Nucleic Acids Research最新文献_第3页

Linkage-based ortholog refinement in bacterial pangenomes with CLARC. 利用CLARC对细菌泛基因组进行基于连锁的同源精化。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf488

Indra González Ojeda, Samantha G Palace, Pamela P Martinez, Taj Azarian, Lindsay R Grant, Laura L Hammitt, William P Hanage, Marc Lipsitch

{"title":"Linkage-based ortholog refinement in bacterial pangenomes with CLARC.","authors":"Indra González Ojeda, Samantha G Palace, Pamela P Martinez, Taj Azarian, Lindsay R Grant, Laura L Hammitt, William P Hanage, Marc Lipsitch","doi":"10.1093/nar/gkaf488","DOIUrl":"10.1093/nar/gkaf488","url":null,"abstract":"Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) (https://github.com/IndraGonz/CLARC) improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8000+ Streptococcus pneumoniae genomes, CLARC reduced accessory gene estimates by >30% and improved evolutionary predictions based on accessory gene frequencies. CLARC is effective across different bacterial species, making it a broadly applicable tool for comparative genomics. By refining COG definitions, CLARC offers critical insights into bacterial evolution, aiding genetic studies across diverse populations.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 12","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12204703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144333576","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

Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA. SSB和RPA直接DNA和RNA链转移和动态蛋白质交换的机制研究。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf642

Tapas Paul, I-Ren Lee, Sushil Pangeni, Fahad Rashid, Olivia Yang, Edwin Antony, James M Berger, Sua Myong, Taekjip Ha

{"title":"Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA.","authors":"Tapas Paul, I-Ren Lee, Sushil Pangeni, Fahad Rashid, Olivia Yang, Edwin Antony, James M Berger, Sua Myong, Taekjip Ha","doi":"10.1093/nar/gkaf642","DOIUrl":"https://doi.org/10.1093/nar/gkaf642","url":null,"abstract":"Single-stranded DNA-binding proteins (SSBs) are essential for genome stability, facilitating replication, repair, and recombination by binding single-stranded DNA (ssDNA), recruiting other proteins, and dynamically relocating in response to cellular demands. Using single-molecule fluorescence resonance energy transfer assays, we elucidated the mechanisms underlying direct strand transfer from one locale to another, protein exchange, and RNA interactions at high resolution. Both bacterial SSB and eukaryotic replication protein A (RPA) exhibited direct strand transfer to competing ssDNA, with rates strongly influenced by ssDNA length. Strand transfer proceeded through multiple failed attempts before a successful transfer, forming a ternary intermediate complex with transient interactions, supporting a direct transfer mechanism. Both proteins efficiently exchanged DNA-bound counterparts with freely diffusing molecules, while hetero-protein exchange revealed that SSB and RPA could replace each other on ssDNA, indicating that protein exchange does not require specific protein-protein interactions. Additionally, both proteins bound RNA and underwent strand transfer to competing RNA, with RPA demonstrating faster RNA transfer kinetics. Competitive binding assays confirmed a strong preference for DNA over RNA. These findings provide critical insights into the dynamic behavior of SSB and RPA in nucleic acid interactions, advancing our understanding of their essential roles in genome stability, regulating RNA metabolism, and orchestrating nucleic acid processes.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 12","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541626","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

i-Motif DNA molecular beacon for microRNA detection. 用于microRNA检测的i-Motif DNA分子信标。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf556

Tengshuo Luo,Ziyue Guan,Yunlong Liu,Jun Zhou,Jean-Louis Mergny,Mingpan Cheng

{"title":"i-Motif DNA molecular beacon for microRNA detection.","authors":"Tengshuo Luo,Ziyue Guan,Yunlong Liu,Jun Zhou,Jean-Louis Mergny,Mingpan Cheng","doi":"10.1093/nar/gkaf556","DOIUrl":"https://doi.org/10.1093/nar/gkaf556","url":null,"abstract":"A molecular beacon (MB) is an oligonucleotide probe with a stem-loop structure designed to fluoresce upon hybridization with a specific target nucleic acid. Herein, we introduce a novel i-motif DNA-based molecular beacon (iMB) designed for nucleic acid detection. DNA chemical sequencing showed that the iMB can be selectively opened when its target is present, thanks to the formation of a duplex between this target and the iMB recognition loop. Phase diagrams were introduced to analyze the binding properties between the iMB and its target, and to optimize the detection conditions with different combinations of pH and temperature. Benefiting from the environment-sensitive stability and special structural feature inherent to the i-motif, this iMB exhibits a controllable sensitivity and specificity through choosing appropriate temperature/pH combination and recognition loop position in the i-motif probe. Leveraging the duplex-specific nuclease (DSN) resistance of the i-motif, we significantly enhanced the sensitivity by more than four orders of magnitude through the implementation of a DSN-assisted amplification strategy. Finally, miRNAs in cell lines and patient plasma were detected by the iMBs, as validated via quantitative reverse transcription polymerase chain reaction (RT-qPCR). This research successfully broadens the structural repertoire of MB stems to include a pH- and temperature-responsive i-motif stem.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"653 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488176","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 DNA-PKcs/JNK/p53 pathway underlies changes in cell fate decision toward death during DNA replication catastrophe. DNA- pkcs /JNK/p53通路是DNA复制灾难中细胞命运决定死亡变化的基础。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf573

Jinal A Patel,Julie Rageul,Natalie Lo,Auntara Nandi,Camryn Zezelic,Cynthia T Lee,Arafat Khan,Hyungjin Kim

{"title":"The DNA-PKcs/JNK/p53 pathway underlies changes in cell fate decision toward death during DNA replication catastrophe.","authors":"Jinal A Patel,Julie Rageul,Natalie Lo,Auntara Nandi,Camryn Zezelic,Cynthia T Lee,Arafat Khan,Hyungjin Kim","doi":"10.1093/nar/gkaf573","DOIUrl":"https://doi.org/10.1093/nar/gkaf573","url":null,"abstract":"Exacerbating the DNA replication problems of cancer cells serves as a viable therapeutic approach. Nevertheless, the cytotoxicity of cancer drugs is often hampered by therapy-induced senescence, leading to unfavorable patient outcomes. Here, we employ acute replisome dysfunction in combination with Ataxia telangiectasia and Rad3-related (ATR) inhibition as a strategy to divert senescent cells toward death by triggering DNA replication catastrophe, a form of irreversible replication fork collapse caused by excessive single-stranded DNA (ssDNA) accumulation. RNA-sequencing revealed a distinct set of p53-responsive genes responsible for death. We identify c-Jun N-terminal kinase (JNK) to be essential for augmenting p53-dependent apoptotic programs and inducing pan-nuclear distribution of γH2AX, together constituting a feed-forward loop to drive cell death. Activation of DNA-PKcs initiates the signaling cascade of replication catastrophe, including CHK1-dependent JNK activation, which relies on MRE11 and PARP1 to expand and recognize ssDNA gaps, defining replication-associated gaps as an underlying basis for replication catastrophe. Our study elucidates the dynamic regulation of proximal and distal effectors along the DNA-PKcs/JNK/p53 axis that govern the cell fate decision between senescence and death. We propose that key determinants of replication catastrophe signaling are targetable vulnerabilities that can be exploited to limit senescent cell populations and increase the efficacy of anti-cancer therapies.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"639 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478639","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

Nonredundant roles of topoisomerase 2α and 2β in the cytosolic replication of vaccinia virus. 拓扑异构酶2α和2β在牛痘病毒胞质复制中的非冗余作用。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf566

Ilaria Dalla Rosa, Lois Kent, Michael Way

{"title":"Nonredundant roles of topoisomerase 2α and 2β in the cytosolic replication of vaccinia virus.","authors":"Ilaria Dalla Rosa, Lois Kent, Michael Way","doi":"10.1093/nar/gkaf566","DOIUrl":"10.1093/nar/gkaf566","url":null,"abstract":"Vaccinia virus is a large enveloped DNA virus, which, like all poxviruses, replicates in the cytoplasm of infected cells. Vaccinia was historically thought to encode all the proteins required for its replication. However, more recent findings have shown that nuclear host proteins are redirected to the cytoplasm to facilitate viral replication. Among these, topoisomerase 2α (TOP2A) and 2β (TOP2B), which mediate nuclear transcription, DNA replication, and chromosome segregation are the most abundant host proteins associated with nascent viral genomes. Here, we investigate the mechanisms driving TOP2A and TOP2B cytoplasmic translocation and their role in viral replication. We found that early viral protein synthesis induces the cytosolic relocalization of both isoforms, which are subsequently recruited to viral factories by an interaction of their C-terminal domains with the viral ligase, A50. TOP2A promotes replication by interacting with the vaccinia DNA replication machinery. In contrast, TOP2B suppresses replication by enhancing the formation of double-stranded RNA and antiviral granules, containing components of the tRNA splicing ligase complex. Our analysis provides new insights into host-pathogen interactions during poxvirus infection and the role of topoisomerase 2 outside of the nucleus.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 12","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485305","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

Catalytic-state structure of Candidatus Hydrogenedentes Cas12b revealed by cryo-EM studies. cro - em研究Candidatus hydrogenentes Cas12b的催化态结构。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf519

Ye Li,Jian Li,Xiaotong Pei,Jingjing Wei,Jianhua Gan,Jinzhong Lin

{"title":"Catalytic-state structure of Candidatus Hydrogenedentes Cas12b revealed by cryo-EM studies.","authors":"Ye Li,Jian Li,Xiaotong Pei,Jingjing Wei,Jianhua Gan,Jinzhong Lin","doi":"10.1093/nar/gkaf519","DOIUrl":"https://doi.org/10.1093/nar/gkaf519","url":null,"abstract":"The CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein) systems are adaptive immune mechanisms that play critical roles in defending archaea and bacteria against invading entities. These systems can be divided into two classes, with class 2 comprising three types (II, V, and VI). Because of their ability to cleave double-stranded DNA, many class 2 CRISPR-Cas proteins have been harnessed as genome editing tools. Unlike the well-studied type II Cas9 proteins, the structural studies of the type V-B Cas12b proteins are limited, hindering their engineering and broader application. Here, we report four complex structures of ChCas12b, which reveal many unique structural features. The folding of the single guide RNA (sgRNA) of ChCas12b is distinct from that of AacCas12b and BthCas12b. Notably, many of these unique features are involved in ChCas12b-sgRNA interaction, suggesting that they are co-evolved. While ChCas12b shares a conserved two-cation-assisted catalytic mechanism with its homologs, it recognizes a longer guide:target heteroduplex, potentially offering higher fidelity in DNA editing. Altogether, our studies suggested that Cas12b family proteins exhibit significant diversity in their folding, sgRNA and target DNA binding. In the future, it is worth characterizing more representative proteins to identify CRISPR-Cas proteins with higher gene editing ability and fidelity.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"16 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329043","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

Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing. 利用全局偶联和高通量测序表征转录因子的DNA识别偏好。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf592

Qin Zhou, Jose Alberto de la Paz, Alexander D Stanowick, Xingcheng Lin, Faruck Morcos

{"title":"Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing.","authors":"Qin Zhou, Jose Alberto de la Paz, Alexander D Stanowick, Xingcheng Lin, Faruck Morcos","doi":"10.1093/nar/gkaf592","DOIUrl":"https://doi.org/10.1093/nar/gkaf592","url":null,"abstract":"DNA-transcription factor (TF) interactions are essential for gene regulation. Fully characterizing TF recognition specificities and identifying their genomic binding targets are important to understand TF function and regulatory networks. Recently, high-throughput sequencing technology HT-SELEX (high-throughput systematic evolution of ligands by exponential enrichment) has been used to measure hundreds of TFs, providing massive datasets that comprise TF binding preferences. However, there is a need to develop comprehensive computational modeling to fully extract and characterize critical TF binding preferences and fail to distinguish genome-wide binding targets. In this study, we developed a global pairwise model called DCA-Scapes trained with experimental HT-SELEX data. Our approach uncovered high-resolution TF recognition specificity landscapes, enabled the prediction of in vivo binding sequences, and was validated with ChIP-seq (ChIP sequencing) data. In addition, the DCA-Scapes model was utilized to refine the locations of binding regions and accurately identify the binding sites within the ChIP-seq enriched peaks. Moreover, we extended our model to cover the entire human genome, uncovering potential TF target sites that exhibit tissue-specific TF recognition across various cellular environments.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 12","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144541586","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

Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research. 在生物生产和基础研究中对哺乳动物细胞基因表达的有效光遗传学调控。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf546

Jeannette Gebel, Elisa Ciglieri, Rainer Stahl, Fraser Duthie, Fabian Frechen, Andreas Möglich, Herbert Müller-Hartmann, Hanns-Martin Schmidt, Dagmar Wachten

{"title":"Potent optogenetic regulation of gene expression in mammalian cells for bioproduction and basic research.","authors":"Jeannette Gebel, Elisa Ciglieri, Rainer Stahl, Fraser Duthie, Fabian Frechen, Andreas Möglich, Herbert Müller-Hartmann, Hanns-Martin Schmidt, Dagmar Wachten","doi":"10.1093/nar/gkaf546","DOIUrl":"10.1093/nar/gkaf546","url":null,"abstract":"Precise temporal and spatial control of gene expression greatly benefits the study of specific cellular circuits and activities. Compared to chemical inducers, light-dependent control of gene expression by optogenetics achieves a higher spatial and temporal resolution. Beyond basic research, this could also prove decisive for manufacturing difficult-to-express proteins in pharmaceutical bioproduction. However, current optogenetic gene-expression systems limit this application in mammalian cells, as expression levels and the degree of induction upon light stimulation are insufficient. To overcome this limitation, we designed a photoswitch by fusing the blue light-activated light-oxygen-voltage receptor EL222 from Erythrobacter litoralis to the three transcriptional activator domains VP64, p65, and Rta in tandem. The resultant photoswitch, dubbed DEL-VPR, allows up to a 570-fold induction of target gene expression by blue light, thereby achieving expression levels of strong constitutive promoters. Here, we used DEL-VPR to enable light-induced expression of complex monoclonal and bispecific antibodies with reduced byproduct expression and increased yield of functional protein complexes. Our approach offers temporally controlled yet strong gene expression and applies to academic and industrial settings.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 12","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144529040","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

Switchable RNA motifs for dynamic transcriptional control of RNA condensates. 可切换RNA基序用于RNA凝聚物的动态转录控制。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf497

Anli A Tang,Martin Vincent Gobry,Shiyi Li,Ebbe Sloth Andersen,Elisa Franco

{"title":"Switchable RNA motifs for dynamic transcriptional control of RNA condensates.","authors":"Anli A Tang,Martin Vincent Gobry,Shiyi Li,Ebbe Sloth Andersen,Elisa Franco","doi":"10.1093/nar/gkaf497","DOIUrl":"https://doi.org/10.1093/nar/gkaf497","url":null,"abstract":"RNA-driven phase separation is emerging as a promising approach for engineering biomolecular condensates with diverse functionalities. Condensates form thanks to weak yet specific RNA-RNA interactions established by design via complementary sequence domains. Here, we demonstrate how RNA condensates formed by star-shaped RNA motifs, or nanostars, can be dynamically controlled when the motifs include additional linear or branch-loop domains that facilitate access of regulatory RNA molecules to the nanostar interaction domains. We show that condensates dissolve in the presence of RNA \"invaders\" that occlude selected nanostar bonds and reduce the valency of the nanostars, preventing phase separation. We further demonstrate that the introduction of \"anti-invader\" strands, complementary to the invaders, makes it possible to restore condensate formation. An important aspect of our experiments is that we demonstrate these behaviors in one-pot reactions, where RNA nanostars, invaders, and anti-invaders are simultaneously transcribed in vitro using short DNA templates. Our results lay the groundwork for engineering RNA-based assemblies with tunable, reversible condensation, providing a promising toolkit for synthetic biology applications requiring responsive, self-organizing biomolecular materials.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329042","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

An engineered glutamic acid tRNA for efficient suppression of pathogenic nonsense mutations. 一种工程谷氨酸tRNA有效抑制致病性无义突变。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-06-20 DOI: 10.1093/nar/gkaf532

Caitlin Specht,Alejandro Tapia,Sarah Penrod,Gabriela A Soriano,Aya Awawdeh,Sarah A Alshawi,Cody A White,Jean-Denis Beaudoin,Emma H Doud,Oscar Vargas-Rodriguez,Yunjie Huang,Jeffery M Tharp

{"title":"An engineered glutamic acid tRNA for efficient suppression of pathogenic nonsense mutations.","authors":"Caitlin Specht,Alejandro Tapia,Sarah Penrod,Gabriela A Soriano,Aya Awawdeh,Sarah A Alshawi,Cody A White,Jean-Denis Beaudoin,Emma H Doud,Oscar Vargas-Rodriguez,Yunjie Huang,Jeffery M Tharp","doi":"10.1093/nar/gkaf532","DOIUrl":"https://doi.org/10.1093/nar/gkaf532","url":null,"abstract":"Nonsense mutations that introduce premature termination codons (PTCs) into protein-coding genes are responsible for numerous genetic diseases; however, there are currently no effective treatment options for individuals affected by these mutations. One approach to combat nonsense-related diseases relies on the use of engineered suppressor transfer RNAs (sup-tRNAs) that facilitate translational stop codon readthrough, thereby restoring full-length protein synthesis. While several sup-tRNAs have shown promising results in preclinical models, many exhibit low PTC suppression efficiency, precluding their use as therapeutics. For example, glutamic acid (Glu) codons represent one of the most common sites for nonsense mutations, yet existing sup-tRNAs are ineffective at suppressing Glu-to-Stop mutations. To address this limitation, here we describe a rationally designed sup-tRNA (tRNAGluV13) with greatly improved ability to suppress PTCs occurring at Glu codons. We demonstrate that tRNAGluV13 efficiently restores protein synthesis from multiple nonsense-containing reporter genes, faithfully installing Glu in response to PTCs. Additionally, we demonstrate that tRNAGluV13 can functionally rescue pathogenic PTCs that cause hereditary breast and ovarian cancer syndrome and cystic fibrosis. The ability of tRNAGluV13 to effectively suppress one of the most common PTC mutations should greatly expand the potential of sup-tRNA-based therapeutics.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"24 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329044","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