Nucleic Acids Research最新文献_第7页

R2DT: a comprehensive platform for visualizing RNA secondary structure.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-02-08 DOI: 10.1093/nar/gkaf032

Holly McCann, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Philip Z Johnson, Anne E Simon, David Hoksza, Eric P Nawrocki, Patricia P Chan, Todd M Lowe, Carlos Eduardo Ribas, Blake A Sweeney, Fábio Madeira, Stephen Anyango, Sri Devan Appasamy, Mandar Deshpande, Mihaly Varadi, Sameer Velankar, Craig L Zirbel, Aleksei Naiden, Fabrice Jossinet, Anton I Petrov

{"title":"R2DT: a comprehensive platform for visualizing RNA secondary structure.","authors":"Holly McCann, Caeden D Meade, Loren Dean Williams, Anton S Petrov, Philip Z Johnson, Anne E Simon, David Hoksza, Eric P Nawrocki, Patricia P Chan, Todd M Lowe, Carlos Eduardo Ribas, Blake A Sweeney, Fábio Madeira, Stephen Anyango, Sri Devan Appasamy, Mandar Deshpande, Mihaly Varadi, Sameer Velankar, Craig L Zirbel, Aleksei Naiden, Fabrice Jossinet, Anton I Petrov","doi":"10.1093/nar/gkaf032","DOIUrl":"https://doi.org/10.1093/nar/gkaf032","url":null,"abstract":"<p><p>RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.</p>","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 4","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459072","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

zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-05 DOI: 10.1093/nar/gkaf045

Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore, Ashlee M Earl, Karthik Anantharaman, Lindsay R Kalan

{"title":"zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters","authors":"Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore, Ashlee M Earl, Karthik Anantharaman, Lindsay R Kalan","doi":"10.1093/nar/gkaf045","DOIUrl":"https://doi.org/10.1093/nar/gkaf045","url":null,"abstract":"Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements, such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to handle thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) performing population genetic investigations of BGCs for a fungal species, and (iii) uncovering evolutionary trends for a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"27 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143125164","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

Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-03 DOI: 10.1093/nar/gkaf059

Zhikang Dai, Yu Chen, Zeyuan Guan, Xueting Chen, Keyi Tan, Kaiyue Yang, Xuhui Yan, Yidong Liu, Zhou Gong, Wenyuan Han, Tingting Zou

{"title":"Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus","authors":"Zhikang Dai, Yu Chen, Zeyuan Guan, Xueting Chen, Keyi Tan, Kaiyue Yang, Xuhui Yan, Yidong Liu, Zhou Gong, Wenyuan Han, Tingting Zou","doi":"10.1093/nar/gkaf059","DOIUrl":"https://doi.org/10.1093/nar/gkaf059","url":null,"abstract":"Prokaryotic Argonaute proteins (pAgos) defend the host against invading nucleic acids, including plasmids and viruses. Short pAgo systems confer immunity by inducing cell death upon detecting invading nucleic acids. However, the activation mechanism of the SiAgo system, comprising a short pAgo from the archaeon Sulfolobus islandicus and its associated proteins SiAga1 and SiAga2, remains largely unknown. Here, we determined the cryo-electron microscopy structures of the SiAgo–Aga1 apo complex and the RNA–DNA-bound SiAgo–Aga1 complex at resolutions of 2.7 and 3.0 Å, respectively. Our results revealed that a positively charged pocket is generated from the interaction between SiAgo and SiAga1, exhibiting an architecture similar to APAZ-pAgo of short pAgo systems and accommodating the nucleic acids. Further investigation elucidated the conserved mechanism of nucleic acid recognition by SiAgo–Aga1. Both the SiAgo–Aga1 interaction and nucleic acid recognition by the complex are essential for antiviral defense. Biochemical and structural analyses demonstrated that SiAgo–Aga1 undergoes extensive conformational changes upon binding to the RNA–DNA duplex, thereby licensing its interaction with the effector SiAga2 to trigger the immune response. Overall, our findings highlight the evolutionary conservation of Agos across phylogenetic clades and provide structural insights into the activation mechanism of the SiAgo system.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"39 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077633","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 short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-03 DOI: 10.1093/nar/gkaf053

Amitabh Ranjan, Sandy Mattijssen, Nithin Charlly, Isabel Cruz Gallardo, Leah F Pitman, Jennifer C Coleman, Maria R Conte, Richard J Maraia

{"title":"The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation","authors":"Amitabh Ranjan, Sandy Mattijssen, Nithin Charlly, Isabel Cruz Gallardo, Leah F Pitman, Jennifer C Coleman, Maria R Conte, Richard J Maraia","doi":"10.1093/nar/gkaf053","DOIUrl":"https://doi.org/10.1093/nar/gkaf053","url":null,"abstract":"LARP4 interacts with poly(A)-binding protein (PABP) to protect messenger RNAs (mRNAs) from deadenylation and decay, and recent data indicate it can direct the translation of functionally related mRNA subsets. LARP4 was known to bind RACK1, a ribosome-associated protein, although the specific regions involved and relevance had been undetermined. Here, through a combination of in-cell and in vitro methodologies, we identified positions 615–625 in conserved region-2 (CR2) of LARP4 (and 646–656 in LARP4B) as directly binding RACK1. Consistent with these results, AlphaFold2-Multimer predicted high-confidence interaction of CR2 with RACK1 propellers 5 and 6. CR2 mutations strongly decreased LARP4 association with cellular RACK1 and ribosomes by multiple assays, whereas PABP association was less affected, consistent with independent interactions. The CR2 mutations decreased LARP4’s ability to stabilize a β-globin mRNA reporter containing an AU-rich element (ARE) to higher degree than β-globin and GFP (green fluorescent protein) mRNAs lacking the ARE. We show LARP4 robustly increases translation of β-glo-ARE mRNA, whereas the LARP4 CR2 mutant is impaired. Analysis of nanoLuc-ARE mRNA for production of luciferase activity confirmed LARP4 promotes translation efficiency, while CR2 mutations are disabling. Thus, LARP4 CR2-mediated interaction with RACK1 can promote translational efficiency of some mRNAs.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"38 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077630","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 membrane-targeting-sequence motif is required for exhibition of recessive resurrection in Escherichia coli RNase E

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-03 DOI: 10.1093/nar/gkaf055

Papri Basak, Manjula Ekka, Apuratha Pandiyan, Smriti Tandon, Jayaraman Gowrishankar

{"title":"The membrane-targeting-sequence motif is required for exhibition of recessive resurrection in Escherichia coli RNase E","authors":"Papri Basak, Manjula Ekka, Apuratha Pandiyan, Smriti Tandon, Jayaraman Gowrishankar","doi":"10.1093/nar/gkaf055","DOIUrl":"https://doi.org/10.1093/nar/gkaf055","url":null,"abstract":"The essential homotetrameric endoribonuclease RNase E of Escherichia coli participates in global RNA turnover as well as stable RNA maturation. The protomer’s N-terminal half (residues 1–529) bears the catalytic, allosteric, and tetramerization domains, including the active site residues D303 and D346. The C-terminal half (CTH, residues 530–1061) is dispensable for viability. We have previously described a phenomenon of recessive resurrection in RNase E that requires the CTH, wherein the wild-type homotetramer apparently displays nearly identical activity in vivo as a heterotetramer comprising three catalytically dead subunits (with D303A or D346A substitutions) and one wild-type subunit. Here, we show that recessive resurrection is exhibited even in dimeric RNase E with the CTH, and that it is largely dependent on the presence of a membrane-targeting-sequence motif (residues 565–582). A single F575E substitution also impaired recessive resurrection, whereas other CTH motifs (such as those for binding of RNA or of partner proteins) were dispensable. The phenomenon was independent of RNA 5′-monophosphate sensing by the enzyme. We propose that membrane-anchoring of RNase E renders it processive for endoribonucleolytic action, and that recessive resurrection and dominant negativity associated with mutant protomers are mutually exclusive manifestations of, respectively, processive and distributive catalytic mechanisms in a homo-oligomeric enzyme.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"166 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077631","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

Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-03 DOI: 10.1093/nar/gkaf052

Jie Liu, Steven K Gore, Wolf-Dietrich Heyer

{"title":"Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments","authors":"Jie Liu, Steven K Gore, Wolf-Dietrich Heyer","doi":"10.1093/nar/gkaf052","DOIUrl":"https://doi.org/10.1093/nar/gkaf052","url":null,"abstract":"Homologous recombination (HR) is a high-fidelity repair mechanism for double-strand breaks. Rad51 is the key enzyme that forms filaments on single-stranded DNA (ssDNA) to catalyze homology search and DNA strand exchange in recombinational DNA repair. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) to ascertain the density map of the wild-type budding yeast Rad51-ssDNA filament bound to ADP-AlF3, achieving a resolution of 2.35 Å without imposing helical symmetry. The model assigned 6 Rad51 protomers, 24 nt of DNA, and 6 bound ADP-AlF3. It shows 6-fold symmetry implying monomeric building blocks, unlike the structure of the Rad51-I345T mutant filament with three-fold symmetry implying dimeric building blocks, for which the structural comparisons provide a satisfying mechanistic explanation. This image analysis enables comprehensive comparisons of individual Rad51 protomers within the filament and reveals local conformational movements of amino acid side chains. Notably, R293 in Loop 1 adopts multiple conformations to facilitate L296 and V331 in separating and twisting the DNA triplets. We also analyzed the crystal structure of Rad51-I345T and the predicted structure of yeast Rad51–K342E using the Rad51–ssDNA structure from this study as a reference.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"207 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077629","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

mRNA-LM: full-length integrated SLM for mRNA analysis

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-03 DOI: 10.1093/nar/gkaf044

Sizhen Li, Shahriar Noroozizadeh, Saeed Moayedpour, Lorenzo Kogler-Anele, Zexin Xue, Dinghai Zheng, Fernando Ulloa Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager

{"title":"mRNA-LM: full-length integrated SLM for mRNA analysis","authors":"Sizhen Li, Shahriar Noroozizadeh, Saeed Moayedpour, Lorenzo Kogler-Anele, Zexin Xue, Dinghai Zheng, Fernando Ulloa Montoya, Vikram Agarwal, Ziv Bar-Joseph, Sven Jager","doi":"10.1093/nar/gkaf044","DOIUrl":"https://doi.org/10.1093/nar/gkaf044","url":null,"abstract":"The success of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) messenger RNA (mRNA) vaccine has led to increased interest in the design and use of mRNA for vaccines and therapeutics. Still, selecting the most appropriate mRNA sequence for a protein remains a challenge. Several recent studies have shown that the specific mRNA sequence can have a significant impact on the translation efficiency, half-life, degradation rates, and other issues that play a major role in determining vaccine efficiency. To enable the selection of the most appropriate sequence, we developed mRNA-LM, an integrated small language model for modeling the entire mRNA sequence. mRNA-LM uses the contrastive language–image pretraining integration technology to combine three separate language models for the different mRNA segments. We trained mRNA-LM on millions of diverse mRNA sequences from several different species. The unsupervised model was able to learn meaningful biology related to evolution and host–pathogen interactions. Fine-tuning of mRNA-LM allowed us to use it in several mRNA property prediction tasks. As we show, using the full-length integrated model led to accurate predictions, improving on prior methods proposed for this task.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"4 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077632","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

Direct repeat region 3′ end modifications regulate Cas12a activity and expand its applications

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-30 DOI: 10.1093/nar/gkaf040

Wei Zhang, Yinyin Zhong, Jiaqi Wang, Guangrong Zou, Qiaozhen Chen, Chaoxing Liu

{"title":"Direct repeat region 3′ end modifications regulate Cas12a activity and expand its applications","authors":"Wei Zhang, Yinyin Zhong, Jiaqi Wang, Guangrong Zou, Qiaozhen Chen, Chaoxing Liu","doi":"10.1093/nar/gkaf040","DOIUrl":"https://doi.org/10.1093/nar/gkaf040","url":null,"abstract":"CRISPR-Cas12a technology has transformative potential, but as its applications grow, enhancing its inherent functionalities is essential to meet diverse demands. Here, we reveal a regulatory mechanism for LbCas12a through direct repeat (DR) region 3′ end modifications and de-modifications, which can regulate LbCas12a’s cis- and trans-cleavage activities. We extensively explored the effects of introducing phosphorylation, DNA, photo-cleavable linker, DNA modifications at the DR 3′ end on LbCas12a’s functionality. We find that the temporary inhibitory function of Cas12a can be reactivated by DR 3′ end modification corresponding substances, such as alkaline phosphatase (ALP), immunoglobulin G (IgG), alpha-fetoprotein (AFP), DNA exonucleases, ultraviolet radiation, and DNA glycosylases, which greatly expand the scope of application of Cas12a. Clinical applications demonstrated promising results in ALP, AFP, and trace Epstein–Barr virus detection compared to gold standard methods. Our research provides valuable insights into regulating LbCas12a activity through direct modification of DR and significantly expands its potential clinical detection targets, paving the way for future universal clustered regularly interspaced short palindromic repeats (CRISPR) diagnostic strategies.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"36 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056333","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

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-30 DOI: 10.1093/nar/gkaf033

Rahul Jaiswal, Brandon Braud, Karen C Hernandez-Ramirez, Vishaka Santosh, Alexander Washington, Carlos R Escalante

{"title":"Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting","authors":"Rahul Jaiswal, Brandon Braud, Karen C Hernandez-Ramirez, Vishaka Santosh, Alexander Washington, Carlos R Escalante","doi":"10.1093/nar/gkaf033","DOIUrl":"https://doi.org/10.1093/nar/gkaf033","url":null,"abstract":"The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"124 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056334","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

A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-30 DOI: 10.1093/nar/gkaf030

James C Taggart, Kathryn Julia Dierksheide, Hannah J LeBlanc, Jean-Benoît Lalanne, Sylvain Durand, Frédérique Braun, Ciarán Condon, Gene-Wei Li

{"title":"A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis","authors":"James C Taggart, Kathryn Julia Dierksheide, Hannah J LeBlanc, Jean-Benoît Lalanne, Sylvain Durand, Frédérique Braun, Ciarán Condon, Gene-Wei Li","doi":"10.1093/nar/gkaf030","DOIUrl":"https://doi.org/10.1093/nar/gkaf030","url":null,"abstract":"RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches—transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites—that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5′- and 3′-exonuclease-deficient cells revealed &gt;103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"54 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056335","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