Nucleic Acids Research最新文献_第2页

Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction–modification enzyme 不含 DNA 和与 DNA 结合的 BsaXI 的冷冻电镜结构：IIB 型限制性修饰酶的结构

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-15 DOI: 10.1093/nar/gkaf291

Betty W Shen, Dan Heiter, Weiwei Yang, Shuang-yong Xu, Barry L Stoddard

{"title":"Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction–modification enzyme","authors":"Betty W Shen, Dan Heiter, Weiwei Yang, Shuang-yong Xu, Barry L Stoddard","doi":"10.1093/nar/gkaf291","DOIUrl":"https://doi.org/10.1093/nar/gkaf291","url":null,"abstract":"We have determined multiple cryogenic electron microscopy (cryo-EM) structures of the Type IIB restriction–modification enzyme BsaXI. Such enzymes cleave DNA on both sides of their recognition sequence and share features of Types I, II, and III restriction systems. BsaXI forms a heterotrimeric (RM)2S assemblage in the presence and absence of bound DNA. Two unique structural motifs—a multi-helical “knob” and a long antiparallel double-helical “paddle”—are involved in DNA binding and cleavage. Binding of the DNA target triggers a large conformational change from an ‘open’ to ‘closed’ configuration, resulting in a mixture of two different conformations with respect to the positioning of the S subunit and its target recognition domains on the enzyme’s bipartite DNA target site. Structure-guided mutagenesis studies implicated two clusters of residues in the RM subunit as being critical for DNA cleavage, both are located proximal to a DNA cleavage site. One corresponds to a canonical PD-(D/E)xK endonuclease site in the N-terminal endonuclease domain, while the other corresponds to residues clustered within the paddle motif (near to the C-terminal end of the RM subunit). This analysis facilitates a comparison of three potential mechanisms by which such enzymes cleave DNA on each side of the bound target.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"3 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143832505","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 yeast CST and Polα/primase complexes act in concert to ensure proper telomere maintenance and protection

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-15 DOI: 10.1093/nar/gkaf245

Kimberly Calugaru, Eun Young Yu, Sophie Huang, Nayim González-Rodríguez, Javier Coloma, Neal F Lue

{"title":"The yeast CST and Polα/primase complexes act in concert to ensure proper telomere maintenance and protection","authors":"Kimberly Calugaru, Eun Young Yu, Sophie Huang, Nayim González-Rodríguez, Javier Coloma, Neal F Lue","doi":"10.1093/nar/gkaf245","DOIUrl":"https://doi.org/10.1093/nar/gkaf245","url":null,"abstract":"Polα/primase (PP), the polymerase that initiates DNA synthesis at replication origins, also completes the task of genome duplication by synthesizing the telomere C-strand under the control of the CTC1/CDC13-STN1-TEN1 (CST) complex. Using cryo-electron microscopy (cryo-EM) structures of the human CST-Polα/primase-DNA complex as guides in conjunction with AlphaFold modeling, we identified structural elements in yeast CST and PP that promote complex formation. Mutating these structures in Candida glabrata Stn1, Ten1, Pri1, and Pri2 abrogated the stimulatory activity of CST on PP in vitro, supporting the functional relevance of the physical contacts in cryo-EM structures as well as the conservation of mechanisms between yeast and humans. Introducing these mutations into C. glabrata yielded two distinct groups of mutants. One group exhibited progressive, telomerase-dependent telomere elongation without evidence of DNA damage. The other manifested slow growth, telomere length heterogeneity, single-stranded DNA accumulation and elevated C-circles, which are indicative of telomere deprotection. These telomere deprotection phenotypes are altered or suppressed by mutations in multiple DNA damage response (DDR) and DNA repair factors. We conclude that in yeast, the telomerase inhibition and telomere protection function previously ascribed to the CST complex are mediated jointly by both CST and Polα/primase, highlighting the critical importance of a replicative DNA polymerase in telomere regulation.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"238 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143837034","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

Maternal histone mRNAs are uniquely processed through polyadenylation in a Stem-Loop Binding Protein (SLBP) dependent manner 母体组蛋白 mRNA 以茎环结合蛋白 (SLBP) 依赖性方式通过多腺苷酸化进行独特加工

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-15 DOI: 10.1093/nar/gkaf288

Juan Pérez-Roldán, László Henn, Jordi Bernués, Mònica Torras-LLort, Srividya Tamirisa, Eulàlia Belloc, Laura Rodríguez-Muñoz, Gyula Timinszky, Gerardo Jiménez, Raúl Méndez, Albert Carbonell, Fernando Azorín

{"title":"Maternal histone mRNAs are uniquely processed through polyadenylation in a Stem-Loop Binding Protein (SLBP) dependent manner","authors":"Juan Pérez-Roldán, László Henn, Jordi Bernués, Mònica Torras-LLort, Srividya Tamirisa, Eulàlia Belloc, Laura Rodríguez-Muñoz, Gyula Timinszky, Gerardo Jiménez, Raúl Méndez, Albert Carbonell, Fernando Azorín","doi":"10.1093/nar/gkaf288","DOIUrl":"https://doi.org/10.1093/nar/gkaf288","url":null,"abstract":"During early embryogenesis the zygotic genome remains transcriptionally silent and expression relies on maternally deposited products. Maternal deposition of histones is crucial to preserve chromatin integrity during early embryo development, when the number of nuclei exponentially increases in the absence of zygotic expression. In the Drosophila embryo, histones are maternally deposited as both proteins and mRNAs. Histone transcripts are the only nonpolyadenylated cellular mRNAs. They contain a highly conserved 3′UTR stem-loop structure, which is recognized by the Stem-Loop Binding Protein (SLBP) that, in conjunction with U7 snRNP, regulates their unique 3′-end processing. Here we report that, unexpectedly, maternal histone mRNAs are polyadenylated and have a truncated 3′ stem-loop. This noncanonical 3′-end processing of maternal histone mRNAs occurs at their synthesis during oogenesis and requires SLBP, but not U7 snRNP. We show that maternal histone transcripts are subjected to cytoplasmic poly(A) tail elongation by Wisp, which results in their stabilization and is a requisite for translation. We also show that maternal histone transcripts remain largely quiescent and that their translation is activated upon loss of the embryonic linker histone dBigH1, which impairs chromatin assembly and induces DNA damage. Here, we discuss possible models to integrate these observations.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"38 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143832506","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

Transcriptional induction by ecdysone in Drosophila salivary glands involves an increase in chromatin accessibility and acetylation 果蝇唾液腺中蜕皮激素的转录诱导涉及染色质可及性和乙酰化的增加

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-15 DOI: 10.1093/nar/gkaf284

Aleksandra A Evdokimova, Tatyana D Kolesnikova, Marina Yu Mazina, Aleksey N Krasnov, Maksim Erokhin, Darya Chetverina, Nadezhda E Vorobyeva

{"title":"Transcriptional induction by ecdysone in Drosophila salivary glands involves an increase in chromatin accessibility and acetylation","authors":"Aleksandra A Evdokimova, Tatyana D Kolesnikova, Marina Yu Mazina, Aleksey N Krasnov, Maksim Erokhin, Darya Chetverina, Nadezhda E Vorobyeva","doi":"10.1093/nar/gkaf284","DOIUrl":"https://doi.org/10.1093/nar/gkaf284","url":null,"abstract":"Transcriptional activation by 20-hydroxyecdysone (20E) in Drosophila provides an excellent model for studying tissue-specific responses to steroids. An increase in the 20E concentration regulates the degradation of larval and the proliferation of adult tissues during metamorphosis. To study 20E-dependent transcription, we used the natural system for controlling the 20E concentration—the E23 membrane transporter—which exports 20E from the cell. We artificially expressed E23 in tissues to suppress the first wave of 20E-inducible transcription at metamorphosis. E23 expression revealed a plethora of 20E-dependent genes in salivary glands, while mildly affecting transcription in brain. We described the mechanisms controlling transcriptional activation by 20E in salivary glands. 20E depletion decreased the binding of Pol II and the TFIID subunit, TBP, to the promoters of primary targets, demonstrating the role of 20E in transcription initiation. At target loci, 20E depletion resulted in the malfunctioning of sites co-bound with EcR and CBP/Nejire and enriched for the H3K27Ac mark inherent to active enhancers. At these sites, the 20E concentration was found to control chromatin accessibility and acetylation. We suggest that the activity of these ‘active’ ecdysone-sensitive elements was responsible for the active status of 20E targets in the salivary glands of wandering larvae.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"16 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143832468","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

Autophagy induction enhances homologous recombination-associated CRISPR–Cas9 gene editing

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-15 DOI: 10.1093/nar/gkaf258

Hye Jin Nam, Jun Hee Han, Jihyeon Yu, Chang Sik Cho, Dongha Kim, Young Eun Kim, Min Ji Kim, Jeong Hun Kim, Dong Hyun Jo, Sangsu Bae

{"title":"Autophagy induction enhances homologous recombination-associated CRISPR–Cas9 gene editing","authors":"Hye Jin Nam, Jun Hee Han, Jihyeon Yu, Chang Sik Cho, Dongha Kim, Young Eun Kim, Min Ji Kim, Jeong Hun Kim, Dong Hyun Jo, Sangsu Bae","doi":"10.1093/nar/gkaf258","DOIUrl":"https://doi.org/10.1093/nar/gkaf258","url":null,"abstract":"CRISPR (clustered regularly interspaced short palindromic repeats)–Cas9 (CRISPR-associated protein 9)-based gene editing via homologous recombination (HR) enables precise gene correction and insertion. However, its low efficiency poses a challenge due to the predominance of nonhomologous end-joining during DNA repair processes. Although numerous efforts have been made to boost HR efficiency, there remains a critical need to devise a novel method that can be universally applied across cell types and in vivo animals, which could ultimately facilitate therapeutic treatments. This study demonstrated that autophagy induction using different protocols, including nutrient deprivation or chemical treatment, significantly improved HR-associated gene editing at diverse genomic loci in mammalian cells. Notably, interacting cofactor proteins that bind to Cas9 under the autophagic condition have been identified, and autophagy induction could also enhance in vivo HR-associated gene editing in mice. These findings pave the way for effective gene correction or insertion for in vivo therapeutic treatments.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"16 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143832504","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

pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-14 DOI: 10.1093/nar/gkaf289

J Carlos Angel, Narjis El Amraoui, Gamze Gürsoy

{"title":"pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data","authors":"J Carlos Angel, Narjis El Amraoui, Gamze Gürsoy","doi":"10.1093/nar/gkaf289","DOIUrl":"https://doi.org/10.1093/nar/gkaf289","url":null,"abstract":"The three-dimensional (3D) organization of the genome is crucial for gene regulation, with disruptions linked to various diseases. High-throughput Chromosome Conformation Capture (Hi-C) and related technologies have advanced our understanding of 3D genome organization by mapping interactions between distal genomic regions. However, capturing enhancer–promoter interactions at high resolution remains challenging due to the high sequencing depth required. We introduce pC-SAC (probabilistically Constrained Self-Avoiding Chromatin), a novel computational method for producing accurate high-resolution Hi-C matrices from low-resolution data. pC-SAC uses adaptive importance sampling with sequential Monte Carlo to generate ensembles of 3D chromatin chains that satisfy physical constraints derived from low-resolution Hi-C data. Our method achieves over 95% accuracy in reconstructing high-resolution chromatin maps and identifies novel interactions enriched with candidate cis-regulatory elements (cCREs) and expression quantitative trait loci (eQTLs). Benchmarking against state-of-the-art deep learning models demonstrates pC-SAC’s performance in both short- and long-range interaction reconstruction. pC-SAC offers a cost-effective solution for enhancing the resolution of Hi-C data, thus enabling deeper insights into 3D genome organization and its role in gene regulation and disease. Our tool can be found at https://github.com/G2Lab/pCSAC.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"108 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143827678","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 ZBTB24-CDCA7-HELLS axis suppresses the totipotent 2C-like reprogramming by maintaining Dux methylation and repression

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-14 DOI: 10.1093/nar/gkaf302

Dan Guo, Zeling Du, Youqi Liu, Meiqi Lin, Yue Lu, Swanand Hardikar, Yanna Xue, Jinghong Zhang, Taiping Chen, Jiameng Dan

{"title":"The ZBTB24-CDCA7-HELLS axis suppresses the totipotent 2C-like reprogramming by maintaining Dux methylation and repression","authors":"Dan Guo, Zeling Du, Youqi Liu, Meiqi Lin, Yue Lu, Swanand Hardikar, Yanna Xue, Jinghong Zhang, Taiping Chen, Jiameng Dan","doi":"10.1093/nar/gkaf302","DOIUrl":"https://doi.org/10.1093/nar/gkaf302","url":null,"abstract":"Two-cell-like cells (2CLCs), a rare population (∼0.5%) in mouse embryonic stem cell (mESC) cultures, are in a transient totipotent-like state resembling that of 2C-stage embryos, and their discovery and characterization have greatly facilitated the study of early developmental events, such as zygotic genome activation. However, the molecular determinants governing 2C-like reprogramming remain to be elucidated. Here, we show that ZBTB24, CDCA7, and HELLS, components of a molecular pathway that is involved in the pathogenesis of immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, function as negative regulators of 2C-like reprogramming by maintaining DNA methylation of the Dux cluster, a master inducer of the 2C-like state. Disruption of the ZBTB24-CDCA7-HELLS axis results in Dux hypomethylation and derepression, leading to dramatic upregulation of 2C-specific genes, which can be reversed by site-specific re-methylation in the Dux promoter. We also provide evidence that CDCA7 is enriched at the Dux cluster and recruits the CDCA7–HELLS chromatin remodeling complex to constitutive heterochromatin. Our study uncovers a key role for the ZBTB24-CDCA7-HELLS axis in safeguarding the mESC state by suppressing the 2C-like reprogramming.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"66 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143827677","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

tRNA binding to Kti12 is crucial for wobble uridine modification by Elongator

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-14 DOI: 10.1093/nar/gkaf296

David Scherf, Alexander Hammermeister, Pauline Böhnert, Alicia Burkard, Mark Helm, Sebastian Glatt, Raffael Schaffrath

{"title":"tRNA binding to Kti12 is crucial for wobble uridine modification by Elongator","authors":"David Scherf, Alexander Hammermeister, Pauline Böhnert, Alicia Burkard, Mark Helm, Sebastian Glatt, Raffael Schaffrath","doi":"10.1093/nar/gkaf296","DOIUrl":"https://doi.org/10.1093/nar/gkaf296","url":null,"abstract":"In yeast, tRNA modifications that are introduced by the Elongator complex are recognized by zymocin, a fungal tRNase killer toxin that cleaves the anticodon. Based on zymocin resistance conferred by mutations in KTI12, a gene coding for an Elongator interactor, we further examined the yet vaguely defined cellular role of Kti12. Guided by structural similarities between Kti12 and PSTK, a tRNA kinase involved in selenocysteine synthesis, we identified conserved basic residues in the C-terminus of Kti12, which upon site-directed mutagenesis caused progressive loss of tRNA binding in vitro. The inability of Kti12 to bind tRNA led to similar phenotypes caused by Elongator inactivation in vivo. Consistently, tRNA binding deficient kti12 mutants drastically suppressed Elongator dependent tRNA anticodon modifications and reduced the capacity of Kti12 to interact with Elongator. We further could distinguish Elongator unbound pools of Kti12 in a tRNA dependent manner from bound ones. In summary, the C-terminal domain of Kti12 is crucial for tRNA binding and Kti12 recruitment to Elongator, which are both requirements for Elongator function suggesting Kti12 is a tRNA carrier that interacts with Elongator for modification of the tRNA anticodon.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"23 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143827676","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

Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-14 DOI: 10.1093/nar/gkaf305

Qilong Lai, Shuai Yao, Yuguo Zha, Haohong Zhang, Haobo Zhang, Ying Ye, Yonghui Zhang, Hong Bai, Kang Ning

{"title":"Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model","authors":"Qilong Lai, Shuai Yao, Yuguo Zha, Haohong Zhang, Haobo Zhang, Ying Ye, Yonghui Zhang, Hong Bai, Kang Ning","doi":"10.1093/nar/gkaf305","DOIUrl":"https://doi.org/10.1093/nar/gkaf305","url":null,"abstract":"Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC prediction and classification. Leveraging the transformer encoder, BGC-Prophet captures location-dependent relationships between genes. As one of the pioneering ultrahigh-throughput tools, BGC-Prophet significantly surpasses existing methods in efficiency and fidelity, enabling comprehensive pan-phylogenetic and whole-metagenome BGC screening. Through the analysis of 85 203 genomes and 9428 metagenomes, BGC-Prophet has profiled an extensive array of sub-million BGCs. It highlights notable enrichment in phyla like Actinomycetota and the widespread distribution of polyketide, NRP, and RiPP BGCs across diverse lineages. It reveals enrichment patterns of BGCs following important geological events, suggesting environmental influences on BGC evolution. BGC-Prophet’s capabilities in detection of BGCs and evolutionary patterns offer contributions to deeper understanding of microbial secondary metabolites and application in synthetic biology.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"1 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143827682","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

CRISPR RNA binding drives structural ordering that primes Cas7-11 for target cleavage

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-04-14 DOI: 10.1093/nar/gkaf271

Calvin P Lin, Harry Li, Daniel J Brogan, Tianqi Wang, Omar S Akbari, Elizabeth A Komives

{"title":"CRISPR RNA binding drives structural ordering that primes Cas7-11 for target cleavage","authors":"Calvin P Lin, Harry Li, Daniel J Brogan, Tianqi Wang, Omar S Akbari, Elizabeth A Komives","doi":"10.1093/nar/gkaf271","DOIUrl":"https://doi.org/10.1093/nar/gkaf271","url":null,"abstract":"Type III-E CRISPR–Cas effectors, referred to as Cas7-11 or giant Repeat-Associated Mysterious Protein, are single proteins that cleave target RNAs (tgRNAs) without nonspecific collateral cleavage, opening new possibilities for RNA editing. Here, biochemical assays combined with amide hydrogen–deuterium exchange mass spectrometry (HDX–MS) experiments reveal the dynamics of apo Cas7-11. The HDX–MS results suggest a mechanism by which CRISPR RNA (crRNA) stabilizes the folded state of the protein and subsequent tgRNA binding remodels it to the active form. HDX–MS shows that the four Cas7 RNA recognition motif (RRM) folds are well-folded, but insertion sequences, including disordered catalytic loops and β-hairpins of the Cas7.2/Cas7.3 active sites, fold upon binding crRNA leading to stronger interactions at domain–domain interfaces, and folding of the Cas7.1 processing site. TgRNA binding causes conformational changes around the catalytic loops of Cas7.2 and Cas7.3. We show that Cas7-11 cannot independently process the CRISPR array and that binding of partially processed crRNA induces multiple states in Cas7-11 and reduces tgRNA cleavage. The insertion domain interacts most stably with mature crRNA. Finally, we show a crRNA-induced conformational change in one of the tetratricopeptide repeat fused with Cas/HEF1-associated signal transducer (TPR-CHAT) binding sites providing an explanation for why crRNA binding facilitates TPR-CHAT binding.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"183 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143827679","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