IF 4.2 3区生物学

RNA Pub Date : 2025-06-06 DOI: 10.1261/rna.080600.125

Qiupei Du, Anna Cherian, Raymond J Louie, Giulia Barcia, Natasha Rudy, Rima Nabbout, Eugenie Sarda, Maelle Charpie, Wesley G Patterson, Liam Peter Keegan, Mary A O'Connell

{"title":"Novel ADAR2 variants in children with seizures, intellectual disability and motor delay have reduced RNA editing.","authors":"Qiupei Du, Anna Cherian, Raymond J Louie, Giulia Barcia, Natasha Rudy, Rima Nabbout, Eugenie Sarda, Maelle Charpie, Wesley G Patterson, Liam Peter Keegan, Mary A O'Connell","doi":"10.1261/rna.080600.125","DOIUrl":"https://doi.org/10.1261/rna.080600.125","url":null,"abstract":"The ADARB1 gene encodes the ADAR2 RNA editing enzyme, which edits the GRIA2 transcript Q/R editing site with almost 100% efficiency in the nervous system. The edited GRIA2R transcript encodes the GLUA2 R subunit isoform of tetrameric AMPA receptors, which is essential to prevent seizures associated with aberrantly elevated AMPA receptor cation permeability. Rare biallelic variants in ADARB1 cause severe infant and childhood seizures and developmental delays in seven cases we previously described. Here, we report two new homozygous ADARB1 variants and study ADAR2 variant editing activities at the GRIA2 Q/R site and other editing sites in cell cultures. One new variant in the second dsRNA binding domain (dsRBD II) retains up to 60% editing activity, whereas another, in the deaminase domain, eliminates RNA editing activity. Reduced GRIA2 Q/R site editing increases AMPA receptor permeability by upregulating the expression of the GLUA2 Q isoform and reducing overall GLUA2 subunit levels, resulting in AMPA receptors that lack GLUA2 and are calcium-permeable. Since failure to edit the GRIA2 Q/R site leads to failure of intron 11 splicing, we also examined the effects of ADAR2 variants on the splicing of a mouse Gria2-based reporter and concluded that ADAR2 variants affect splicing only through their effects on RNA editing activity. To expand the number of variants in ADARB1, some variants reported in ClinVar have also been analysed by in silico methods to predict which are likely to be most deleterious and associated with seizures in patients.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Rho-dependent transcription termination: mechanisms and roles in bacterial fitness and adaptation to environmental changes. rho依赖性转录终止：细菌适应度和适应环境变化的机制和作用。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-03 DOI: 10.1261/rna.080486.125

Thuy Duong Do, Nara Figueroa-Bossi, Johnathan C Black, Eric Eveno, Mildred Delaleau, Lionello Bossi, Marc Boudvillain

{"title":"Rho-dependent transcription termination: mechanisms and roles in bacterial fitness and adaptation to environmental changes.","authors":"Thuy Duong Do, Nara Figueroa-Bossi, Johnathan C Black, Eric Eveno, Mildred Delaleau, Lionello Bossi, Marc Boudvillain","doi":"10.1261/rna.080486.125","DOIUrl":"https://doi.org/10.1261/rna.080486.125","url":null,"abstract":"The bacterial transcription termination factor Rho is a rare example of an RNA helicase that functions as a ring-shaped ATP-powered six-subunit motor. Recent studies have linked Rho's distinctive architecture to a variety of regulatory mechanisms that shape the bacterial transcriptome at the global scale and control the transcription of individual genes in a context-dependent manner. In this review, we provide a comprehensive overview of the molecular mechanisms by which Rho triggers transcription termination. We examine the two prevailing modes of Rho's action: the \"catch-up\" mode, where Rho actively translocates along RNA and collides with the RNA polymerase to terminate transcription, and the \"stand-by\" mode where Rho, recruited by transcription elongation factor NusG, remains poised to engage RNA polymerase at specific sites or under particular constraints. Additionally, we highlight Rho's interplay with nucleoid-structuring protein H-NS in the regulation of bacterial chromatin transcription, as well as the crucial role played by Rho in the conditional regulation of specific genomic loci. We discuss how these mechanisms contribute to the fine-tuning of gene activity and integrate into broader regulatory networks, supporting bacterial adaptation to environmental changes and resilience to external challenges.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Constructing an active chimeric pRNA ring with a stoichiometry of six and identifying 12 domains of the pRNA ring binding to the 12-subunit channel of phi29 DNA-packaging motor. 构建了一个化学计量为6的活性嵌合pRNA环，并鉴定了与phi29 DNA包装马达的12个亚基通道结合的12个pRNA环结构域。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080383.125

Margaret Bohmer, Daniel W Binzel, Wen Zhang, Peixuan Guo

{"title":"Constructing an active chimeric pRNA ring with a stoichiometry of six and identifying 12 domains of the pRNA ring binding to the 12-subunit channel of phi29 DNA-packaging motor.","authors":"Margaret Bohmer, Daniel W Binzel, Wen Zhang, Peixuan Guo","doi":"10.1261/rna.080383.125","DOIUrl":"10.1261/rna.080383.125","url":null,"abstract":"During the last stage of replication of double-stranded RNA or DNA viruses, their genome is packaged into a preassembled protein capsid. The bacterial virus phi29 dsDNA-packaging motor uses a noncoding packaging RNA (pRNA) molecule to gear its genomic DNA translocation. In this study, we constructed chimeric pRNAs by fusing the pRNA of bacterial virus M2 and that of phi29. The chimeric pRNAs can form dimers or trimers. The dimeric or trimeric pRNAs were active in the packaging of the phi29 dsDNA genome into the purified procapsid, which was subsequently converted into the infectious viruses, as proven by counting plaque-forming units (PFUs). These data show that the stoichiometry of the chimeric pRNAs on the motor is six subunits, a multiple of 2 and 3. Furthermore, AFM studies on pRNA fused to an RNA-triangle revealed hexamer formation. But how do the six identical RNAs anchor on the 12-subunit connector with the double stoichiometry? Structural analysis in combination with enzymatic and chemical probing data revealed that each native pRNA contributes two domains to bind to the 12-subunit DNA-packaging channel at three positively charged residues RKR, proving the formation of the hexameric ring. Resolving the hexamer versus pentamer debate clarifies the mechanism of dsDNA translocation in living organisms.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"836-849"},"PeriodicalIF":4.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 pseudouridine synthase D (TruD) from Thermus thermophilus modifies U13 in tRNA^Asp, tRNA^Glu, and tRNA^Gln and U35 in tRNA^Tyr. 来自嗜热热菌的tRNA假尿嘧啶合成酶D （TruD）修饰tRNA Asp中的U13， tRNA Glu中的U13， tRNA Tyr中的tRNA Gln和U35。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080405.125

Ryota Yamagami, Kojiro Takahashi, Shogo Shingu, Miyu Namba, Kohsuke Kamizaki, Hiroyuki Hori

{"title":"tRNA pseudouridine synthase D (TruD) from Thermus thermophilus modifies U13 in tRNAAsp, tRNAGlu, and tRNAGln and U35 in tRNATyr.","authors":"Ryota Yamagami, Kojiro Takahashi, Shogo Shingu, Miyu Namba, Kohsuke Kamizaki, Hiroyuki Hori","doi":"10.1261/rna.080405.125","DOIUrl":"10.1261/rna.080405.125","url":null,"abstract":"Pseudouridine is a modified nucleoside found in various RNA species, including tRNA, rRNA, mRNA, and other noncoding RNAs. Pseudouridine is synthesized from uridine by pseudouridine synthases. While the landscape of pseudouridines in RNA has been extensively studied, much less is known about substrate RNA recognition mechanisms of pseudouridine synthases. Herein, we investigate the tRNA pseudouridine synthase D (TruD), which catalyzes the formation of pseudouridine at position 13 in tRNAAsp in Thermus thermophilus, a thermophilic eubacterium. To identify the tRNA substrates of TruD, we compared results of next-generation sequencing experiments combined with bisulfite probing of pseudouridine in tRNAs from both wild-type and a truD gene disruption mutant. Our data reveal that TruD recognizes tRNAAsp, tRNAGlu, and tRNAGln as substrate tRNAs. In addition, we discover that TruD modifies U35 in tRNATyr, which has previously been reported as a substrate of RluF in Escherichia coli These findings were validated through in vitro assays with recombinant TruD, which further demonstrated that TruD can act on other RNAs, including a CDC8 mRNA fragment, a known substrate of Pus7, the eukaryotic counterpart of TruD. Systematic mutational analysis of CDC8 transcripts reveals that TruD preferentially pseudouridylates the UNUAR sequence in tRNA substrates (N = any nucleotide, R = purine, U = target site). Finally, we identify over 600 mRNA fragments containing this recognition sequence in T. thermophilus ORFs and demonstrate the ability of TruD to act on these potential mRNA substrates. Our findings suggest the possibility that many other RNAs are modified by TruD in vivo.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"850-867"},"PeriodicalIF":4.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143731506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Dissecting the stress granule RNA world: dynamics, strategies, and data. 剖析应激颗粒RNA世界：动力学、策略和数据。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080409.125

Giulia Biancon, Emma Busarello, Matthew Cheng, Stephanie Halene, Toma Tebaldi

引用次数: 0

Deciphering the influence of the [4Fe-4S] cluster of tRNA thiolation enzymes on tRNA binding. 解读tRNA巯基化酶[Fe-S]簇对tRNA结合的影响。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080292.124

Sylvain Gervason, Sambuddha Sen, Jean-Luc Ravanat, Sylvain Caillat, Djemel Hamdane, Béatrice Golinelli-Pimpaneau

{"title":"Deciphering the influence of the [4Fe-4S] cluster of tRNA thiolation enzymes on tRNA binding.","authors":"Sylvain Gervason, Sambuddha Sen, Jean-Luc Ravanat, Sylvain Caillat, Djemel Hamdane, Béatrice Golinelli-Pimpaneau","doi":"10.1261/rna.080292.124","DOIUrl":"10.1261/rna.080292.124","url":null,"abstract":"Iron-sulfur clusters [Fe-S] play crucial roles in diverse biological reactions, often serving as prosthetic groups for enzymes. Specifically, certain tRNA-modifying enzymes utilize these clusters to catalyze the thiolation of specific nucleosides. While the participation of [4Fe-4S] clusters in such catalytic processes is known, their potential influence on tRNA binding remains unexplored. In this study, we examine the impact of the cluster on the affinity for tRNA of TtuI from the archeon Methanococcus maripaludis, an enzyme responsible for the formation of 4-thiouridine at position 8 in tRNAs of archaea and bacteria, as well as Escherichia coli TtcA that catalyzes the biosynthesis of 2-thiocytidine at position 32 in bacterial tRNAs. For this purpose, we compare the change of fluorescence properties of judiciously located tryptophans upon tRNA binding between the apo-enzyme (lacking the cluster) and the holo-enzyme (incorporating a reconstituted cluster). Our results indicate that the presence of the [4Fe-4S] cluster does not alter the affinity of the thiolases for tRNA, thus ruling out any direct involvement of the cluster in tRNA binding and emphasizing the purely catalytic role of the [4Fe-4S] cluster in tRNA thiolation.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"735-742"},"PeriodicalIF":4.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

RNA-binding protein Miso/CG44249 is crucial for minor splicing during oogenesis in Drosophila. rna结合蛋白Miso/CG44249对果蝇卵发生过程中的微小剪接至关重要。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080311.124

Yuki Taira, Li Zhu, Ryuya Fukunaga

{"title":"RNA-binding protein Miso/CG44249 is crucial for minor splicing during oogenesis in Drosophila.","authors":"Yuki Taira, Li Zhu, Ryuya Fukunaga","doi":"10.1261/rna.080311.124","DOIUrl":"10.1261/rna.080311.124","url":null,"abstract":"Pre-mRNA introns are removed by two distinct spliceosomes: the major (U2-type) spliceosome, which splices over 99.5% of introns, and the minor (U12-type) spliceosome, responsible for a rare class of introns known as minor introns. While the major spliceosome contains U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs) along with numerous associated proteins, the minor spliceosome comprises U11, U12, U4atac, U5, and U6atac snRNAs and includes specialized proteins. The function and regulation of the minor spliceosome are critical. Mutations in its specific component, RNA-binding protein RNPC3/65K, are linked to human diseases such as primary ovarian insufficiency. In this study, we identify RNA-binding protein Miso (CG44249), which shares 31% and 27% amino acid sequence identity with human RNPC3 and RBM41, respectively, as a key factor in minor splicing and oogenesis in Drosophila Miso associates with U11 and U12 snRNAs in ovaries. miso mutant females exhibit smaller ovaries, reduced germline stem cell numbers, disrupted oogenesis, reduced fecundity, and lower fertility. In miso mutant ovaries, significant minor intron retention is observed, accompanied by a reduction in spliced RNAs and protein products. Our findings establish Miso as a critical factor for minor intron splicing and underscore its essential role in Drosophila oogenesis.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"822-835"},"PeriodicalIF":4.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering. 已发表的兔核糖体rRNAs的不一致性：序列和位点编号一致性的建议。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080294.124

Swastik De, Michelle Zhou, Zuben P Brown, Raymond N Burton-Smith, Yaser Hashem, Tatyana V Pestova, Christopher U T Hellen, Joachim Frank

引用次数: 0

Natural human tRNA^Ala anticodon variants mistranslate the genetic code. 天然人类tRNAAla反密码子变体错误翻译遗传密码。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080450.125

Rasangi Tennakoon, Teija M I Bily, Farah Hasan, Kyle S Hoffman, Patrick O'Donoghue

{"title":"Natural human tRNAAla anticodon variants mistranslate the genetic code.","authors":"Rasangi Tennakoon, Teija M I Bily, Farah Hasan, Kyle S Hoffman, Patrick O'Donoghue","doi":"10.1261/rna.080450.125","DOIUrl":"10.1261/rna.080450.125","url":null,"abstract":"Transfer RNAs (tRNAs) play an essential role in protein synthesis by linking the nucleic acid sequences of gene products to the amino acid sequences of proteins. There are >400 functional tRNA genes in humans, and adding to this diversity, there are many single-nucleotide polymorphisms in tRNAs across our population, including anticodon variants that mistranslate the genetic code. In human genomes, we identified three rare alanine tRNA (tRNAAla) variants with nonsynonymous anticodon mutations: tRNAAla CGC G35T, tRNAAla UGC G35A, and tRNAAla AGC C36T. Since alanyl-tRNA synthetase (AlaRS) does not recognize the anticodon, we hypothesized that these tRNAAla variants will misincorporate Ala at glutamate (Glu), valine (Val), and threonine (Thr) codons, respectively. We found that expressing the naturally occurring tRNAAla variants in human cells led to defects in protein production without a substantial impact on cell growth. Using mass spectrometry, we confirmed and estimated Ala misincorporation levels at Glu (0.7%), Val (5%), and Thr (0.1%) codons. Although Ala misincorporation was higher at Val codons, cells misincorporating Ala at Glu codons had the most severe defect in protein production. The data demonstrate the ability of natural human tRNAAla variants to generate mistranslation, leading to defects in protein production that depend on the nature of the amino acid replacement.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"791-806"},"PeriodicalIF":4.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Corrigendum: An incredible life in science: Joseph G. Gall (1928-2024). 勘误：不可思议的科学生活：约瑟夫·g·加尔（1928-2024）。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080473.125

Svetlana Deryusheva, Ji-Long Liu, Zehra F Nizami, Gaëlle J S Talross, Susan A Gerbi

引用次数: 0

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