Nucleic Acids Research最新文献_第6页

KRAS-induced STN1 (OBFC1) promotes proper CTC1-STN1-TEN1 complex-independent DNA double-strand break repair and cell cycle checkpoint maintenance in pancreatic cancer. kras诱导的STN1 （OBFC1）在胰腺癌中促进CTC1-STN1-TEN1复合体非依赖性DNA双链断裂修复和细胞周期检查点维持。

IF 13.1 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf983

Changxian Shen, Tiantian Cui, Linlin Yang, Ling Gui, Sergio Corrales-Guerrero, Sindhu Nair, Haiqing Li, Joanna M Karasinska, James T Topham, Daniel J Renouf, David F Schaeffer, Anthony Fernandez, Xiaoli Ping, Binghui Shen, Jeremy M Stark, Terence M Williams

{"title":"KRAS-induced STN1 (OBFC1) promotes proper CTC1-STN1-TEN1 complex-independent DNA double-strand break repair and cell cycle checkpoint maintenance in pancreatic cancer.","authors":"Changxian Shen, Tiantian Cui, Linlin Yang, Ling Gui, Sergio Corrales-Guerrero, Sindhu Nair, Haiqing Li, Joanna M Karasinska, James T Topham, Daniel J Renouf, David F Schaeffer, Anthony Fernandez, Xiaoli Ping, Binghui Shen, Jeremy M Stark, Terence M Williams","doi":"10.1093/nar/gkaf983","DOIUrl":"10.1093/nar/gkaf983","url":null,"abstract":"KRAS activating mutations occur in 90%-95% of pancreatic adenocarcinoma (PC) and contribute to tumor progression and resistance to therapy, including radiotherapy. A screen in isogenic cells revealed that KRAS activation positively modulates STN1 expression, a component of the CTC1-STN1-TEN1 (CST) complex. We find that STN1 is significantly upregulated in PC and its elevation is correlated with KRAS oncogenic mutations, while inhibition of KRAS signaling decreases STN1 expression. Interestingly, depletion of STN1 increases DNA damage and replication stress, and sensitizes PC cells to ionizing radiation independent of CTC1 and TEN1. STN1 silencing reduces both homologous recombination and non-homologous end joining repair of double-strand breaks (DSBs), suggesting STN1 ensures proper DSB repair. Furthermore, knockdown of STN1 impairs cell cycle arrest at G2/M phase in response to ionizing radiation, which is accompanied by increased mitotic catastrophe. Proteomic analysis reveals that STN1 physically interacts with proteins important for DNA repair, replication, and cell cycle progression, including ATM, DICER, CEP164, and CEP250. In particular, STN1 appears to stabilize ATM expression and promote proper ATM signaling after DNA damage. Our findings have revealed a novel CST complex-independent role of STN1 in DSB repair and suggest STN1 may be a promising target for cancer therapy.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12489472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206998","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}

引用次数: 0

Reactive sulfur species mediated persulfidation cascade regulation mechanism of novel transcription factor SscRAc in extremophile Acidithiobacillus caldus under extreme copper stress. 极端铜胁迫下嗜酸硫杆菌新转录因子SscRAc介导的过硫化级联调控机制

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf943

Xingyu Huo,Yanjun Tong,Mingwei Wang,Ruian Ji,Yiwen Zhu,Hailin Yang,Shoushuai Feng

{"title":"Reactive sulfur species mediated persulfidation cascade regulation mechanism of novel transcription factor SscRAc in extremophile Acidithiobacillus caldus under extreme copper stress.","authors":"Xingyu Huo,Yanjun Tong,Mingwei Wang,Ruian Ji,Yiwen Zhu,Hailin Yang,Shoushuai Feng","doi":"10.1093/nar/gkaf943","DOIUrl":"https://doi.org/10.1093/nar/gkaf943","url":null,"abstract":"Severe environmental conditions enhance the resilience of biomining microorganisms to elevated metal ion concentrations. The mechanism of how biomining microorganisms resist metal ions is poorly understood. We identified a novel reactive sulfur species (RSS)-sensitive MarR family transcription factor (SscRAc) in Acidithiobacillus caldus by persulfidation proteomics and observed increase in RSS and protein persulfidation levels under 250 mM Cu2+ stress. The deletion of sscRAc gene via CRISPR-Cas9 and conjugative transfer technology enhanced copper sensitivity in A. caldus. ChIP-seq/qRT-PCR revealed that SscRAc regulates copper detoxification by blocking efflux pumps and stimulating RSS metabolism. LC-MS/MS analysis revealed that both Cys74 and Cys78 in SscRAc interact with RSS and undergo persulfidation, resulting in the dissociation of the protein from the promoter-DNA of target genes. Upstream signaling analysis indicated that copper-sensitive repressor CsoRAc, regulated by SscRAc, inversely regulates SscRAc, thereby jointly enabling copper-RSS signal transduction. In conclusion, we identify SscRAc as the first RSS-dependent transcriptional switch directly linking copper toxicity with the persulfidation signaling pathway in extremophiles.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"82 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145116680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SPACE: Spatially variable gene clustering adjusting for cell type effect for improved spatial domain detection. 空间：调节细胞类型效应的空间可变基因聚类，以改进空间域检测。

IF 13.1 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf936

Sikta Das Adhikari, Nina G Steele, Brian Theisen, Jianrong Wang, Yuehua Cui

{"title":"SPACE: Spatially variable gene clustering adjusting for cell type effect for improved spatial domain detection.","authors":"Sikta Das Adhikari, Nina G Steele, Brian Theisen, Jianrong Wang, Yuehua Cui","doi":"10.1093/nar/gkaf936","DOIUrl":"10.1093/nar/gkaf936","url":null,"abstract":"Recent advances in spatial transcriptomics (ST) have significantly deepened our understanding of biology. A primary focus in ST analysis is to identify spatially variable genes (SVGs) which are crucial for downstream tasks like spatial domain detection. Spatial domains reflect underlying tissue architecture and distinct biological processes. Traditional methods often use a set number of top SVGs for this purpose, and embedding these SVGs simultaneously can confound unrelated spatial signals, dilute weaker patterns, leading to obscured latent structure. Instead, grouping SVGs and getting low-dimensional embedding within each group preserves specific patterns, reduces signal mixing, and enhances the detection of diverse structures. Furthermore, classifying SVGs is akin to identifying cell-type marker genes, offering valuable biological insights. The challenge lies in accurately categorizing SVGs into relevant clusters, aggravated by the absence of prior knowledge regarding the number and spatial gene patterns. Here, we propose SPACE, a framework that classifies SVGs based on their spatial patterns by adjusting for shared cell-type confounding effects, to improve spatial domain detection. This method does not require prior knowledge of gene cluster numbers, spatial patterns, or cell type information. Both simulation and real data analyses demonstrate that SPACE is an efficient and promising tool for ST analysis.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145125292","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}

引用次数: 0

Stable Cas9 expression regulates cell growth by facilitating mTORC2 activation. 稳定的Cas9表达通过促进mTORC2激活来调节细胞生长。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf965

Le Yu,Yi Jin,Jianfeng Chen,Zhichuan Zhu,Siyuan Su,Emily M Wilkerson,Joanna Gongora,Erica W Cloer,Michael B Major,Pengda Liu

{"title":"Stable Cas9 expression regulates cell growth by facilitating mTORC2 activation.","authors":"Le Yu,Yi Jin,Jianfeng Chen,Zhichuan Zhu,Siyuan Su,Emily M Wilkerson,Joanna Gongora,Erica W Cloer,Michael B Major,Pengda Liu","doi":"10.1093/nar/gkaf965","DOIUrl":"https://doi.org/10.1093/nar/gkaf965","url":null,"abstract":"Clustered regularly interspaced short palindromic repeats (CRISPR), widely used for gene editing, relies on bacterial endonucleases like Cas9 to study gene functions and develop therapies. However, its potential effects on mammalian cellular behavior remain unclear. Here, we systematically profiled effects of stable Cas9 expression on growth of 32 cell lines spanning 9 cancer types and non-cancerous cells, finding growth alterations in a subset. To investigate mechanisms, we established the SpCas9 interactome in DU145 and MDA-MB-231 cells, both showing Cas9-enhanced growth, and identified ribosomal proteins as the top shared interactors. RNA-seq analysis revealed that Cas9 expression in DU145 cells activated PI3K signaling. Mechanistic studies showed that ribosomal proteins, including RPL26 and RPL23a, bind to Sin1, a core mTORC2 component, leading to mTORC2 activation. Notably, SpCas9 interacts with both RPL26/RPL23a and Sin1, acting as a scaffold to stabilize their association and enhance mTORC2 activation, even in the absence of growth factors. Our study systematically characterizes Cas9's effects on cell growth regulation and uncovers a novel Cas9-ribosome-mTORC2 signaling axis that promotes cell growth. These findings underscore the need to consider unintended cellular effects in CRISPR applications and highlight the importance of engineering safer Cas9 variants for biomedical research and clinical therapies.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"31 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145182662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to 'The Shu complex promotes error-free tolerance of alkylation-induced base excision repair products'. 修正“Shu复合物促进烷基化诱导的碱基切除修复产物的无错误耐受性”。

IF 13.1 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf1042

引用次数: 0

Engineering of BZ transposase and transposon donor vector for enhanced efficiency and safety in gene delivery applications. BZ转座酶和转座子供体载体的工程设计，以提高基因传递应用的效率和安全性。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf935

Saisai Wang,Pingjing Zhang,Yan Sun,Yuan Fang,Pei Wang,Meiqi Shao,Ningning Zhang,Shasha Shi,Xin Chen,Haixia Gao,Jingbo Cheng,Bo Gao,Tao Liu,Qijun Qian,Chengyi Song

{"title":"Engineering of BZ transposase and transposon donor vector for enhanced efficiency and safety in gene delivery applications.","authors":"Saisai Wang,Pingjing Zhang,Yan Sun,Yuan Fang,Pei Wang,Meiqi Shao,Ningning Zhang,Shasha Shi,Xin Chen,Haixia Gao,Jingbo Cheng,Bo Gao,Tao Liu,Qijun Qian,Chengyi Song","doi":"10.1093/nar/gkaf935","DOIUrl":"https://doi.org/10.1093/nar/gkaf935","url":null,"abstract":"Transposons, as non-viral vectors, provide an efficient and secure method for stable gene delivery and have been successfully applied in human gene therapies. The engineering of transposase has significantly improved the efficiency of various transposon systems, including chimeric antigen receptor (CAR)-T cell engineering. In this study, multiple engineering strategies were implemented to enhance the efficiency and safety of the Baize (BZ) transposon system, which was derived from the ZB (the wild-type BZ, BZwt) and has been proven to be an effective tool for genetic manipulation in vertebrates. Through designed engineering and combinatorial mutagenesis in vitro, several hyperactive BZ transposase variants with higher transposition activity, cargo capacity, and integration safety were developed. At optimal activity levels, BZ325 surpassed BZwt by ∼1.2-fold and 2.3-fold at 500 ng and 10 ng dosages of donor plasmids, respectively. Furthermore, reducing the size of BZ donor vector backbone significantly increased CAR-T modification efficiency without compromising its function. Notably, BZ325, BZ326, and especially BZ327 exhibited significantly higher CAR-T engineering rates and CAR expression levels than BZwt. Overall, the engineering of the BZ transposon system significantly enhanced its transposition activity, cargo capacity, and safety, providing a compelling tool for gene transfer applications and emphasizing its potential in gene therapy.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"17 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145116681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RNF4 and USP7 coordinate spatial regulation of SLX4 stability within the PML nuclear bodies. RNF4和USP7在PML核体内协调SLX4稳定性的空间调控。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf941

Eunyoung Jung,Myung-Jin Kim,Orlando D Schärer,Yonghwan Kim

{"title":"RNF4 and USP7 coordinate spatial regulation of SLX4 stability within the PML nuclear bodies.","authors":"Eunyoung Jung,Myung-Jin Kim,Orlando D Schärer,Yonghwan Kim","doi":"10.1093/nar/gkaf941","DOIUrl":"https://doi.org/10.1093/nar/gkaf941","url":null,"abstract":"To protect the genome from the formation of DNA breaks by nucleases involved in DNA repair, cells have evolved multiple levels of regulatory strategies. One key regulator of nuclease activity is the scaffold protein SLX4, which plays important roles in repairing DNA damage induced by mitomycin C (MMC) and camptothecin (CPT) as well as in the resolution of stalled replication forks. Since SLX4 regulates the activity of nucleases such as SLX1, MUS81, and XPF, whose uncontrolled activity could jeopardize genome integrity, the protein level and localization of SLX4 must be tightly regulated. Here, we show that the ubiquitin E3 ligase RNF4 is associated with SLX4 and is responsible for the ubiquitin-dependent proteasomal degradation of excessive SLX4 under normal conditions. Conversely, promyelocytic leukemia nuclear bodies (PML NBs) promote SLX4 stability. In PML NBs, the stability of SLX4 is maintained by the deubiquitinase USP7, managing the amount of SLX4 necessary for a rapid response to DNA damage. These findings suggest that SLX4 and its associate nucleases are confined within PML NBs and that the optimal protein level of SLX4 is maintained by the coordinated activities of RNF4 and USP7. Our findings provide insight into how cells effectively control the potentially harmful activities of nucleases in the absence of DNA damage by a spatial regulatory mechanism.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"51 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The arabidopsis GyraseB3 contributes to transposon silencing by promoting histone deacetylation. 拟南芥GyraseB3通过促进组蛋白去乙酰化参与转座子沉默。

IF 13.1 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf985

Isabelle Gy, Sébastien Beaubiat, Nicolas Bouché

{"title":"The arabidopsis GyraseB3 contributes to transposon silencing by promoting histone deacetylation.","authors":"Isabelle Gy, Sébastien Beaubiat, Nicolas Bouché","doi":"10.1093/nar/gkaf985","DOIUrl":"10.1093/nar/gkaf985","url":null,"abstract":"DNA methylation and histone modifications are key epigenetic marks controlling chromatin structure, gene expression, and transposable element (TE) activity. In plants, the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1) prevents heterochromatic silencing marks from accumulating on actively transcribed genes. Through a genetic screen of mutants defective in IBM1 production, we identified suppressor mutations in genes essential for maintaining balanced genome-wide epigenetic states. The gyrb3 mutation partly reversed DNA hypermethylation in IBM1-deficient plants, revealing a novel role for GyrB3, a nuclear protein combining domains from cyanobacterial gyrases and ELM2/SANT proteins involved in histone acetylation. In gyrb3 mutants, TEs exhibit transcriptional activity, showing reduced DNA methylation and increased histone H3 acetylation, both of which are epigenetic marks associated with expression activation. GyrB3 physically interacts with histone deacetylases like HISTONE DEACETYLASE6 (HDA6), likely mediating their activities at TEs. The functional overlap between HDA6 and GyrB3 is further supported by the observation that, similar to gyrb3, a mutation in hda6 suppresses the Ibm2 phenotype. Our findings reinforce that histone deacetylation is essential for TE silencing and that loss of IBM1 in plants abolished the frontiers between genes and TEs, emphasizing its importance in maintaining epigenomic stability.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12489469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206987","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}

引用次数: 0

A quantitative model of enzyme-free copying of RNA with dimers. 二聚体无酶复制RNA的定量模型。

IF 13.1 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf987

Ludwig Burger, Franziska Welsch, Eric Kervio, Marc Henker, Gabrielle Leveau, Ulrich Gerland, Clemens Richert

{"title":"A quantitative model of enzyme-free copying of RNA with dimers.","authors":"Ludwig Burger, Franziska Welsch, Eric Kervio, Marc Henker, Gabrielle Leveau, Ulrich Gerland, Clemens Richert","doi":"10.1093/nar/gkaf987","DOIUrl":"10.1093/nar/gkaf987","url":null,"abstract":"The transfer of genetic information from one RNA strand to a daughter strand in the absence of polymerases could have initiated prebiotic evolution. This reaction, driven by base pairing and chemical reactivity alone, is slow and low yielding. The molecular basis of its inefficiency has remained unclear. We conducted a systems chemistry analysis of the most effective enzyme-free RNA copying system to date. This system uses the strongly pairing dimers (CC, CG, GC, and GG) and in situ activation. Rate constants for activation were obtained from nuclear magnetic resonance-monitored model reactions, effective dissociation constants in the sub-millimolar range were obtained from inhibitor assays, and rates of phosphodiester formation for bound and activated dimers were determined by fitting extension kinetics, with the latter ranging from 1.4-16 × 10-3 h-1. Using a kinetic model that incorporates all experimentally determined parameters, we simulated primer extension. This identified phosphodiester formation on templates as the rate-limiting step. Our model shows copying of up to 12 template bases through a combination of primer extension, dimer-dimer coupling, and fragment ligation steps. The fluxes through reaction channels provide an unprecedented view of genetic copying in a protein-free RNA system. Our analysis identifies the remaining bottlenecks of enzyme-free pathways and provides the basis for rationally searching for more efficient self-replicating systems.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 18","pages":""},"PeriodicalIF":13.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12507520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145252071","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}

引用次数: 0

Novel fold and wing structure of Forkhead transcription factor facilitate DNA binding. 叉头转录因子新颖的折叠和翅膀结构促进DNA结合。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-09-23 DOI: 10.1093/nar/gkaf946

George L Wang,Yibei Jiang,Yuying Sun,Fariborz Nasertorabi,Jesse A Weller,Raktim Mitra,Alexander Batyuk,Oscar M Aparicio,Vadim Cherezov,Remo Rohs

{"title":"Novel fold and wing structure of Forkhead transcription factor facilitate DNA binding.","authors":"George L Wang,Yibei Jiang,Yuying Sun,Fariborz Nasertorabi,Jesse A Weller,Raktim Mitra,Alexander Batyuk,Oscar M Aparicio,Vadim Cherezov,Remo Rohs","doi":"10.1093/nar/gkaf946","DOIUrl":"https://doi.org/10.1093/nar/gkaf946","url":null,"abstract":"Forkhead homologue 1 (Fkh1) is a yeast transcription factor that plays essential roles in cell-cycle dynamics. Here, we report the co-crystal structure of the DNA-binding domain (DBD) of the yeast Fkh1 protein in complex with a 19-base pair oligonucleotide containing the core binding site and flanking regions. The three-dimensional structure of the Fkh1-DBD reveals a previously unknown protein fold among all known Forkhead proteins. The winged-helix fold forms base-specific contacts of α-helix H3 with the major groove of the core binding site. Wing 1 and Wing 2 form DNA shape-mediated contacts with the minor groove of the binding site flanking regions. The conformation of Wing 2 is distinct from all known Forkhead proteins, with α-helices H5 and H6 wrapping back onto the protein core, creating a stable Wing 2 loop. Backbone interactions with β-strands S1 and S2 reveal a structural mechanism for previously observed flanking region preferences in SELEX-seq experiments. In vivo yeast experiments on Fkh1 mutants demonstrate that wing residues interacting with flanking regions are important for Fkh1 function. Molecular dynamics simulations relate Fkh1 function to conformational flexibility of wing residues. The novel Forkhead fold enables Fkh1 function with implications, such as structure-based protein design, for other DNA-binding proteins.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"15 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145127150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0