Pub Date : 2025-12-12DOI: 10.1016/j.gene.2025.149957
Hao Ding, Qilu Deng, Zhenhua Guo
Musculoskeletal injuries and interindividual variability in recovery remain critical challenges for sustaining elite athletic performance. Despite advances in diagnostics, training, and rehabilitation, unexplained differences in injury risk and recovery efficiency persist. Growing evidence implicates genetic and epigenetic mechanisms in these disparities, influencing collagen integrity, inflammatory regulation, oxidative stress, and muscle regeneration. Key contributors include single-nucleotide polymorphisms (SNPs) in COL1A1, COL5A1, ACTN3, and IL6, as well as novel loci identified by genome-wide association studies (GWAS). Polygenic risk scores (PRS), which integrate the effects of multiple low-impact variants, enhance prediction compared to single-gene markers. Epigenetic regulators, including DNA methylation and exercise-responsive microRNAs (e.g., miR-206, miR-133a, miR-486), provide a dynamic interface linking genetic predisposition with environmental factors such as training load and nutrition. Integration of genomic data with wearable technologies and artificial intelligence enables real-time monitoring, adaptive recovery, and precision load management. Yet, clinical translation faces challenges including limited population diversity, interpretative complexity, and ethical concerns over data privacy and potential misuse. Advancing precision sports medicine will require multidisciplinary, systems-level strategies that unite molecular insights with practical implementation, ultimately enabling individualized injury prevention, optimized rehabilitation, and the preservation of long-term athlete health and performance.
{"title":"Genetic and epigenetic determinants of injury risk and recovery in elite athletes: toward precision sports medicine.","authors":"Hao Ding, Qilu Deng, Zhenhua Guo","doi":"10.1016/j.gene.2025.149957","DOIUrl":"https://doi.org/10.1016/j.gene.2025.149957","url":null,"abstract":"<p><p>Musculoskeletal injuries and interindividual variability in recovery remain critical challenges for sustaining elite athletic performance. Despite advances in diagnostics, training, and rehabilitation, unexplained differences in injury risk and recovery efficiency persist. Growing evidence implicates genetic and epigenetic mechanisms in these disparities, influencing collagen integrity, inflammatory regulation, oxidative stress, and muscle regeneration. Key contributors include single-nucleotide polymorphisms (SNPs) in COL1A1, COL5A1, ACTN3, and IL6, as well as novel loci identified by genome-wide association studies (GWAS). Polygenic risk scores (PRS), which integrate the effects of multiple low-impact variants, enhance prediction compared to single-gene markers. Epigenetic regulators, including DNA methylation and exercise-responsive microRNAs (e.g., miR-206, miR-133a, miR-486), provide a dynamic interface linking genetic predisposition with environmental factors such as training load and nutrition. Integration of genomic data with wearable technologies and artificial intelligence enables real-time monitoring, adaptive recovery, and precision load management. Yet, clinical translation faces challenges including limited population diversity, interpretative complexity, and ethical concerns over data privacy and potential misuse. Advancing precision sports medicine will require multidisciplinary, systems-level strategies that unite molecular insights with practical implementation, ultimately enabling individualized injury prevention, optimized rehabilitation, and the preservation of long-term athlete health and performance.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149957"},"PeriodicalIF":2.4,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145755941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fusarium oxysporum f. sp. cubense (Foc), the causal agent of banana Fusarium wilt, is one of the most destructive plant pathogens worldwide. However, the molecular mechanisms that integrate fungal growth, metabolism, and virulence remain poorly understood. This study identifies and functionally characterizes FoSrk1, a serine/arginine-rich protein kinase (SRPK), in Foc. Deletion of FoSrk1 markedly impaired vegetative growth, reduced aerial mycelium formation and conidiation, and significantly attenuated virulence toward banana plantlets. The mutant also exhibited compromised utilization of diverse carbon sources, accompanied by altered expression of 32 genes involved in carbon metabolism. Complementation with the wild-type FoSrk1 allele restored normal growth and pathogenicity, confirming the gene's essential role. Transcriptomic analyses revealed that loss of FoSrk1 altered the expression of 2,500 genes and was associated with changes in 37 alternative splicing events, predominantly intron retention, affecting transcripts linked to protein metabolism, ribosome biogenesis, and redox processes. Moreover, several virulenceassociated genes encoding ABC transporters, cytochrome P450 enzymes, and hydrophobins were downregulated in the FoSrk1-deficient strain. These findings suggest that FoSrk1 acts as an important regulator that couples RNA processing with metabolic and pathogenic pathways and is required for normal fungal development and virulence. This study provides new insight into the molecular basis of pathogenic adaptation and identifies FoSrk1 as a potential target for antifungal intervention strategies.
香蕉枯萎病病原菌Fusarium oxysporum f. sp. cubense (Foc)是世界上最具破坏性的植物病原体之一。然而,整合真菌生长、代谢和毒力的分子机制仍然知之甚少。本研究鉴定并功能表征了FoSrk1,一种在Foc中富含丝氨酸/精氨酸的蛋白激酶(SRPK)。缺失FoSrk1显著损害香蕉植株的营养生长,减少气生菌丝的形成和分生,并显著降低对香蕉植株的毒力。该突变体还表现出对不同碳源的利用受损,并伴有涉及碳代谢的32个基因的表达改变。与野生型FoSrk1等位基因的互补恢复了正常的生长和致病性,证实了该基因的重要作用。转录组学分析显示,FoSrk1的缺失改变了2500个基因的表达,并与37个可变剪接事件的变化有关,主要是内含子保留,影响与蛋白质代谢、核糖体生物发生和氧化还原过程相关的转录本。此外,编码ABC转运蛋白、细胞色素P450酶和疏水蛋白的几个毒力相关基因在fosrk1缺陷菌株中下调。这些发现表明,FoSrk1是一个重要的调节因子,将RNA加工与代谢和致病途径结合起来,是正常真菌发育和毒力所必需的。该研究为致病适应的分子基础提供了新的见解,并确定了FoSrk1作为抗真菌干预策略的潜在靶点。
{"title":"SR protein kinase FoSrk1 integrates RNA splicing, carbon metabolism, and virulence in Fusarium oxysporum f. sp. cubense.","authors":"Han Ouyang, Jiayi Peng, Zhouqi Huang, Yicong Huang, Yinglan Wen, Yuan Xu, Yu Long, Huijiao Lin, Qiyan Fu, Zhaojian Ding","doi":"10.1016/j.gene.2025.149954","DOIUrl":"https://doi.org/10.1016/j.gene.2025.149954","url":null,"abstract":"<p><p>Fusarium oxysporum f. sp. cubense (Foc), the causal agent of banana Fusarium wilt, is one of the most destructive plant pathogens worldwide. However, the molecular mechanisms that integrate fungal growth, metabolism, and virulence remain poorly understood. This study identifies and functionally characterizes FoSrk1, a serine/arginine-rich protein kinase (SRPK), in Foc. Deletion of FoSrk1 markedly impaired vegetative growth, reduced aerial mycelium formation and conidiation, and significantly attenuated virulence toward banana plantlets. The mutant also exhibited compromised utilization of diverse carbon sources, accompanied by altered expression of 32 genes involved in carbon metabolism. Complementation with the wild-type FoSrk1 allele restored normal growth and pathogenicity, confirming the gene's essential role. Transcriptomic analyses revealed that loss of FoSrk1 altered the expression of 2,500 genes and was associated with changes in 37 alternative splicing events, predominantly intron retention, affecting transcripts linked to protein metabolism, ribosome biogenesis, and redox processes. Moreover, several virulenceassociated genes encoding ABC transporters, cytochrome P450 enzymes, and hydrophobins were downregulated in the FoSrk1-deficient strain. These findings suggest that FoSrk1 acts as an important regulator that couples RNA processing with metabolic and pathogenic pathways and is required for normal fungal development and virulence. This study provides new insight into the molecular basis of pathogenic adaptation and identifies FoSrk1 as a potential target for antifungal intervention strategies.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149954"},"PeriodicalIF":2.4,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145755939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-11DOI: 10.1016/j.gene.2025.149955
Amber R Paulson, Maureen O'Callaghan, Xue-Xian Zhang, Naran Naren, Marion Schoof, Mark R H Hurst
Entomopathogenic bacteria express virulence genes in a temperature-dependent manner, but the underlying molecular mechanisms remain poorly understood. Here, we describe the roles of an unusual LytTR-containing transcription factor Yen6 in determining the virulence of Yersinia entomophaga (MH96). An initial transcriptome analysis in vivo revealed that yen6, located 1,372 bp upstream from genes encoding the Yen Toxin complex (Yen-Tc), exhibited significantly higher transcriptional activity at 37 °C compared to 25 °C (adjusted p-value < 0.001) during intrahemocoelic infection in the insect model Galleria mellonella. Deletion of yen6 also significantly reduced MH96's virulence in G. mellonella by up to three-fold. Next, comparing the transcriptome of wild-type MH96 and its derived Δyen6 mutant revealed genes for ribose utilization were downregulated whereas genes for fructose utilization and the RNA-binding protein YhbY were upregulated in the yen6-deficient mutant. Subsequent electromobility shift assays showed that purified Yen6His6 protein was capable of specifically binding to the promoter regions of the ribose and fructose utilization-related gene clusters, as well as yhbY. A 645-nucleotide-long 3' untranslated region, designated yen7_AS, was identified extending from the yen6 coding region. Notably, yen7_AS completely overlaps the yen7 gene on the opposing strand and may therefore act as a cis anti-sense RNA regulating yen7 expression, which encodes a putative transcriptional regulator of the Yen-Tc. This study highlights the critical role of the yen6-yen7 locus in MH96 virulence during G. mellonella infection, including the complex mechanisms controlling insecticidal exoprotein production.
{"title":"Two transcription factors and one antisense RNA underlie the thermoregulated insect pathogenicity of Yersinia entomophaga MH96.","authors":"Amber R Paulson, Maureen O'Callaghan, Xue-Xian Zhang, Naran Naren, Marion Schoof, Mark R H Hurst","doi":"10.1016/j.gene.2025.149955","DOIUrl":"https://doi.org/10.1016/j.gene.2025.149955","url":null,"abstract":"<p><p>Entomopathogenic bacteria express virulence genes in a temperature-dependent manner, but the underlying molecular mechanisms remain poorly understood. Here, we describe the roles of an unusual LytTR-containing transcription factor Yen6 in determining the virulence of Yersinia entomophaga (MH96). An initial transcriptome analysis in vivo revealed that yen6, located 1,372 bp upstream from genes encoding the Yen Toxin complex (Yen-Tc), exhibited significantly higher transcriptional activity at 37 °C compared to 25 °C (adjusted p-value < 0.001) during intrahemocoelic infection in the insect model Galleria mellonella. Deletion of yen6 also significantly reduced MH96's virulence in G. mellonella by up to three-fold. Next, comparing the transcriptome of wild-type MH96 and its derived Δyen6 mutant revealed genes for ribose utilization were downregulated whereas genes for fructose utilization and the RNA-binding protein YhbY were upregulated in the yen6-deficient mutant. Subsequent electromobility shift assays showed that purified Yen6<sub>His6</sub> protein was capable of specifically binding to the promoter regions of the ribose and fructose utilization-related gene clusters, as well as yhbY. A 645-nucleotide-long 3' untranslated region, designated yen7_AS, was identified extending from the yen6 coding region. Notably, yen7_AS completely overlaps the yen7 gene on the opposing strand and may therefore act as a cis anti-sense RNA regulating yen7 expression, which encodes a putative transcriptional regulator of the Yen-Tc. This study highlights the critical role of the yen6-yen7 locus in MH96 virulence during G. mellonella infection, including the complex mechanisms controlling insecticidal exoprotein production.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149955"},"PeriodicalIF":2.4,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-11DOI: 10.1016/j.gene.2025.149952
M.A.H. Dilshan , Gaeun Kim , W.K.M. Omeka , D.S. Liyanage , H.M.V. Udayantha , D.C.G. Rodrigo , G.A.N.P. Ganepola , H.A.C.R. Hanchapola , Y.K. Kodagoda , Po Gong , Jihun Lee , Sukkyoung Lee , Jeongeun Kim , Jehee Lee
Hypoxia, caused by reduced dissolved oxygen (DO) levels in water, is a critical challenge in aquaculture and often results in stress, anorexia, and mass mortality in fish. The olive flounder (Paralichthys olivaceus) is a key species in South Korea’s global aquaculture exports. However, aquaculture production of P. olivaceus experiences significant economic losses caused by hypoxia-induced fish mortality, highlighting the critical need for developing genetically improved hypoxia-tolerant strains. In this study, a genome-wide association study (GWAS) was performed to unveil single-nucleotide polymorphisms (SNPs) associated with acute hypoxia tolerance and elucidate underlying regulatory mechanisms. A total of 382 P. olivaceus fish were measured for blood serum cortisol level using enzyme-linked immunosorbent assay (ELISA) upon acute hypoxia stress. Blood plasma cortisol levels were used as a proxy phenotype of hypoxia tolerance, with the hypothesis that elevated concentrations indicate low tolerance, and minimized concentrations indicate high tolerance to acute hypoxia stress. Then, fish were genotyped using the Affymetrix® Axiom® myDesign™ genotype array, and 57,651 SNPs were retained after quality control filtering. A significant SNP was identified on chromosome 15 of the P. olivaceus genome, above the suggestive threshold (p < 1 × 10−4) for the stress cortisol level trait. A strongly associated SNP with accession number AX-419149718 was located in the zona pellucida-like domain-containing protein 1 (Zpld1) gene. Gene ontology (GO) analysis suggests that Zpld1 is involved in signaling pathways, including the integrin-mediated signaling pathway, thereby contributing to the mitigation of hypoxia stress effects. Collectively, this study provides insights into the genetic basis of acute hypoxia tolerance in P. olivaceus and may serve as a foundation for establishing genomic selection of olive flounders with acute hypoxia stress tolerance in aquaculture breeding programs.
{"title":"Genome-wide association study of tolerance to acute hypoxia in the olive flounder (Paralichthys olivaceus) using individual blood cortisol levels as a physiological phenotype","authors":"M.A.H. Dilshan , Gaeun Kim , W.K.M. Omeka , D.S. Liyanage , H.M.V. Udayantha , D.C.G. Rodrigo , G.A.N.P. Ganepola , H.A.C.R. Hanchapola , Y.K. Kodagoda , Po Gong , Jihun Lee , Sukkyoung Lee , Jeongeun Kim , Jehee Lee","doi":"10.1016/j.gene.2025.149952","DOIUrl":"10.1016/j.gene.2025.149952","url":null,"abstract":"<div><div>Hypoxia, caused by reduced dissolved oxygen (DO) levels in water, is a critical challenge in aquaculture and often results in stress, anorexia, and mass mortality in fish. The olive flounder (<em>Paralichthys olivaceus</em>) is a key species in South Korea’s global aquaculture exports. However, aquaculture production of <em>P. olivaceus</em> experiences significant economic losses caused by hypoxia-induced fish mortality, highlighting the critical need for developing genetically improved hypoxia-tolerant strains. In this study, a genome-wide association study (GWAS) was performed to unveil single-nucleotide polymorphisms (SNPs) associated with acute hypoxia tolerance and elucidate underlying regulatory mechanisms. A total of 382 <em>P. olivaceus</em> fish were measured for blood serum cortisol level using enzyme-linked immunosorbent assay (ELISA) upon acute hypoxia stress. Blood plasma cortisol levels were used as a proxy phenotype of hypoxia tolerance, with the hypothesis that elevated concentrations indicate low tolerance, and minimized concentrations indicate high tolerance to acute hypoxia stress. Then, fish were genotyped using the Affymetrix® Axiom® myDesign™ genotype array, and 57,651 SNPs were retained after quality control filtering. A significant SNP was identified on chromosome 15 of the <em>P. olivaceus</em> genome, above the suggestive threshold (<em>p</em> < 1 × 10<sup>−4</sup>) for the stress cortisol level trait. A strongly associated SNP with accession number AX-419149718 was located in the zona pellucida-like domain-containing protein 1 (<em>Zpld1</em>) gene. Gene ontology (GO) analysis suggests that <em>Zpld1</em> is involved in signaling pathways, including the integrin-mediated signaling pathway, thereby contributing to the mitigation of hypoxia stress effects. Collectively, this study provides insights into the genetic basis of acute hypoxia tolerance in <em>P. olivaceus</em> and may serve as a foundation for establishing genomic selection of olive flounders with acute hypoxia stress tolerance in aquaculture breeding programs.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"980 ","pages":"Article 149952"},"PeriodicalIF":2.4,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145735922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-11DOI: 10.1016/j.gene.2025.149956
Seongmin Kim, Hankyeol Jeong, Ga-Eun Kim, Kwan-Woo Kim, Woncheoul Park, Jaemin Kim, Bong-Hwan Choi
Korean indigenous goats are maintained as purebred lineages in geographically isolated populations such as Dangjin, Gyeongsang National University (GNU), Jangsu, and Tongyeong. However, their small population size and high rates of inbreeding have raised concerns regarding the preservation of genetic diversity. We generated SNP genotypes for 217 Korean indigenous goats using the GoatSNP50 BeadChip, and standardized body size measurements with complete metadata were available for 64 adult individuals. Principal component analysis (PCA) clearly separated the four lineages, with the GNU population showing particularly high values of inbreeding coefficient and proportion of runs of homozygosity, reflecting the impact of recent closed breeding. Genome-wide patterns of haplotype sharing revealed exploratory trends suggesting that introgression from global breeds tended to coincide with larger body size, whereas intensified inbreeding within the Korean population showed a general tendency toward reduced body size. Furthermore, cross-population extended haplotype homozygosity (XP-EHH) analysis revealed candidate genes, including ADGRL3, SP8, and ARL6IP5, that are likely involved in adaptation to seasonal environmental stress. Our findings highlight the global connectivity, functional relevance of body conformation traits, and selective signatures of Korean indigenous goats, providing a genomic foundation for preserving diversity and guiding future breeding.
{"title":"Differential genomic signatures of homozygosity and a haplotype sharing Extents across breeds associated with body size variation in Korean indigenous goats.","authors":"Seongmin Kim, Hankyeol Jeong, Ga-Eun Kim, Kwan-Woo Kim, Woncheoul Park, Jaemin Kim, Bong-Hwan Choi","doi":"10.1016/j.gene.2025.149956","DOIUrl":"https://doi.org/10.1016/j.gene.2025.149956","url":null,"abstract":"<p><p>Korean indigenous goats are maintained as purebred lineages in geographically isolated populations such as Dangjin, Gyeongsang National University (GNU), Jangsu, and Tongyeong. However, their small population size and high rates of inbreeding have raised concerns regarding the preservation of genetic diversity. We generated SNP genotypes for 217 Korean indigenous goats using the GoatSNP50 BeadChip, and standardized body size measurements with complete metadata were available for 64 adult individuals. Principal component analysis (PCA) clearly separated the four lineages, with the GNU population showing particularly high values of inbreeding coefficient and proportion of runs of homozygosity, reflecting the impact of recent closed breeding. Genome-wide patterns of haplotype sharing revealed exploratory trends suggesting that introgression from global breeds tended to coincide with larger body size, whereas intensified inbreeding within the Korean population showed a general tendency toward reduced body size. Furthermore, cross-population extended haplotype homozygosity (XP-EHH) analysis revealed candidate genes, including ADGRL3, SP8, and ARL6IP5, that are likely involved in adaptation to seasonal environmental stress. Our findings highlight the global connectivity, functional relevance of body conformation traits, and selective signatures of Korean indigenous goats, providing a genomic foundation for preserving diversity and guiding future breeding.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149956"},"PeriodicalIF":2.4,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Phosphoenolpyruvate carboxylase (PEPC) is a bicarbonate fixation enzyme that is associated with nitrogen metabolism. We previously observed that NO3- affected the expression levels of PEPC genes differently in detached wheat leaves. Three types of PEPC isogenes, including the orthologous isogene group (Tappc1b) for C4-photosynthetic PEPC, exhibited distinct transcriptionally up-regulated patterns from one another. However, it remains unclear which nitrogen compounds exactly trigger the gene expression responses and their light dependency. Here, we investigated the cause of isogene-specific expression responses of PEPCs to different forms of nitrogen supplementation. Detached leaves from wheat seedlings cultivated under a nitrogen-deficient condition were incubated with NO3-, NH4+, and urea under both light and dark conditions. Notably, the genes analyzed exhibited markedly different expression patterns across the nitrogen forms under the light condition. Tappc1a, which did non-respond to NO3-, was up-regulated by NH4+ exclusively under light. Tappc2 was also up-regulated by NO3- and NH4+ only under light, and these up-regulations were suppressed under the dark condition. The candidate transcriptional regulator DOF1 for Tappc1b in wheat was also up-regulated by NO3- only under light condition, but earlier than Tappc1b, implicating a DOF1-mediated transcriptional response of Tappc1b to NO3-. Comparison of Tappc1b promoter sequences with that of NO3--responsive maize C4PEPC revealed conserved light-responsive elements near the Dof1 binding site. These findings suggest that distinct transcriptional regulatory cascades would exist for non-photosynthetic PEPCs in response to different inorganic nitrogen forms.
{"title":"Inorganic nitrogen sources and light cooperatively stimulate gene regulation for non-photosynthetic phosphoenolpyruvate carboxylase in wheat leaves.","authors":"Naoki Yamamoto, Jingru Jiang, Haoyu Deng, Ken-Ichi Kurotani, Jiang Zou, Zaijun Yang","doi":"10.1016/j.gene.2025.149950","DOIUrl":"https://doi.org/10.1016/j.gene.2025.149950","url":null,"abstract":"<p><p>Phosphoenolpyruvate carboxylase (PEPC) is a bicarbonate fixation enzyme that is associated with nitrogen metabolism. We previously observed that NO<sub>3</sub><sup>-</sup> affected the expression levels of PEPC genes differently in detached wheat leaves. Three types of PEPC isogenes, including the orthologous isogene group (Tappc1b) for C<sub>4</sub>-photosynthetic PEPC, exhibited distinct transcriptionally up-regulated patterns from one another. However, it remains unclear which nitrogen compounds exactly trigger the gene expression responses and their light dependency. Here, we investigated the cause of isogene-specific expression responses of PEPCs to different forms of nitrogen supplementation. Detached leaves from wheat seedlings cultivated under a nitrogen-deficient condition were incubated with NO<sub>3</sub><sup>-</sup>, NH<sub>4</sub><sup>+</sup>, and urea under both light and dark conditions. Notably, the genes analyzed exhibited markedly different expression patterns across the nitrogen forms under the light condition. Tappc1a, which did non-respond to NO<sub>3</sub><sup>-</sup>, was up-regulated by NH<sub>4</sub><sup>+</sup> exclusively under light. Tappc2 was also up-regulated by NO<sub>3</sub><sup>-</sup> and NH<sub>4</sub><sup>+</sup> only under light, and these up-regulations were suppressed under the dark condition. The candidate transcriptional regulator DOF1 for Tappc1b in wheat was also up-regulated by NO<sub>3</sub><sup>-</sup> only under light condition, but earlier than Tappc1b, implicating a DOF1-mediated transcriptional response of Tappc1b to NO<sub>3</sub><sup>-</sup>. Comparison of Tappc1b promoter sequences with that of NO<sub>3</sub><sup>-</sup>-responsive maize C<sub>4</sub>PEPC revealed conserved light-responsive elements near the Dof1 binding site. These findings suggest that distinct transcriptional regulatory cascades would exist for non-photosynthetic PEPCs in response to different inorganic nitrogen forms.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149950"},"PeriodicalIF":2.4,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145741963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-09DOI: 10.1016/j.gene.2025.149949
Yang Li, Xiang Dong, Jian Guo, Ya-Feng Lv
Globoid cell leukodystrophy (GLD) is an autosomal recessive lysosomal storage disorder caused by mutations in the β-galactosylceramidase(GALC) gene, resulting in enzyme deficiency and the progressive accumulation of galactosylsphingosine and galactosylceramide in the white matter of the central nervous system and in peripheral nerves, which in turn triggers demyelination. Although no curative therapy is currently available, studies in animal models in recent years have shown that gene therapy can ameliorate pathological and biochemical abnormalities and holds considerable promise for clinical translation. This article reviews advances in gene therapy in animal models of GLD and discusses key directions and challenges for future treatments.
{"title":"Gene therapy for Krabbe disease: evidence from mouse and canine models.","authors":"Yang Li, Xiang Dong, Jian Guo, Ya-Feng Lv","doi":"10.1016/j.gene.2025.149949","DOIUrl":"10.1016/j.gene.2025.149949","url":null,"abstract":"<p><p>Globoid cell leukodystrophy (GLD) is an autosomal recessive lysosomal storage disorder caused by mutations in the β-galactosylceramidase(GALC) gene, resulting in enzyme deficiency and the progressive accumulation of galactosylsphingosine and galactosylceramide in the white matter of the central nervous system and in peripheral nerves, which in turn triggers demyelination. Although no curative therapy is currently available, studies in animal models in recent years have shown that gene therapy can ameliorate pathological and biochemical abnormalities and holds considerable promise for clinical translation. This article reviews advances in gene therapy in animal models of GLD and discusses key directions and challenges for future treatments.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149949"},"PeriodicalIF":2.4,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145741704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
As organisms age, physiological and pathological changes occur, with altered lncRNA expression playing a key role. However, their regulatory mechanisms in aging remain unclear. This study investigates the differential expression of lncRNAs between aged and young mice, and explores the lncRNA–miRNA–mRNA interplay to gain insights into the molecular basis of aging.
Methods
We performed whole-transcriptome sequencing on tibialis anterior muscles from four aged (20-month-old) and four young (3-month-old) mice. Hub genes were identified via PPI and WGCNA analyses, followed by functional enrichment. Integrative analysis revealed interactions among differentially expressed lncRNAs, miRNAs, and mRNAs, leading to the construction of cis-/trans-regulatory and ceRNA networks.
Results
Our results revealed 746 significantly differentially expressed known lncRNAs (465 upregulated, 281 downregulated) and 27 novel lncRNAs in aged mouse TA muscle, alongside 50 miRNAs and 1124 mRNAs. Based on lncRNA classification (antisense, intergenic, intronic), we constructed subtype-specific cis- and trans-regulatory networks. Hub genes were identified via PPI and WGCNA analyses to further refine these networks. Highly expressed and variable genes were also integrated into regulatory mapping. Enrichment analyses indicated involvement in extracellular matrix remodeling, epithelial cell migration, and immune response.
Conclusions
This study systematically profiled age-related changes in lncRNAs, miRNAs, and mRNAs in TA muscle, and constructed core regulatory networks based on lncRNA subtypes. This study systematically profiled age-related transcriptomic changes in mouse skeletal muscle and constructed lncRNA–miRNA–mRNA regulatory networks associated with aging. These results provide a valuable resource and generate hypotheses for future experimental validation of lncRNA-mediated regulatory mechanisms in muscle aging.
{"title":"Comprehensive transcriptomic profiling reveals lncRNA–miRNA–mRNA regulatory networks in skeletal muscle aging of mice","authors":"Jinrui Jia, Qingyan Wang, Xuanye Jiang, Hao Chen, Minwei Huang, Bing Ni, Huiying Zhang, Xin’e Shi, Jianjun Jin","doi":"10.1016/j.gene.2025.149946","DOIUrl":"10.1016/j.gene.2025.149946","url":null,"abstract":"<div><h3>Purpose</h3><div>As organisms age, physiological and pathological changes occur, with altered lncRNA expression playing a key role. However, their regulatory mechanisms in aging remain unclear. This study investigates the differential expression of lncRNAs between aged and young mice, and explores the lncRNA–miRNA–mRNA interplay to gain insights into the molecular basis of aging.</div></div><div><h3>Methods</h3><div>We performed whole-transcriptome sequencing on tibialis anterior muscles from four aged (20-month-old) and four young (3-month-old) mice. Hub genes were identified via PPI and WGCNA analyses, followed by functional enrichment. Integrative analysis revealed interactions among differentially expressed lncRNAs, miRNAs, and mRNAs, leading to the construction of cis-/<em>trans</em>-regulatory and ceRNA networks.</div></div><div><h3>Results</h3><div>Our results revealed 746 significantly differentially expressed known lncRNAs (465 upregulated, 281 downregulated) and 27 novel lncRNAs in aged mouse TA muscle, alongside 50 miRNAs and 1124 mRNAs. Based on lncRNA classification (antisense, intergenic, intronic), we constructed subtype-specific cis- and <em>trans</em>-regulatory networks. Hub genes were identified via PPI and WGCNA analyses to further refine these networks. Highly expressed and variable genes were also integrated into regulatory mapping. Enrichment analyses indicated involvement in extracellular matrix remodeling, epithelial cell migration, and immune response.</div></div><div><h3>Conclusions</h3><div>This study systematically profiled age-related changes in lncRNAs, miRNAs, and mRNAs in TA muscle, and constructed core regulatory networks based on lncRNA subtypes. This study systematically profiled age-related transcriptomic changes in mouse skeletal muscle and constructed lncRNA–miRNA–mRNA regulatory networks associated with aging. These results provide a valuable resource and generate hypotheses for future experimental validation of lncRNA-mediated regulatory mechanisms in muscle aging.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149946"},"PeriodicalIF":2.4,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145722080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-07DOI: 10.1016/j.gene.2025.149933
Soumi Chowdhury , Harsh Pawar
The Target of Rapamycin (TOR) kinase family is a central regulator of eukaryotic cell growth and metabolism. Unlike most eukaryotes that possess one or two TOR genes, Leishmania species encode four distinct paralogs, suggesting lineage-specific expansion and functional diversification. In this study, we performed a comprehensive phylogenetic and domain analysis of TOR paralogs across multiple Leishmania species, with Trypanosoma brucei serving as a comparative reference. TOR1 and TOR2 were found to be highly conserved, possessing canonical FAT, FRB, and PI3Kc domains, consistent with their roles in the essential TORC1 and TORC2 complexes. TOR3 and TOR4 displayed significant sequence divergence and altered domain structures, particularly in visceral and mucocutaneous species. TOR3 lacks the FRB domain but retains kinase activity and is implicated in arginine sensing and acidocalcisome biogenesis. TOR4 shows the highest divergence, including truncated domains and species-specific clustering, suggesting a role in parasite adaptation or stage differentiation. Functional annotations further support this, as TOR1 and TOR2 are enriched in kinase functions, while TOR3 and TOR4 are associated with hypothetical or uncharacterized proteins. The conserved PI3Kc domain across all paralogs offers a target for drug development. These findings enhance our understanding of TOR evolution and its therapeutic potential in leishmaniasis.
{"title":"Target of rapamycin (TOR) kinases in Leishmania: Insights from comparative analyses with Trypanosomatids","authors":"Soumi Chowdhury , Harsh Pawar","doi":"10.1016/j.gene.2025.149933","DOIUrl":"10.1016/j.gene.2025.149933","url":null,"abstract":"<div><div>The Target of Rapamycin (TOR) kinase family is a central regulator of eukaryotic cell growth and metabolism. Unlike most eukaryotes that possess one or two TOR genes, <em>Leishmania</em> species encode four distinct paralogs, suggesting lineage-specific expansion and functional diversification. In this study, we performed a comprehensive phylogenetic and domain analysis of TOR paralogs across multiple <em>Leishmania</em> species, with <em>Trypanosoma brucei</em> serving as a comparative reference. TOR1 and TOR2 were found to be highly conserved, possessing canonical FAT, FRB, and PI3Kc domains, consistent with their roles in the essential TORC1 and TORC2 complexes. TOR3 and TOR4 displayed significant sequence divergence and altered domain structures, particularly in visceral and mucocutaneous species. TOR3 lacks the FRB domain but retains kinase activity and is implicated in arginine sensing and acidocalcisome biogenesis. TOR4 shows the highest divergence, including truncated domains and species-specific clustering, suggesting a role in parasite adaptation or stage differentiation. Functional annotations further support this, as TOR1 and TOR2 are enriched in kinase functions, while TOR3 and TOR4 are associated with hypothetical or uncharacterized proteins. The conserved PI3Kc domain across all paralogs offers a target for drug development. These findings enhance our understanding of TOR evolution and its therapeutic potential in leishmaniasis.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149933"},"PeriodicalIF":2.4,"publicationDate":"2025-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145713995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-06DOI: 10.1016/j.gene.2025.149944
Ziling Tao , Shiyu Cai , YiMing Wang, Fengxiu li, Lu Lv, Haimeng Bai, Ludan Li, Jihong Jiang, Xiaoying Cao
Dendrobium officinale is renowned as the foremost among the “Nine Immortal Herbs of China”. Our previous research showed enhanced flavonoid accumulation following induction by the endophyte Wickerhamomyces sp. KLBMPSYLp8. Transcriptome data analysis identified multiple upregulated transcription factor (TF) genes. We conducted transient overexpression analysis of 10 significantly upregulated TF genes in D. officinale leaves. The results demonstrated that transient overexpression of the DoWRKY26 significantly enhanced flavonoid accumulation, with a 33 % increase compared to the empty vector control group. Furthermore, DoWRKY26 overexpression also upregulated the expression levels of key enzyme genes implicated in the flavonoid biosynthesis pathway. Subcellular localization confirmed its nuclear presence. DoWRKY26 expression was induced by salicylic acid (SA), abscisic acid (ABA), 1-Aminocyclopropane-1-carboxylic Acid (ACC) and methyl jasmonate (MeJA). Yeast one-hybrid (Y1H), Electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter assays verified that DoWRKY26 could bind and activate the promoter of DoCCoAOMT. These findings provide a foundational basis for further exploring the biosynthesis and transcriptional regulation mechanisms of flavonoids in D. officinale.
{"title":"DoWRKY26 positively regulating flavonoid biosynthesis in Dendrobium officinale","authors":"Ziling Tao , Shiyu Cai , YiMing Wang, Fengxiu li, Lu Lv, Haimeng Bai, Ludan Li, Jihong Jiang, Xiaoying Cao","doi":"10.1016/j.gene.2025.149944","DOIUrl":"10.1016/j.gene.2025.149944","url":null,"abstract":"<div><div><em>Dendrobium officinale</em> is renowned as the foremost among the “Nine Immortal Herbs of China”. Our previous research showed enhanced flavonoid accumulation following induction by the endophyte <em>Wickerhamomyces</em> sp. KLBMPSYLp8. Transcriptome data analysis identified multiple upregulated transcription factor (TF) genes. We conducted transient overexpression analysis of 10 significantly upregulated TF genes in <em>D. officinale</em> leaves. The results demonstrated that transient overexpression of the <em>DoWRKY26</em> significantly enhanced flavonoid accumulation, with a 33 % increase compared to the empty vector control group. Furthermore, <em>DoWRKY26</em> overexpression also upregulated the expression levels of key enzyme genes implicated in the flavonoid biosynthesis pathway. Subcellular localization confirmed its nuclear presence. <em>DoWRKY26</em> expression was induced by salicylic acid (SA), abscisic acid (ABA), 1-Aminocyclopropane-1-carboxylic Acid (ACC) and methyl jasmonate (MeJA). Yeast one-hybrid (Y1H), Electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter assays verified that DoWRKY26 could bind and activate the promoter of <em>DoCCoAOMT</em>. These findings provide a foundational basis for further exploring the biosynthesis and transcriptional regulation mechanisms of flavonoids in <em>D. officinale</em>.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"979 ","pages":"Article 149944"},"PeriodicalIF":2.4,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145707083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}