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Methyl-dependent auto-regulation of the DNA N6-adenine methyltransferase AMT1 in the unicellular eukaryote Tetrahymena thermophila
IF 14.9 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-25 DOI: 10.1093/nar/gkaf022
Lili Duan, Haicheng Li, Aili Ju, Zhe Zhang, Junhua Niu, Yumiao Zhang, Jinghan Diao, Yongqiang Liu, Ni Song, Honggang Ma, Kensuke Kataoka, Shan Gao, Yuanyuan Wang
{"title":"Methyl-dependent auto-regulation of the DNA N6-adenine methyltransferase AMT1 in the unicellular eukaryote Tetrahymena thermophila","authors":"Lili Duan, Haicheng Li, Aili Ju, Zhe Zhang, Junhua Niu, Yumiao Zhang, Jinghan Diao, Yongqiang Liu, Ni Song, Honggang Ma, Kensuke Kataoka, Shan Gao, Yuanyuan Wang","doi":"10.1093/nar/gkaf022","DOIUrl":"https://doi.org/10.1093/nar/gkaf022","url":null,"abstract":"DNA N6-methyladenine (6mA) is a potential epigenetic mark involved in gene transcription in eukaryotes, yet the regulatory mechanism governing its methyltransferase (MTase) activity remains obscure. Here, we exploited the 6mA MTase AMT1 to elucidate its auto-regulation in the unicellular eukaryote Tetrahymena thermophila. The detailed endogenous localization of AMT1 in vegetative and sexual stages revealed a correlation between the 6mA reestablishment in the new MAC and the occurrence of zygotically expressed AMT1. Catalytically inactive AMT1 reduced 6mA level on the AMT1 gene and its expression, suggesting that AMT1 modulated its own transcription via 6mA. Furthermore, AMT1-dependent 6mA regulated the transcription of its target genes, thereby affecting cell fitness. Our findings unveil a positive feedback loop of transcriptional activation on the AMT1 gene and highlight the crucial role of AMT1-dependent 6mA in gene transcription.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"20 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044196","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
Proximity-activated guide RNA of CRISPR–Cas12a for programmable diagnostic detection and gene regulation
IF 14.9 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-25 DOI: 10.1093/nar/gkaf017
Zhian Hu, Shen Ling, Jialin Duan, Zixiao Yu, Yanfei Che, Song Wang, Sichun Zhang, Xinrong Zhang, Zhengping Li
{"title":"Proximity-activated guide RNA of CRISPR–Cas12a for programmable diagnostic detection and gene regulation","authors":"Zhian Hu, Shen Ling, Jialin Duan, Zixiao Yu, Yanfei Che, Song Wang, Sichun Zhang, Xinrong Zhang, Zhengping Li","doi":"10.1093/nar/gkaf017","DOIUrl":"https://doi.org/10.1093/nar/gkaf017","url":null,"abstract":"The flexibility and programmability of CRISPR–Cas technology have made it one of the most popular tools for biomarker diagnostics and gene regulation. Especially, the CRISPR–Cas12 system has shown exceptional clinical diagnosis and gene editing capabilities. Here, we discovered that although the top loop of the 5′ handle of guide RNA can undergo central splitting, deactivating CRISPR–Cas12a, the segments can dramatically restore CRISPR function through nucleic acid self-assembly or interactions with small molecules and aptamers. This discovery forms the basis of an engineered Cas12a system with a programmable proximity-activated guide RNA (PARC–Cas12a) that links targets of interest to dsDNA. Leveraging the efficient trans- and cis-cleavage of Cas12, our findings further inspired a detection platform design for RNAs or non-nucleic acid biomarkers, enabling highly sensitive and multiplexed analysis. We further demonstrated the feasibility of RNA-controllable gene knockout/knockdown in Escherichia coli. Notably, we successfully validated the gene regulatory capabilities of the PARC–Cas12a system within mammalian cell systems by utilizing the classical theophylline molecule–aptamer system. Our results introduce a programmable toolbox for precise diagnostics and cell regulation, allowing the development of versatile diagnostic tools, complex synthetic biological circuits, and cellular biosensors.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"47 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143035146","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
c-JUN: a chromatin repressor that limits mesoderm differentiation in human pluripotent stem cells
IF 14.9 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-25 DOI: 10.1093/nar/gkaf001
Ran Zhang, Guihuan Li, Qi Zhang, Zhenhua Wang, Dan Xiang, Xiaofei Zhang, Jiekai Chen, Andrew P Hutchins, Dajiang Qin, Huanxing Su, Duanqing Pei, Dongwei Li
{"title":"c-JUN: a chromatin repressor that limits mesoderm differentiation in human pluripotent stem cells","authors":"Ran Zhang, Guihuan Li, Qi Zhang, Zhenhua Wang, Dan Xiang, Xiaofei Zhang, Jiekai Chen, Andrew P Hutchins, Dajiang Qin, Huanxing Su, Duanqing Pei, Dongwei Li","doi":"10.1093/nar/gkaf001","DOIUrl":"https://doi.org/10.1093/nar/gkaf001","url":null,"abstract":"Cell fate determination at the chromatin level is not fully comprehended. Here, we report that c-JUN acts on chromatin loci to limit mesoderm cell fate specification as cells exit pluripotency. Although c-JUN is widely expressed across various cell types in early embryogenesis, it is not essential for maintaining pluripotency. Instead, it functions as a repressor to constrain mesoderm development while having a negligible impact on ectoderm differentiation. c-JUN interacts with MBD3–NuRD complex, which helps maintain chromatin in a low accessibility state at mesoderm-related genes during the differentiation of human pluripotent stem cells into mesoderm. Furthermore, c-JUN specifically inhibits the activation of key mesoderm factors, such as EOMES and GATA4. Knocking out c-JUN or inhibiting it with a JNK inhibitor can alleviate this suppression, promoting mesoderm cell differentiation. Consistently, knockdown of MBD3 enhances mesoderm generation, whereas MBD3 overexpression impedes it. Overexpressing c-JUN redirects differentiation toward a fibroblast-like lineage. Collectively, our findings suggest that c-JUN acts as a chromatin regulator to restrict the mesoderm cell fate.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"111 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143035144","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
Fam170a deficiency causes male infertility by impairing histone-to-protamine exchange during mouse spermiogenesis
IF 14.9 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-25 DOI: 10.1093/nar/gkaf023
Jinmei Cheng, Yimin Gu, Yueming Wang, Junjie Xun, Guishuan Wang, Yu Wang, Jianyu Wang, Yinchuan Li, Fei Sun
{"title":"Fam170a deficiency causes male infertility by impairing histone-to-protamine exchange during mouse spermiogenesis","authors":"Jinmei Cheng, Yimin Gu, Yueming Wang, Junjie Xun, Guishuan Wang, Yu Wang, Jianyu Wang, Yinchuan Li, Fei Sun","doi":"10.1093/nar/gkaf023","DOIUrl":"https://doi.org/10.1093/nar/gkaf023","url":null,"abstract":"Chromatin remodeling, which involves the histone-to-protamine exchange process during spermiogenesis, is crucial for sperm nuclear condensation and male fertility. However, the key regulators and underlying molecular mechanisms involved in this process remain largely unexplored. In this study, we discovered that deficiency in the family with sequence similarity 170 member A (Fam170a) led to abnormal sperm nuclear morphology and male infertility in mice, mirroring the observation of very low Fam170a transcription levels in sperm of infertile men with teratozoospermia. Further investigation revealed that Fam170a plays a significant role in the histone-to-protamine chromatin remodeling process. This was evidenced by the earlier core histone removal, accelerated translation and degradation of transition proteins, and reduced protamine incorporation during spermiogenesis in Fam170a-deleted mice. Mechanistically, we found that Fam170a interacts with chromatin remodeling-associated proteins and regulates the transcription of genes related to chromatin remodeling. Notably, Fam170a directly interacts with the deubiquitinating enzyme Usp7 and facilitates its nuclear translocation in elongating sperm, enhancing the deubiquitinating activity of Usp7 on testis-specific histone H2A and H2B variants. Collectively, our findings identify Fam170a as a previously unrecognized key regulator of sperm chromatin remodeling and suggest that histone deubiquitination may play an essential role in the histone-to-protamine exchange process.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"29 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143035142","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
Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes
IF 14.9 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-25 DOI: 10.1093/nar/gkaf014
Mariko Sasaki, Takehiko Kobayashi
{"title":"Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes","authors":"Mariko Sasaki, Takehiko Kobayashi","doi":"10.1093/nar/gkaf014","DOIUrl":"https://doi.org/10.1093/nar/gkaf014","url":null,"abstract":"DNA copy number changes via chromosomal rearrangements or the production of extrachromosomal circular DNA. Here, we demonstrate that the histone deacetylase Sir2 maintains the copy number of budding yeast ribosomal RNA gene [ribosomal DNA (rDNA)] by suppressing end resection of DNA double-strand breaks (DSBs) formed upon DNA replication fork arrest in the rDNA and their subsequent homologous recombination (HR)-mediated rDNA copy number changes during DSB repair. Sir2 represses transcription from the regulatory promoter E-pro located near the fork arresting site. When Sir2 is absent, this transcription is stimulated but terminated by arrested replication forks. This transcription–replication collision induces DSB formation, DSB end resection and the Mre11-Rad50-Xrs2 complex-dependent DSB repair that is prone to chromosomal rDNA copy number changes and the production of extrachromosomal rDNA circles. Therefore, repression of transcription near arrested replication forks is critical for the maintenance of rDNA stability by directing DSB repair into the HR-independent, rearrangement-free pathway.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"19 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143035141","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
ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.
IF 16.6 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf009
Joon Young Park, Minchang Jang, Eunna Choi, Sang-Mok Lee, Ina Bang, Jihoon Woo, Seonggyu Kim, Eun-Jin Lee, Donghyuk Kim
{"title":"ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.","authors":"Joon Young Park, Minchang Jang, Eunna Choi, Sang-Mok Lee, Ina Bang, Jihoon Woo, Seonggyu Kim, Eun-Jin Lee, Donghyuk Kim","doi":"10.1093/nar/gkaf009","DOIUrl":"10.1093/nar/gkaf009","url":null,"abstract":"<p><p>Genome-wide identification of binding profiles for DNA-binding proteins from the limited number of intracellular pathogens in infection studies is crucial for understanding virulence and cellular processes but remains challenging, as the current ChIP-exo is designed for high-input bacterial cells (>1010). Here, we developed an optimized ChIP-mini method, a low-input ChIP-exo utilizing a 5,000-fold reduced number of initial bacterial cells and an analysis pipeline, to identify genome-wide binding dynamics of DNA-binding proteins in host-infected pathogens. Applying ChIP-mini to intracellular Salmonella Typhimurium, we identified 642 and 1,837 binding sites of H-NS and RpoD, respectively, elucidating changes in their binding position and binding intensity during infection. Post-infection, we observed 21 significant reductions in H-NS binding at intergenic regions, exposing the promoter region of virulence genes, such as those in Salmonella pathogenicity islands-2, 3 and effectors. Furthermore, we revealed the crucial phenomenon that novel and significantly increased RpoD bindings were found within regions exhibiting diminished H-NS binding, thereby facilitating substantial upregulation of virulence genes. These findings markedly enhance our understanding of how H-NS and RpoD simultaneously coordinate the transcription initiation of virulence genes within macrophages. Collectively, this work demonstrates a broadly adaptable tool that will enable the elucidation of DNA-binding protein dynamics in diverse intracellular pathogens during infection.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 3","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11770342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047299","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
R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning. R-DeeP/TripepSVM鉴定rna结合ob -fold样蛋白PatR是异囊模式化的调节因子。
IF 16.6 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkae1247
Manuel Brenes-Álvarez, Halie R Ropp, Dimitrios Papagiannidis, Clement M Potel, Frank Stein, Ingeborg Scholz, Claudia Steglich, Mikhail M Savitski, Agustín Vioque, Alicia M Muro-Pastor, Wolfgang R Hess
{"title":"R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning.","authors":"Manuel Brenes-Álvarez, Halie R Ropp, Dimitrios Papagiannidis, Clement M Potel, Frank Stein, Ingeborg Scholz, Claudia Steglich, Mikhail M Savitski, Agustín Vioque, Alicia M Muro-Pastor, Wolfgang R Hess","doi":"10.1093/nar/gkae1247","DOIUrl":"10.1093/nar/gkae1247","url":null,"abstract":"<p><p>RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation of RNA-protein complexes after RNase treatment in density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates in Nostoc sp. PCC 7120. We validated in vivo the RNA-binding capacity of six RBP candidates. Some participate in essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst differentiation (PrpA, PatU3), but their association with RNA was unknown. Validated RBPs Asl3888 and Alr1700 were not previously characterized. Alr1700 is an RBP with two oligonucleotide/oligosaccharide-binding (OB)-fold-like domains that is differentially expressed in heterocysts and interacts with non-coding regulatory RNAs. Deletion of alr1700 led to complete deregulation of the cell differentiation process, a striking increase in the number of heterocyst-like cells, and was ultimately lethal in the absence of combined nitrogen. These observations characterize this RBP as a master regulator of the heterocyst patterning and differentiation process, leading us to rename Alr1700 to PatR.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854843","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
tRNA hypomodification facilitates 5-fluorocytosine resistance via cross-pathway control system activation in Aspergillus fumigatus. tRNA低修饰通过烟曲霉的交叉通路控制系统激活促进5-氟胞嘧啶抗性。
IF 16.6 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkae1205
Alexander Bruch, Valentina Lazarova, Maximilian Berg, Thomas Krüger, Sascha Schäuble, Abdulrahman A Kelani, Birte Mertens, Pamela Lehenberger, Olaf Kniemeyer, Stefanie Kaiser, Gianni Panagiotou, Fabio Gsaller, Matthew G Blango
{"title":"tRNA hypomodification facilitates 5-fluorocytosine resistance via cross-pathway control system activation in Aspergillus fumigatus.","authors":"Alexander Bruch, Valentina Lazarova, Maximilian Berg, Thomas Krüger, Sascha Schäuble, Abdulrahman A Kelani, Birte Mertens, Pamela Lehenberger, Olaf Kniemeyer, Stefanie Kaiser, Gianni Panagiotou, Fabio Gsaller, Matthew G Blango","doi":"10.1093/nar/gkae1205","DOIUrl":"10.1093/nar/gkae1205","url":null,"abstract":"<p><p>Increasing antifungal drug resistance is a major concern associated with human fungal pathogens like Aspergillus fumigatus. Genetic mutation and epimutation mechanisms clearly drive resistance, yet the epitranscriptome remains relatively untested. Here, deletion of the A. fumigatus transfer RNA (tRNA)-modifying isopentenyl transferase ortholog, Mod5, led to altered stress response and unexpected resistance against the antifungal drug 5-fluorocytosine (5-FC). After confirming the canonical isopentenylation activity of Mod5 by liquid chromatography-tandem mass spectrometry and Nano-tRNAseq, we performed simultaneous profiling of transcriptomes and proteomes to reveal a comparable overall response to 5-FC stress; however, a premature activation of cross-pathway control (CPC) genes in the knockout was further increased after antifungal treatment. We identified several orthologues of the Aspergillus nidulans Major Facilitator Superfamily transporter nmeA as specific CPC-client genes in A. fumigatus. Overexpression of Mod5-target tRNATyrGΨA in the Δmod5 strain rescued select phenotypes but failed to reverse 5-FC resistance, whereas deletion of nmeA largely, but incompletely, reverted the resistance phenotype, implying additional relevant exporters. In conclusion, 5-FC resistance in the absence of Mod5 and i6A likely originates from multifaceted transcriptional and translational changes that skew the fungus towards premature CPC-dependent activation of antifungal toxic-intermediate exporter nmeA, offering a potential mechanism reliant on RNA modification to facilitate transient antifungal resistance.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797069/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877621","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 gate-clamp mechanism for ssDNA translocation by DdmD in Vibrio cholerae plasmid defense.
IF 16.6 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf064
Ruoyu Li, Yusong Liu, Haishan Gao, Zhonghui Lin
{"title":"A gate-clamp mechanism for ssDNA translocation by DdmD in Vibrio cholerae plasmid defense.","authors":"Ruoyu Li, Yusong Liu, Haishan Gao, Zhonghui Lin","doi":"10.1093/nar/gkaf064","DOIUrl":"10.1093/nar/gkaf064","url":null,"abstract":"<p><p>The DdmDE antiplasmid system, consisting of the helicase-nuclease DdmD and the prokaryotic Argonaute (pAgo) protein DdmE, plays a crucial role in defending Vibrio cholerae against plasmids. Guided by DNA, DdmE specifically targets plasmids, disassembles the DdmD dimer, and forms a DdmD-DdmE handover complex to facilitate plasmid degradation. However, the precise ATP-dependent DNA translocation mechanism of DdmD has remained unclear. Here, we present cryo-EM structures of DdmD bound to single-stranded DNA (ssDNA) in nucleotide-free, ATPγS-bound, and ADP-bound states. These structures, combined with biochemical analysis, reveal a unique \"gate-clamp\" mechanism for ssDNA translocation by DdmD. Upon ATP binding, arginine finger residues R855 and R858 reorient to interact with the γ-phosphate, triggering HD2 domain movement. This shift repositions the gate residue Q781, causing a flip of the 3' flank base, which is then clamped by residue F639. After ATP hydrolysis, the arginine finger releases the nucleotide, inducing HD2 to return to its open state. This conformational change enables DdmD to translocate along ssDNA by one nucleotide in the 5' to 3' direction. This study provides new insights into the ATP-dependent translocation of DdmD and contributes to understanding the mechanistic diversity within SF2 helicases.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 3","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11795196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190040","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
Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.
IF 16.6 2区 生物学
Nucleic Acids Research Pub Date : 2025-01-24 DOI: 10.1093/nar/gkaf025
Maria Chernigovskaya, Milena Pavlović, Chakravarthi Kanduri, Sofie Gielis, Philippe A Robert, Lonneke Scheffer, Andrei Slabodkin, Ingrid Hobæk Haff, Pieter Meysman, Gur Yaari, Geir Kjetil Sandve, Victor Greiff
{"title":"Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.","authors":"Maria Chernigovskaya, Milena Pavlović, Chakravarthi Kanduri, Sofie Gielis, Philippe A Robert, Lonneke Scheffer, Andrei Slabodkin, Ingrid Hobæk Haff, Pieter Meysman, Gur Yaari, Geir Kjetil Sandve, Victor Greiff","doi":"10.1093/nar/gkaf025","DOIUrl":"10.1093/nar/gkaf025","url":null,"abstract":"<p><p>Machine learning (ML) has shown great potential in the adaptive immune receptor repertoire (AIRR) field. However, there is a lack of large-scale ground-truth experimental AIRR data suitable for AIRR-ML-based disease diagnostics and therapeutics discovery. Simulated ground-truth AIRR data are required to complement the development and benchmarking of robust and interpretable AIRR-ML methods where experimental data is currently inaccessible or insufficient. The challenge for simulated data to be useful is incorporating key features observed in experimental repertoires. These features, such as antigen or disease-associated immune information, cause AIRR-ML problems to be challenging. Here, we introduce LIgO, a software suite, which simulates AIRR data for the development and benchmarking of AIRR-ML methods. LIgO incorporates different types of immune information both on the receptor and the repertoire level and preserves native-like generation probability distribution. Additionally, LIgO assists users in determining the computational feasibility of their simulations. We show two examples where LIgO supports the development and validation of AIRR-ML methods: (i) how individuals carrying out-of-distribution immune information impacts receptor-level prediction performance and (ii) how immune information co-occurring in the same AIRs impacts the performance of conventional receptor-level encoding and repertoire-level classification approaches. LIgO guides the advancement and assessment of interpretable AIRR-ML methods.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 3","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053084","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
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