and Bhutan, has a mysterious evolutionary origin. Shaped by natural selection, its unique traits make it a valuable genetic resource; however, its populations are rapidly declining. In this study, comprehensive whole-genome resequencing of fifty-eight samples of Gayal from China, India, Myanmar and Bangladesh was performed. We identified over 44 million SNPs across four Gayal populations. Nucleotide diversity analysis revealed variations in genetic diversity, with the lowest occurring in India and the highest occurring in China. Phylogenetic tree analysis revealed three distinct clades representing China, India and Bangladesh-Myanmar, which were further confirmed by principal component and admixture analyses. The genetic exchanges between Gayal and other bovine species indicate limited influence from domestic cattle in both the Chinese and Bangladeshi Gayal populations. Mitochondrial DNA sequences and a phylogenetic tree highlighted the unique mitochondrial genome of Gayal. Genome-wide selection signals pinpointed candidate genes linked to mitochondrial function, immunity, musculoskeletal development, reproduction and growth performance. Distinct haplotype patterns emerged for the CCDC157, KIAA0753 and MTFP1 genes in the Chinese and Bangladesh-Myanmar Gayal populations, indicating artificial selection in the Chinese population. KEGG pathway and gene ontology enrichment analyses provided insights into processes related to neurodevelopment, cardiac function, tissue growth, immunity and metabolism. In summary, our study enhances our understanding of Gayal genetics, population structure and selection signals across four countries. This knowledge is crucial for conserving this endangered species amid its rapid decline.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"61"},"PeriodicalIF":5.8,"publicationDate":"2025-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12553695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145370509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-26DOI: 10.1007/s44154-025-00265-2
Kun Wang, Yaqin Wang, Shuai Fu, Yuchong Tan, Liang Wu, Yi Xu, Jianxiang Wu, Xueping Zhou
Modification of proteins by ubiquitin is a dynamic and reversible process. It is unclear whether rice stripe virus (RSV) can modulate the plant deubiquitination pathway. In this study, we found that RSV infection can specifically upregulate the expression of the deubiquitinase NbUBP16. Further analysis revealed that NbUBP16 stabilizes serine hydroxymethyltrasferase (SHMT1) by binding to NbSHMT1 and removing its polyubiquitination modification mediated by E3 ligase MEL, which inhibits downstream SHMT1-mediated ROS accumulation and thereby facilitates RSV infection. Our findings provide new insights into the molecular arms race between pathogens and plants, demonstrating how a plant virus can undermine plant defenses by hijacking host deubiquitination pathways.
{"title":"Upregulation of deubiquitinase UBP16 induced by rice stripe virus infection stabilizes SHMT1 to suppress ROS accumulation and facilitate virus infection in Nicotiana benthamiana.","authors":"Kun Wang, Yaqin Wang, Shuai Fu, Yuchong Tan, Liang Wu, Yi Xu, Jianxiang Wu, Xueping Zhou","doi":"10.1007/s44154-025-00265-2","DOIUrl":"10.1007/s44154-025-00265-2","url":null,"abstract":"<p><p>Modification of proteins by ubiquitin is a dynamic and reversible process. It is unclear whether rice stripe virus (RSV) can modulate the plant deubiquitination pathway. In this study, we found that RSV infection can specifically upregulate the expression of the deubiquitinase NbUBP16. Further analysis revealed that NbUBP16 stabilizes serine hydroxymethyltrasferase (SHMT1) by binding to NbSHMT1 and removing its polyubiquitination modification mediated by E3 ligase MEL, which inhibits downstream SHMT1-mediated ROS accumulation and thereby facilitates RSV infection. Our findings provide new insights into the molecular arms race between pathogens and plants, demonstrating how a plant virus can undermine plant defenses by hijacking host deubiquitination pathways.</p>","PeriodicalId":74874,"journal":{"name":"Stress biology","volume":"5 1","pages":"62"},"PeriodicalIF":5.8,"publicationDate":"2025-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12553715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145370513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}