Functional & Integrative Genomics最新文献

{"title":"Decoding fungal communication networks: molecular signaling, genetic regulation, and ecological implications.","authors":"Shumila Ishfaq, Hadiqa Anum, Tayyaba Shaheen, Sana Zulfiqar, Anila Ishfaq, Arslan Anjum, Umera Ramzan, Amna Rafiq, Mehboob-Ur-Rahman, Wei Guo","doi":"10.1007/s10142-025-01620-2","DOIUrl":"https://doi.org/10.1007/s10142-025-01620-2","url":null,"abstract":"<p><p>Fungal communication networks regulate essential biological processes, enabling fungi to adapt to environmental changes, coordinate development, and establish interactions within microbial communities. These networks are mediated by diverse signaling molecules, including volatile organic compounds (VOCs), peptide signaling molecules, and quorum-sensing molecules, which facilitate intra- and interspecies communication. The intricate regulation of these signals occurs through specialized signal transduction pathways such as G-protein-coupled receptors (GPCRs) and two-component regulatory systems, allowing fungi to sense external cues and modulate their physiological responses. Genetic mechanisms also play a critical role in fungal communication, influencing community dynamics through regulatory genes governing hyphal fusion, pheromone signaling, and secondary metabolite biosynthesis. Crosstalk between these signaling pathways is further modulated by epigenetic modifications, which fine-tune gene expression in response to environmental conditions. The integration of these molecular networks shapes fungal interactions, impacting resource acquisition, symbiosis, and pathogenicity. Additionally, fungal communication has significant ecological and evolutionary implications, contributing to niche establishment, microbial competition, and host-pathogen interactions. Despite significant progress in understanding fungal communication, key knowledge gaps remain regarding the interplay between signaling molecules, genetic regulation, and environmental adaptation. Future research should focus on unraveling the molecular mechanisms underlying fungal signaling networks and their potential applications in biotechnology, agriculture, and medicine. Harnessing fungal communication could lead to novel strategies for improving crop protection, developing antifungal therapies, and optimizing industrial fermentation processes. This review synthesizes recent advancements in fungal signaling research, providing a comprehensive perspective on its complexity and evolutionary significance.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"111"},"PeriodicalIF":3.9,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Zebrafish metabolomics: a comprehensive approach to understanding health and disease.","authors":"A Vivekaa, Jayshree Nellore, Swetha Sunkar","doi":"10.1007/s10142-025-01621-1","DOIUrl":"https://doi.org/10.1007/s10142-025-01621-1","url":null,"abstract":"<p><p>Zebrafish (Danio rerio) have become a valuable model in biomedical research due to their genetic similarity to humans, rapid development, and suitability for high-throughput studies. Metabolomic analyses in zebrafish provide critical insights into the biochemical pathways underlying health and disease. This review explores the applications of metabolomics in zebrafish research, highlighting its contributions to understanding embryonic development, tuberculosis, neurodegenerative disorders such as Alzheimer's disease, obesity-related metabolic dysfunction, and drug-induced toxicity through a thorough literature review. Zebrafish metabolomics reveals dynamic metabolite shifts during vertebrate development. In tuberculosis research, zebrafish models have helped identify metabolic biomarkers with potential translational relevance. Studies on Alzheimer's disease suggest that metabolomics can elucidate neuroprotective mechanisms, while investigations into obesity have provided insights into metabolic imbalances associated with kidney dysfunction. Furthermore, toxicometabolomic studies have demonstrated the utility of zebrafish in assessing drug-induced renal injury. Despite their advantages, zebrafish metabolomics faces challenges, including differences in metabolic rates compared to mammals, the need for standardized protocols, and limitations in metabolite database annotations. Nonetheless, integrating metabolomics with other omics approaches holds great promise for advancing disease research and paving the way for personalized medicine.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"110"},"PeriodicalIF":3.9,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New hope and promise with CRISPR-Cas9 technology for the treatment of HIV","authors":"Hesham M. Hassan,&nbsp;Akmal Zubair,&nbsp;Mohamed H. Helal,&nbsp;Wesam Taher Almagharbeh,&nbsp;Ranya Mohammed Elmagzoub","doi":"10.1007/s10142-025-01613-1","DOIUrl":"10.1007/s10142-025-01613-1","url":null,"abstract":"<div><p>The commencement of Highly Active Antiretroviral Therapy almost completely stopped viral replication, enabling the immune system to restore its full functionality. The rise in life expectancy has resulted in a decrease in the incidence of classical infections and HIV-associated cancers. HAART has raised concerns, including its exorbitant cost (which hinders its implementation in developing nations), the need for strict adherence, and the potential for both immediate and prolonged ill effects. Lipodystrophy is a significant long-term consequence of HIV that may result in central fat accumulation and severe peripheral fat depletion. Current initiatives to tackle these difficulties include the global expansion of access to HAART, the development of novel drugs that mitigate early side effects, and the introduction of once-daily drug combinations that enhance adherence. The CRISPR-Cas9 system has facilitated the creation of a powerful instrument for precise gene editing. This method has lately established itself as the gold standard for efficient HIV-1 genome editing in HIV therapy, owing to progress in related disciplines. CRISPR may be customized to cleave specific sequences by altering Cas9. This article offers a concise overview of promising CRISPR-Cas9 technology. This technique has the potential to halt the transmission of HIV-1 and alleviate its symptoms. CRISPR-Cas9 technology will be significant in the fight against HIV-1 in the future.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144125861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precise genome editing process and its applications in plants driven by AI","authors":"Bo Jiang,&nbsp;Zeyu An,&nbsp;Linlin Niu,&nbsp;Debin Qin","doi":"10.1007/s10142-025-01619-9","DOIUrl":"10.1007/s10142-025-01619-9","url":null,"abstract":"<div><p>Genome editing technologies have emerged as the keystone of biotechnological research, enabling precise gene modification. The field has evolved rapidly through revolutionary advancements, transitioning from early explorations to the breakthrough of the CRISPR-Cas system. The emergence of the CRISPR-Cas system represents a huge leap in genome editing, prompting the development of advanced tools such as base and prime editors, thereby enhancing precise genomic engineering capabilities. The rapid integration of AI across disciplines is now driving another transformative phase in genome editing, streamlining workflows and enhancing precision. The application prospects of genome editing technology are extensive, particularly in plant breeding, where it has already presented unparalleled opportunities for improving plant traits. Here, we review early genome editing technologies, including meganucleases, ZFNs, TALENs, and CRISPR-Cas systems. We also provide a detailed introduction to next-generation editing tools—such as base editors and prime editors—and their latest applications in plants. At the same time, we summarize and prospect the cutting-edge developments and future trends of genome editing technologies in combination with the rapidly rising AI technology, including optimizing editing systems, predicting the efficiency of editing sites and designing editing strategies. We are convinced that as these technologies progress and their utilization expands, they will provide pioneering solutions to global challenges, ushering in an era of health, prosperity, and sustainability.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144131677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"N4-acetylcytidine modification of LncRNA GFOD1-AS1 promotes high glucose-induced dysfunction in human dermal microvascular endothelial cells through stabilization of DNMT1 protein","authors":"Jingjing Yuan,&nbsp;Lusha Li,&nbsp;Yang Lv,&nbsp;Wenjun Yang","doi":"10.1007/s10142-025-01617-x","DOIUrl":"10.1007/s10142-025-01617-x","url":null,"abstract":"<div><p>Emerging evidence supports that angiogenesis is essential for the wound healing of diabetic foot ulcer (DFU), and high glucose (HG)-induced dysfunction of human dermal microvascular endothelial cells is a key factor that hinders angiogenesis. However, the underlying mechanisms by which HG leads to the dysfunction of human dermal microvascular endothelial cells has not been fully elucidated. In the present investigation, we discovered a significant upregulation of the long non-coding RNA GFOD1-AS1(GFOD1-AS1) in the ulcer margin samples of patients with DFU and the HG-induced dysfunction model of human dermal microvascular endothelial cells, attributing its dysregulation to the stabilizing effect of NAT10-mediated ac4C modification, as corroborated by an integrated approach of data mining and experimental validation. Subsequently, a series of in vitro functional analyses showed that ectopic expression of GFOD1-AS1 promoted impaired function of human dermal microvascular endothelial cells. In contrast, knockdown of GFOD1-AS1 significantly alleviated the HG-induced functional impairment in human dermal microvascular endothelial cells, as indicated by the enhanced cell proliferation, migration, and tube formation. Mechanistically, GFOD1-AS1 directly interacts with DNA methyltransferase DNMT1 to block its ubiquitin-proteasome degradation, thereby enhancing the protein stability of DNMT1.This stability elevates DNMT1 protein expression, ultimately inducing HG-induced dysfunction in human dermal microvascular endothelial cells. In summary, our results reveal that GFOD1-AS1 serves as a potential therapeutic target for DFU, and highlight the critical role of the NAT10/GFOD1-AS1/DNMT1 axis in the dysfunction of human dermal microvascular endothelial cells in DFU.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01617-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144125863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ferroptosis-related gene GGTLC2 is identified as a novel biomarker for gastric cancer within the GGT family, with associations to immune infiltration and liver metastasis","authors":"Nan Yan,&nbsp;Jianhong Liu,&nbsp;Gaofu Li,&nbsp;Linglin Zhao,&nbsp;Jie Yang,&nbsp;Qijing Guo,&nbsp;Wei Zhou,&nbsp;Yushuang Luo,&nbsp;Yue Gao","doi":"10.1007/s10142-025-01614-0","DOIUrl":"10.1007/s10142-025-01614-0","url":null,"abstract":"<div><p>Gastric cancer (GC) has a high incidence and poor prognosis, often metastasizing to the liver. Gamma-glutamyl transferase (GGT) is a key indicator of liver damage, and its family members are associated with various cancers. However, their expression and prognostic significance in GC remain unclear. This study utilized R to analyze the expression and prognosis of GGT family members using RNA-seq and clinical data from the TCGA database, applying Lasso regression for key gene identification. We identified GGTLC2 as a significant gene related to GC prognosis. We examined the clinical relevance, methylation levels, and copy number variations of GGTLC2 using the MEXPRESS database and performed GSEA analysis to identify enriched pathways. Additionally, we explored the relationship between GGTLC2 and immune cell infiltration, as well as immune-related genes, and established GGTLC2 knockdown and overexpression cell lines. The results indicate that GGTLC2 is highly expressed in GC and is associated with DNA methylation, copy number variation, and liver metastasis. Functionally, GGTLC2 is primarily enriched in oxidative stress and immune-related pathways, affecting immune infiltration and the expression of inflammatory factors in the tumor microenvironment. In vivo and in vitro studies demonstrate that knocking down GGTLC2 inhibits GC proliferation, invasion, and migration while promoting apoptosis and ferroptosis. Conversely, overexpressing GGTLC2 significantly increases the number of metastatic tumors in the liver. Overall, GGTLC2 may influence the occurrence, development, and liver metastasis of GC by inhibiting ferroptosis, making it a promising novel biomarker for the diagnosis and treatment of GC and its metastasis.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144108512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"mlstverse-web: advancing real-time identification of mycobacteria from sputum using targeted sequencing NALC-Seq","authors":"Yuki Matsumoto,&nbsp;Kiyoharu Fukushima,&nbsp;Shunran Zhang,&nbsp;Yuzy Fauzyah,&nbsp;Daisuke Motooka,&nbsp;Haruko Saito,&nbsp;June Yamauchi,&nbsp;Tadayoshi Nitta,&nbsp;Takuro Nii,&nbsp;Takanori Matsuki,&nbsp;Kazuyuki Tsujino,&nbsp;Keisuke Miki,&nbsp;Hiroshi Kida,&nbsp;Shota Nakamura","doi":"10.1007/s10142-025-01609-x","DOIUrl":"10.1007/s10142-025-01609-x","url":null,"abstract":"<div><p>The identification of mycobacteria, including Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacteria (NTM), remains a critical challenge in clinical and public health settings due to their pathogenicity and increasing drug resistance. Traditional diagnostic methods, such as PCR and mass spectrometry, are limited by species detectability and prolonged culture requirements. To address these limitations, this study introduces a novel approach, named NALC-Seq, which integrates next-generation sequencing (NGS) and target capture sequencing for the direct and comprehensive identification of mycobacteria from sputum samples. A total of 54 patients were prospectively or retrospectively enrolled between April 6, 2021, and November 8, 2022, and sputum samples were subjected to next generation sequencing. The NALC-Seq methodology utilizes custom-designed RNA probes for targeted enrichment of mycobacterial DNA, coupled with species identification via the mlstverse-web system. This system integrates web, upload, head, and cloud nodes to streamline data management and analysis. Our evaluation demonstrated that NALC-Seq achieved high sensitivity (98.1%) and accuracy (83.3%) in detecting diverse mycobacterial species, including rare and drug-resistant subspecies. There were discrepancies with MGIT-Seq in nine samples. These samples exhibited low smear positivity rates, and the detection of environmental mycobacteria suggested potential contamination. Furthermore, real-time identification using the MinION device significantly reduced the turnaround time from 686 to 19 h.These findings highlight the potential of NALC-Seq and mlstverse-web as an integrated diagnostic solution for overcoming the limitations of current methods. The proposed approach offers a rapid, accurate, and comprehensive strategy for mycobacterial identification, with significant implications for clinical diagnostics and public health surveillance.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01609-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive profiling of Bcl-2-associated athanogene (BAG) genes and their genetic potential role under cold stress in Cotton","authors":"Aamir Ali Abro,&nbsp;Cong Sun,&nbsp;Mubashir Abbas,&nbsp;Qiankun Liu,&nbsp;Zheng Jie,&nbsp;Yanchao Xu,&nbsp;Yuqing Hou,&nbsp;Zhongli Zhou,&nbsp;Rashid Iqbal,&nbsp;Fang Liu,&nbsp;Xiaoyan Cai","doi":"10.1007/s10142-025-01618-w","DOIUrl":"10.1007/s10142-025-01618-w","url":null,"abstract":"<div><p><i>Bcl-2-associated athanogene</i> (BAG) gene family is important in stress tolerance and death regulation in plants. Cotton (<i>Gossypium hirsutum</i>) is an important cash crop with strong functional significance, while the BAG gene family in cotton has been little studied. Remains largely unexplored. Of these, the genome-wide identification and characterization of BAG genes were performed in <i>Gossypium hirsutum, Gossypium barbadense, Gossypium raimondii,</i> and <i>Gossypium arboreum</i> in this study. In <i>G. hirsutum, G. barbadense, G. raimondii,</i> and <i>G. arboreum</i>, there were 30, 32, 12, and 11 BAG genes found, respectively. Phylogenetic classification groupgrouped these genes into five classes (A–E), depending on their evolutionary relatedness with the BAG genes from other plant species. Investigation of the gene structures and expression patterns of BAG proteins indicated conserved domain architectures, gene motifs, and subcellular localizations among <i>Gossypium</i> species. Within tetraploid species, whole-genome and segmental duplications were determined to be the main contributors to BAG gene expansion, while diploid progenitors had few gene duplication events. Comparative sequence approaches and analyses of conserved motifs revealed jagged evolutionary conservation of the BAG domain indicating their possible functional roles in stress response and programmed cell death. Detailed expression profiling under abiotic stress conditions (drought, salt, and cold) showed that several BAG genes significantly differentially expressed which indicating their participation in adaptation mechanisms to stress conditions. In addition, the identification of essential <i>cis-regulatory</i> factors in the promoter regions suggested potential regulation by environmental changes. BAG gene family Structure, evolutionary relationship and expression pattern in cotton in response to different stresses study with predictable implications. Deciphering how the BAG gene functions at a molecular and evolutionary scale will help guide future research into genetic engineering approaches aimed at enhancing cotton tolerance to environmental stressors.\u0000</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"3’UTR RNA editing driven by ADAR1 modulates MDM2 expression in breast cancer cells","authors":"Elanur Almeric,&nbsp;Deniz Karagozoglu,&nbsp;Mustafa Cicek,&nbsp;Didem Naz Dioken,&nbsp;Huseyin Avni Tac,&nbsp;Esra Cicek,&nbsp;Busra Aytul Kirim,&nbsp;Irmak Gurcuoglu,&nbsp;Osman Ugur Sezerman,&nbsp;Nurhan Ozlu,&nbsp;Ayse Elif Erson-Bensan","doi":"10.1007/s10142-025-01611-3","DOIUrl":"10.1007/s10142-025-01611-3","url":null,"abstract":"<div><p>Epitranscriptomic changes in the transcripts of cancer related genes could modulate protein levels. RNA editing, particularly A-to-I(G) editing catalyzed by ADAR1, has been implicated in cancer progression. RNA editing events in the 3’ untranslated region (3’UTR) can regulate mRNA stability, localization, and translation, underscoring the importance of exploring their impact in cancer. Here, we performed an in silico analysis to detect breast cancer enriched RNA editing sites using the TCGA breast cancer RNA-seq dataset. Notably, the majority of differential editing events mapped to 3’ untranslated regions (3’UTRs). We confirmed A-to-I(G) editing in the 3’UTRs of <i>MDM2</i> (Mouse Double Minute 2 homolog), <i>GINS1</i> (GINS Complex Subunit 1), and <i>F11R</i> (Junctional Adhesion Molecule A) in breast cancer cells. RNA immunoprecipitation with ADAR1 antibody confirmed the interaction between ADAR1 and <i>MDM2</i>, <i>GINS1</i>, and <i>F11R</i> 3’UTRs. ADAR1 knockdown revealed decreased editing levels, establishing ADAR1 as the editing enzyme. A reporter assay for <i>MDM2</i>, an oncogene overexpressed mostly in luminal breast cancers, demonstrated that RNA editing enhances protein expression, in agreement with reduced MDM2 protein levels in ADAR1 knockdown cells. Further exploration into the mechanisms of 3’UTR editing events revealed an interaction between ADAR1 and CSTF2, a core component of the polyadenylation machinery, as identified through biotin-based proximity labeling mass spectroscopy, and co-immunoprecipitation experiments. Furthermore, CSTF2 knockdown reduced both ADAR1 and MDM2 protein levels. Our findings highlight implications for <i>MDM2</i> regulation by ADAR1-dependent 3’UTR RNA editing and present an interplay between RNA editing on 3’UTRs and the mRNA polyadenylation machinery. These results improve our understanding of ADAR1’s role in cancer-associated 3’ UTR RNA editing and its potential as a therapeutic target.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01611-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Durum wheat nuclear factor Y (NF-Y) a subfamily: structure, phylogeny, and expression analysis in response to hormones and abiotic stresses","authors":"Yosra Chouaibi,&nbsp;Mohamed Taieb Bouteraa,&nbsp;Walid Ben Romdhane,&nbsp;Narjes Baazaoui,&nbsp;Mohammad Y. Alfaifi,&nbsp;Miroslava Kačániová,&nbsp;Natália Čmiková,&nbsp;Anis Ben Hsouna,&nbsp;Stefania Garzoli,&nbsp;Alina Wiszniewska,&nbsp;Rania Ben Saad","doi":"10.1007/s10142-025-01607-z","DOIUrl":"10.1007/s10142-025-01607-z","url":null,"abstract":"<div><p>Nuclear factor-Y (NF-Y) transcription factors are heterotrimeric complexes that are widely distributed in eukaryotes and play essential roles in many biological processes. Although NF-YA proteins have been characterized in numerous plants, their contribution to the response of durum wheat (<i>Triticum turgidum</i> ssp. <i>durum</i>) to environmental factors has not been reported. Thus, this study was aimed at identification and characterization of <i>Triticum turgidum TtNF-YA</i> family members through genome-wide analysis. Twelve <i>NF-YA</i> genes were discovered in <i>Triticum turgidum</i>. Discovered genes were distributed across eight chromosomes, while their encoded proteins were localized in cell nucleus. Structure and motif pattern analyses revealed that the <i>TtNF-YA</i> genes were relatively conserved. The expression of <i>TtNF-YAs</i> genes was significantly induced by several stressors and their expression profiles differed in various tissues and at various development stages. Notably, <i>TtNF-YA2 A-1</i> and <i>TtNF-YA2B-1</i> exhibited the greatest increase in response to Polyethylene glycol, while <i>TtNF-YA4 A</i> and <i>TtNF-YA4B-1</i> showed the highest increase under salt stress. Additionally, <i>TtNF-YA5B-1</i> and <i>TtNF-YA6 A-1</i> displayed pronounced upregulation when exposed to exogenous Abscisic acid, suggesting that <i>TtNF-YA</i> are involved in a series of cellular and developmental events. This finding was corroborated by the recognition of several <i>cis</i>-regulatory elements in the <i>TtNF-YAs</i> promoter region, associated with the applied treatments. Overexpression of <i>TtNF-YA2 A-1</i>, <i>TtNF-YA2B-1</i>, <i>TtNF-YA4 A</i>, <i>TtNF-YA4 A-1, TtNF-YA4B-1</i>, and <i>TtNF-YA5 A-2</i> genes in <i>Saccharomyces cerevisiae</i> showed that these genes increase cell tolerance to multiple stresses. Our results will facilitate subsequent functional analysis of <i>TtNF-YAs</i> genes, which emerge as promising targets for genetic engineering for increasing wheat tolerance to multiple stresses.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01607-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143944205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}