生物学最新文献

{"title":"Substrate secretion by different EHEC secretion systems during their interaction with epithelial cells.","authors":"Landy Zambrano-Arguello, Jaime Vazquez-Lopez, Fernando Navarro-Garcia","doi":"10.1080/21505594.2026.2634461","DOIUrl":"10.1080/21505594.2026.2634461","url":null,"abstract":"<p><p>Enterohemorrhagic <i>Escherichia coli</i> (EHEC) causes severe foodborne illness in humans. EHEC harbors five types of secretion systems (SSs) and unlike the type three secretion system (T3SS), the other SSs are less explored. Some substrates secreted by these SSs have been described; however, how these SSs collectively participate in EHEC-epithelial cell interaction during infection remains unknown. Here, we optimized protein secretion by four of the EHEC SSs in the absence and presence of epithelial cells, since the T6SS is not expressed <i>in vitro</i>. The secretion of substrates through the EHEC SSs followed a hierarchical pattern when bacteria encountered epithelial cells. Epithelial cells increase the protein secretion by EHEC and mutants in SSs (Western-blot and proteomics). Remarkably, mutants in one particular SS affect protein secretion by other SSs. Analysis of the EHEC secretome in the absence/presence of cells vs different SS mutants showed that epithelial cells increase the abundance of specific substrates; the lack of one SS affects the secretion by other SSs; epithelial cells diminish the effects caused by mutating some SS; bioinformatics analyses identified new potential substrates for each SS. Western blot analysis validated the interdependence in substrate secretion between SSs. Consequently, a complex interaction exists between SSs during epithelial cell infection, affecting the epithelial cells-bacteria interaction and the EHEC pathogenesis.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":" ","pages":"2634461"},"PeriodicalIF":6.8,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12962677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146221316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and profiling of HLA-A*02:01-restricted <i>Toxoplasma gondii</i> peptides through immunopeptidomics in HLA-A2.1 transgenic mice.","authors":"Ruiying Liang, Xinru Luo, Weixiang Xia, Haotian Gu, Dan Li, Yongyu Gao, Zonghui Zuo, Fengshan Gao, Jiabo Ding, Xinming Tang, Zibin Li","doi":"10.1080/21505594.2026.2697091","DOIUrl":"10.1080/21505594.2026.2697091","url":null,"abstract":"<p><p>HLA class I presentation of pathogen-derived peptides is essential for CD8+ T-cell recognition of <i>Toxoplasma gondii</i>. While <i>in vitro</i> MHC ligands have been documented, the <i>in vivo</i> ligandome during infection progression remains poorly characterized. Here, we employed an MS-based immunopeptidomics approach to directly profile the <i>T. gondii</i> immunopeptidome presented by HLA-A *02:01 in transgenic mice. By employing a hierarchical discovery funnel, our analysis identified a comprehensive repertoire of 3,744 unique <i>T. gondii</i>-derived peptides. Subsequent filtering for canonical 8-12mers, matching the typical binding length for HLA-A *02:01 ligands, established a high-confidence foundational ligandome of 3,433 peptides. Source protein analysis revealed that these peptides originate from diverse parasite proteins, including a substantial proportion of previously uncharacterized hypothetical proteins. Notably, specific ligands were consistently detected across both acute and chronic stages, suggesting stable MHC-I presentation throughout the infection cycle. By integrating <i>in silico</i> predictions with experimental validation, we prioritized 73 high-affinity candidates, five of which exhibited robust HLA-A *02:01 binding capacity <i>in vitro</i> and <i>in vivo</i>. Specifically, we identified a novel ligand derived from glycogen synthase (PGS) and determined its co-crystal structure with HLA-A *02:01, revealing favorable binding architecture. Overall, these findings expand the known HLA-A *02:01-restricted ligand landscape of <i>T. gondii</i> and provide a high-priority list of candidates for future functional validation of CD8+ T-cell immunogenicity.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"17 1","pages":"2697091"},"PeriodicalIF":6.8,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13348963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148388117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rotavirus-NSP5 interacts with and hijacks host ATP citrate lyase to viroplasms, enhancing lipid biosynthesis for facilitating rotavirus infection.","authors":"Ranjana Sharma, Shreya Banerjee, Ratul Datta Chaudhuri, Kaushik Kumar Dey, Animesh Gope, Shin-Ichi Miyoshi, Daisuke Imamura, Mamta Chawla-Sarkar","doi":"10.1080/21505594.2026.2709258","DOIUrl":"10.1080/21505594.2026.2709258","url":null,"abstract":"<p><p>Rotavirus (RV) replication occurs within viroplasms (VMs) and is initiated by two RV non-structural proteins NSP2 and NSP5. Viruses exploit host cellular components for their replication and assembly; however, information on the roles of host proteins in VM dynamics and RV replication is limited. Thus, in the current study, we used proteomics to identify host proteins that interact with NSP5 during RV infection to delineate their role in virus replication. A large number of host proteins (<i>n</i> = 128) were found to interact with NSP5, and Gene Ontology enrichment analysis revealed the enrichment of various metabolic processes during RV infection. One of the essential host proteins, ATP citrate lyase (ACLY), which is involved in the <i>de novo</i> lipid synthesis pathway, was found to interact with C-terminal region of RV-NSP5 and colocalize within VMs. Following RV infection, the serine 455 phosphorylation of ACLY was induced, suggesting increased enzymatic activation. This correlates with enhanced lipid droplet production <i>via</i> increased acetyl-coenzyme A expression levels, which in turn supports VM formation. The ACLY inhibitors SB204990 or hydroxycitric acid tripotassium hydrate significantly reduced RV-infection <i>in vitro</i>. This anti-rotaviral effect of drug was further validated in BALB/<i>c</i> suckling mice by measuring viral protein expression and viral titers. In the presence of ACLY inhibitor, reduced viral titers, reduced viral protein expression, and improved small intestinal histopathology were observed. These findings suggest a protective effect of drugs against RV infection <i>in vivo</i> and highlight ACLY as a potential anti-rotaviral target for the development of new therapeutics.</p>","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"17 1","pages":"2709258"},"PeriodicalIF":6.8,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13483473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148761519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uric acid alleviates the inflammatory response in LPS-induced BV2 cells and MPTP-induced PD mice by resisting ferroptosis through the Nrf2 signalling pathway.","authors":"Dongmei Zhou, Tian Xiong, Bing Yang, Fanjie Liu, Xianglai Mo, Ting Chen, Peipei Lu, Xinghuan Liang, Li Li, Yingfen Qin, Decheng Lu, Feng Huang, Xi Yang","doi":"10.1080/13510002.2026.2668238","DOIUrl":"10.1080/13510002.2026.2668238","url":null,"abstract":"<p><strong>Background: </strong>Neuroinflammation, oxidative stress, and ferroptosis are implicated in Parkinson' s disease (PD) pathogenesis. Epidemiological studies suggest that elevated uric acid (UA) levels may reduce PD risk, but the precise molecular mechanisms involved remain unclear. In this study, we investigated the effects of UA in lipopolysaccharide (LPS) or MPP+-stimulated BV2 microglia and MPTP-induced PD mouse models.</p><p><strong>Methods: </strong>BV2 cells are recognized as a standardized and reproducible neural inflammatory cell model for mechanism exploration. The anti-ferroptosis and anti-inflammatory effects of UA were assessed in LPS or MPP+ stimulated BV2 microglia and in an MPTP-induced PD mouse model. Western blot, qPCR, ELISA, and immunofluorescence were used to analyse the expression of inflammasome-related markers. ROS, MDA, GSH, and Fe²⁺ levels were measured using testing kits, while mitochondrial ultrastructure was evaluated through transmission electron microscopy. PD-related markers were assessed by ethology and immunohistochemistry. The Nrf2 inhibitor ML385 was employed to validate pathway specificity.</p><p><strong>Results: </strong>We found that UA treatment reduced the expression of proinflammatory cytokines (TNF-<i>α</i>, IL-6, and IL-1β), ROS production, lipid peroxidation, and intracellular Fe²⁺ in BV2 microglia while increasing the antioxidant capacity and preserving the mitochondrial ultrastructure. In MPTP-treated mice, UA improved motor performance, preserved dopaminergic neuron density in the substantia nigra, and reduced neuroinflammation. UA activated Nrf2 signalling and upregulated GPX4 expression, which were attenuated by ML385, confirming the Nrf2 dependence of these effects.</p><p><strong>Conclusion: </strong>UA alleviates ferroptosis and neuroinflammation in LPS or MPP+ stimulated BV2 microglia and MPTP-induced PD mouse models through the activation of the Nrf2 signalling pathway.</p>","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"31 1","pages":"2668238"},"PeriodicalIF":6.9,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13237794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148157932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"γ-Glutamylcysteine alleviates hypertension and vascular remodeling in SHR by suppressing oxidative stress through Keap1 S-glutathionylation.","authors":"Jianzhen Lei, Yueru Kong, Chao Ye, Chuanyue Zhang, Yi Shen, Xin Wu, Qiuyue Wu, Ying Han, Min Chen, Yueqi Song, Qing Yan, Fen Zheng, Xinyi Xia","doi":"10.1080/13510002.2026.2734676","DOIUrl":"10.1080/13510002.2026.2734676","url":null,"abstract":"<p><strong>Objectives: </strong>Pathological arterial remodeling heavily depends on the aberrant proliferation and migration of vascular smooth muscle cells (VSMCs). This study explores how <i>γ</i>-Glutamylcysteine (<i>γ</i>-GC) regulates VSMC signaling to mitigate hypertensive structural damage.</p><p><strong>Methods: </strong>Spontaneously hypertensive rats (SHR) and Wistar-Kyoto (WKY) rats received intraperitoneal injections of <i>γ</i>-GC (100 mg/kg) every two days for 4 weeks. Blood pressure and arterial remodeling were evaluated. Primary aortic VSMCs were cultured for cellular mechanism analysis. To verify Nrf2 pathway requirement, the Nrf2 inhibitor ML385 was applied <i>in vitro</i> and via osmotic pumps <i>in vivo</i>.</p><p><strong>Results: </strong><i>γ</i>-GC lowered systemic blood pressure and prevented arterial medial thickening in SHR, while normotensive controls remained unaffected. In SHR-VSMCs, <i>γ</i>-GC inhibited cell migration, proliferation, and phenotypic switching, and alleviated cellular oxidative stress. RNA-seq revealed significant enrichment of the Nrf2 signaling pathway. Mechanistically, <i>γ</i>-GC induced Keap1 S-glutathionylation, which disrupted the Keap1 and Nrf2 interaction and promoted Nrf2 nuclear translocation. Notably, Nrf2 inhibition with ML385 abolished the protective effects of <i>γ</i>-GC <i>in vivo</i> and <i>in vitro</i>.</p><p><strong>Discussion: </strong><i>γ</i>-GC attenuates hypertensive arterial remodeling by modulating intracellular signaling, specifically through Keap1 S-glutathionylation-dependent Nrf2 activation. The Keap1/Nrf2 signaling axis is required for <i>γ</i>-GC to restore VSMC function, suggesting a targeted molecular mechanism for cardiovascular protection.</p>","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"31 1","pages":"2734676"},"PeriodicalIF":6.9,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149025936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ovalbumin oxidative modification fingerprints depend on gas plasma-driven reactive species profiles.","authors":"Paul Schulan, Kristian Wende, Ramona Clemen, Torsten Gerling, Klaus-Dieter Weltmann, Klaus Ruhnau, Thomas von Woedtke, Michael Lalk, Sander Bekeschus","doi":"10.1080/13510002.2026.2688623","DOIUrl":"10.1080/13510002.2026.2688623","url":null,"abstract":"<p><strong>Objective: </strong>Oxidative protein modifications have been linked to several diseases, but the variety and diversity of modifications are less studied.</p><p><strong>Methods: </strong>We used the chicken egg protein ovalbumin and gas plasma technology, a potent source of various reactive species, for protein oxidation. Using high-resolution mass spectrometry and an in-house workflow, over 80 distinct oxidative protein modifications were mapped at per-amino-acid resolution. To examine how modification profiles depend on changes in reactive species types and concentrations, we generated 12 distinct argon gas plasmas by systematically varying molecular gas admixtures (water, ethanol, oxygen, and nitrogen).</p><p><strong>Results: </strong>Optical emission spectroscopy (OES) and photometric determination of deposited long-lived species (hydrogen peroxide, nitrite, and nitrate) were applied to profile gas plasma conditions, revealing the admixture-dependent impact on the reactive oxygen/nitrogen species (ROS/RNS) fingerprint. Correlation analysis with mass spectrometry data revealed the significant involvement of atomic oxygen and hydrogen peroxide in protein oxidation. The enrichment of specific reactive species created by a defined gas plasma composition generated specific ovalbumin oxidation profiles resolved per amino acid. Feed gas-dependent oxidation hotspots, such as Trp149 for dry argon gas or Met274 for hydroxyl radical-rich humidified argon gas, were identified.</p><p><strong>Discussion: </strong>This first-of-its-kind study reveals intricate relationships between dynamic reactive species environments and protein oxidation profiles using ovalbumin as a model system.</p>","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"31 1","pages":"2688623"},"PeriodicalIF":6.9,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13276820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148265737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 oxidative stress paradigm in arbovirus infections: mechanisms and therapeutic insights.","authors":"Chang Ke Yee, Rafidah Lani, Pouya Hassandarvish","doi":"10.1080/13510002.2026.2659994","DOIUrl":"10.1080/13510002.2026.2659994","url":null,"abstract":"<p><strong>Background: </strong>Arbovirus infections impose a substantial global health burden, further complicated by their ability to induce oxidative stress through excessive generation of reactive oxygen species (ROS). This oxidative stress triggers a cascade that enhances viral replication and dysregulates immune responses, ultimately exacerbating disease pathology.</p><p><strong>Objective: </strong>In this review, we delineate the molecular pathways through which arbovirus-induced ROS activate NF-κB signalling, impair mitochondrial function, and alter the expression of key antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase), culminating in inflammatory tissue damage.</p><p><strong>Discussions: </strong><i>In vitro</i> studies demonstrate that various alkaloids and polyphenols reduce viral load, while N-acetylcysteine has shown the ability to attenuate inflammation and reduce viral titres across both <i>in vitro</i> and <i>in vivo</i> models. Despite these advances, translation to clinical practice is constrained by limited compound bioavailability, variable pharmacokinetics, optimal timing windows, and a lack of standardized redox assays.</p><p><strong>Conclusion: </strong>We propose that targeted redox-modulating strategies, such as integrating genomic and metabolomic profiling, activating Nrf2 pathways, and incorporating advanced imaging techniques, warrant systematic evaluation using rigorous <i>in vivo</i> models and clinical trials. Defining optimal redox-directed interventions has the potential to catalyse the discovery of novel therapeutics that disrupt pro-viral oxidative pathways and improve outcomes in arboviral disease.</p>","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"31 1","pages":"2659994"},"PeriodicalIF":6.9,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13084857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147692201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enzymatic and non-enzymatic oxidation of fibrillar collagen.","authors":"Felipe Caliani Mathias-Netto, Nathalia Margarida Cantuária, Renato Simões Gaspar","doi":"10.1080/13510002.2026.2682046","DOIUrl":"10.1080/13510002.2026.2682046","url":null,"abstract":"<p><strong>Objectives: </strong>Collagen is a long-lived protein present in the extracellular matrix of force-bearing tissues. It has a unique amino acid composition of predominantly glycine, proline and hydroxyproline that repeats throughout its characteristic triple helical structure. In the extracellular space, collagen interact first by a non-enzymatic, entropy-driven process given their high hydrophobicity. Then, enzymes, such as lysyl oxidase (LOX), create covalent bonds (i.e. crosslinks) between triple helices, generating reactive oxygen species (ROS) as a byproduct. Moreover, it was recently discovered that collagen itself generates ROS upon stretching. Therefore, given the close proximity of ROS-generating sources, it seems plausible that collagen undergoes non-enzymatic oxidation.</p><p><strong>Methods: </strong>This review discusses collagen structure, mechanisms of crosslink formation and collagen oxidation.</p><p><strong>Results: </strong>Despite abundant data on the mechanisms of LOX-mediated collagen oxidation, there is sparse data on the effects of non-enzymatic oxidation on collagen chemical and biophysical properties, as well as its effects on cells and tissues.</p><p><strong>Discussion: </strong>The premise that collagen oxidation could lead to persistent damage is discussed in light of the immunogenicity and proteolysis induced by such modifications. Overall, data support that oxidative modifications in collagen should be further explored and could pose as a novel underlying mechanism in ageing and chronic diseases.</p>","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"31 1","pages":"2682046"},"PeriodicalIF":6.9,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13262103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148219499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 extracellular matrix protein SNED1 affects self-renewal, proliferation and adipogenic differentiation of human adipose stem/progenitor cells.","authors":"Sonja Großmann, Petra Waldegger, Tina Deutinger, Werner Zwerschke","doi":"10.1080/21623945.2026.2737919","DOIUrl":"10.1080/21623945.2026.2737919","url":null,"abstract":"<p><p>The fate of adipose stem/progenitor cells (ASCs) is influenced by the extracellular matrix (ECM). However, the interaction between ASCs and components of the ECM in human white adipose tissue (WAT) is not precisely understood. The gene Sushi, nidogen and EGF-like domain-containing protein 1 (SNED1) encodes a secreted ECM glycoprotein of unknown function in AT. In the present study, we show that knockdown of the SNED1 expression in ASCs leads to a significantly reduced self-renewal and proliferation capacity; moreover, the adipogenic differentiation potential is reduced. Our data suggest that SNED1 contributes to a functional interaction between ECM and ASCs, which is important for stemness and commitment to proliferation and differentiation in adult adipose stem/progenitor cells.</p>","PeriodicalId":7226,"journal":{"name":"Adipocyte","volume":"15 1","pages":"2737919"},"PeriodicalIF":3.3,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13625711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069111","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":"Sequence and ionic requirements of pUG fold quadruplexes.","authors":"Saeed Roschdi, Takuma Kume, Riley J Petersen, Abby McCann, Cristian A Escobar Bravo, Anika Richard, Samuel Butcher","doi":"10.1080/15476286.2026.2638283","DOIUrl":"10.1080/15476286.2026.2638283","url":null,"abstract":"<p><p>Poly(UG) repeats or pUG RNAs can fold into a left-handed parallel quadruplex, the pUG fold. The pUG fold directs the epigenetic amplification of RNAi in <i>Caenorhabditis</i> elegans, and pUG sequences are abundant in eukaryotic transcriptomes. Here, we report the sequence and ionic requirements for pUG folding. The pUG fold preferentially incorporates 12 guanosines but has an otherwise flexible sequence requirement. The uridines can be substituted with other nucleotides, with some sequence variants folding better than pUG RNA. The GA repeat sequence (GA)₁₂ also forms a pUG-like fold, albeit with lower thermodynamic stability than (GU)₁₂. The pUG fold can tolerate multiple deoxyribose substitutions but does not fold when the backbone is entirely deoxyribose. It has a high affinity and specificity for potassium ions (<i>K</i>_1/2 = 6 mM) and does not fold in sodium or ammonium. Addition of 2 mM Mg²⁺ does not further stabilize the pUG fold, and the polyamines spermine and spermidine do not affect its stability. Finally, the pUG fold is sensitive to surrounding sequence context and complementary flanking sequences can stabilize pUG folds, while other sequences can interfere with folding. These data provide an improved ability to understand and predict pUG folds.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-16"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12962679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147309758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}