RNAPub Date : 2025-04-01DOI: 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":"https://doi.org/10.1261/rna.080383.125","url":null,"abstract":"<p><p>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 (PFU). These data show that the stoichiometry of the chimeric pRNAs on the motor is a multiple of 2 and 3, which is 6. Furthermore, AFM studies on pRNA fused to an RNA-triangle revealed hexamer formation. But how do the six identical RNA 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 2 domains to bind to the 12-subunit DNA-packaging channel at 3 positively changed residues RKR, proving the formation of the hexameric ring. Resolving the hexamer versus pentamer debate will clarify the mechanism of dsDNA translocation in living organisms.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
RNAPub Date : 2025-04-01DOI: 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":"https://doi.org/10.1261/rna.080311.124","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A dual-effect of FUBP1 on the SPA lncRNA maturation.","authors":"Zheng-Hu Yang, Fang Nan, Guang Xu, Huang Wu, Meng-Yuan Wei, Li Yang, Ling-Ling Chen, Hao Wu","doi":"10.1261/rna.080341.124","DOIUrl":"https://doi.org/10.1261/rna.080341.124","url":null,"abstract":"<p><p>SPAs are noncanonical long noncoding RNAs (lncRNAs) that are 5' small nucleolar RNA (snoRNA) capped and 3' polyadenylated. Two SPAs are processed from a polycistronic transcript embedded in the human 15q11-13 region related to Prader-Willi Syndrome (PWS). Once produced, SPAs accumulate at their transcription site and sequester splicing factors to form PWS-related nuclear bodies that are involved in alternative splicing regulation. But how the processing of SPAs is regulated has remained obscure. Here, we identified both Far upstream element-binding protein 1 (FUBP1) and Myelin expression factor 2 (MYEF2) enriched in the PWS-related nuclear bodies, loss of both, individually, impaired SPAs expression and dampened the size of PWS-related nuclear bodies in H9 and PA1 cells. Specifically, FUBP1 on the one hand enhances SPAs transcription by targeting the FUSE-like sequence upstream of the polycistronic transcript promoter, and on the other hand, is required for SPA1 splicing and maturation by binding the uridine (U)-rich intronic sequences. These findings suggest a comprehensive and distinct regulation of PWS region-derived SPA lncRNAs.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143731445","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}
{"title":"tRNA pseudouridine synthase D (TruD) from <i>Thermus thermophilus</i> modifies U13 in tRNA <sup>Asp</sup>, tRNA <sup>Glu</sup>, and tRNA <sup>Gln</sup> and U35 in tRNA <sup>Tyr</sup>.","authors":"Ryota Yamagami, Kojiro Takahashi, Shogo Shingu, Miyu Namba, Kohsuke Kamizaki, Hiroyuki Hori","doi":"10.1261/rna.080405.125","DOIUrl":"https://doi.org/10.1261/rna.080405.125","url":null,"abstract":"<p><p>Pseudouridine is a modified nucleoside found in various RNA species including tRNA, rRNA, mRNA, and other non-coding 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 tRNA<sup>Asp</sup> in <i>Thermus thermophilus</i>, 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 tRNA<sup>Asp</sup>, tRNA<sup>Glu</sup>, and tRNA<sup>Gln</sup> as substrate tRNAs. In addition, we discover that TruD modifies U35 in tRNA<sup>Tyr</sup>, which has previously been reported as a substrate of RluF in <i>Escherichia coli</i> 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 reveal that TruD preferentially pseudouridylates the UN<b>U</b>AR sequence in tRNA substrates (N = any nucleotide, R = purine; <b>U</b> = target site). Finally, we identify over 600 mRNA fragments containing this recognition sequence in <i>T. thermophilus</i> 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.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
RNAPub Date : 2025-03-25DOI: 10.1261/rna.080426.125
Gabrielle M Schuh, Katharine R Maschhoff, Annastasia Minor, Wenqian Hu
{"title":"Repression of AGO1 by AGO2 via let-7 microRNAs facilitates embryonic stem cell differentiation.","authors":"Gabrielle M Schuh, Katharine R Maschhoff, Annastasia Minor, Wenqian Hu","doi":"10.1261/rna.080426.125","DOIUrl":"https://doi.org/10.1261/rna.080426.125","url":null,"abstract":"<p><p>Argonaute (AGO) proteins are critical regulators of gene expression. Of the four AGOs in mammals, AGO1 and AGO2 are expressed in mouse embryonic stem cells (mESCs). These two proteins have opposing functions in controlling mESCs' fate decisions between pluripotency and differentiation. AGO2 promotes differentiation predominantly via the let-7 microRNAs, whereas AGO1 maintains pluripotency via modulating protein folding independent of small RNAs. These recent findings raise the question of whether and how these two AGOs are mutually regulated in mESCs. Here, using loss-of-function and gain-of-function approaches, we show that AGO2 represses the expression of AGO1 mRNA via a conserved let-7-microRNA-binding site in its 3'UTR. Mutating this binding site at the endogenous locus abolishes the AGO2-mediated repression of AGO1 mRNA and compromises the exit pluripotency of mESCs. These results indicate that the post-transcriptional regulation of AGO1 by AGO2 and let-7 microRNAs is important for stem cell differentiation, but also reveal a regulatory mechanism between the two AGO paralogs with opposing functions in controlling stem cell fate decisions.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710643","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}
RNAPub Date : 2025-03-21DOI: 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":"https://doi.org/10.1261/rna.080450.125","url":null,"abstract":"<p><p>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 non-synonymous anticodon mutations: tRNAAlaCGC G35T, tRNAAlaUGC G35A, and tRNAAlaAGC C36T. Since alanyl-tRNA synthetase (AlaRS) does not recognize the anticodon, we hypothesized that these tRNAAla variants will mis-incorporate 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 mis-incorporation levels at Glu (0.7%), Val (5%) and Thr (0.1%) codons. Although Ala mis-incorporation was higher at Val codons, cells mis-incorporating 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.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Deciphering the influence of the [Fe-S] cluster of tRNA thiolation enzymes on tRNA binding.","authors":"Sylvain Gervason, Sambuddha Sen, Sylvain Caillat, Jean-Luc Ravanat, Djemel Hamdane, Beatrice Golinelli-Pimpaneau","doi":"10.1261/rna.080292.124","DOIUrl":"https://doi.org/10.1261/rna.080292.124","url":null,"abstract":"<p><p>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 archer 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.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
RNAPub Date : 2025-03-18DOI: 10.1261/rna.080347.124
Jörg Vogel, Franziska Faber, Lars Barquist, Anke Sparmann, Linda Popella, Chandradhish Ghosh
{"title":"ASOBIOTICS 2024: an interdisciplinary symposium on antisense-based programmable RNA antibiotics.","authors":"Jörg Vogel, Franziska Faber, Lars Barquist, Anke Sparmann, Linda Popella, Chandradhish Ghosh","doi":"10.1261/rna.080347.124","DOIUrl":"10.1261/rna.080347.124","url":null,"abstract":"<p><p>The international symposium ASOBIOTICS 2024 brought together scientists across disciplines to discuss the challenges of advancing antibacterial antisense oligomers (ASOs) from basic research to clinical application. Hosted by the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, Germany, on September 12-13, 2024, the event featured presentations covering major milestones and current challenges of this antimicrobial technology and its applications against pathogens, commensals, and bacterial viruses. General design principles and modification of ASOs based on peptide nucleic acid (PNA) or phosphorodiamidate-morpholino-oligomer (PMO) chemistry, promising cellular RNA targets, new delivery technologies, as well as putative resistance mechanisms, were discussed. A panel discussion noted the challenge of nomenclature: antibacterial ASOs lack a single, universally used name. To address this, the term \"asobiotics\" was proposed to unite a community of like-minded scientists that are committed to advancing ASOs as antimicrobials. A consistent name will simplify literature searches and help scientists and funders appreciate the potential of programmable RNA antibiotics to combat antimicrobial resistance and enable precise microbiome editing.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"465-474"},"PeriodicalIF":4.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010994","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}
RNAPub Date : 2025-03-18DOI: 10.1261/rna.080406.125
Svetlana Deryusheva, Ji-Long Liu, Zehra F Nizami, Gaëlle J S Talross, Susan A Gerbi
{"title":"An incredible life in science: Joseph G. Gall (1928-2024).","authors":"Svetlana Deryusheva, Ji-Long Liu, Zehra F Nizami, Gaëlle J S Talross, Susan A Gerbi","doi":"10.1261/rna.080406.125","DOIUrl":"10.1261/rna.080406.125","url":null,"abstract":"","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"453-464"},"PeriodicalIF":4.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370284","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}
RNAPub Date : 2025-03-18DOI: 10.1261/rna.080335.124
Sepideh Fakhretaha Aval, Amal Seffouh, Kyung-Mee Moon, Leonard J Foster, Joaquin Ortega, Kurt Fredrick
{"title":"Role of the sarcin-ricin loop of 23S rRNA in biogenesis of the 50S ribosomal subunit.","authors":"Sepideh Fakhretaha Aval, Amal Seffouh, Kyung-Mee Moon, Leonard J Foster, Joaquin Ortega, Kurt Fredrick","doi":"10.1261/rna.080335.124","DOIUrl":"10.1261/rna.080335.124","url":null,"abstract":"<p><p>The sarcin-ricin loop (SRL) is one of the most conserved segments of ribosomal RNA (rRNA). Translational GTPases (trGTPases), such as EF-G, EF-Tu, and IF2, form contacts with the SRL that are critical for GTP hydrolysis and factor function. Previous studies showed that expression of 23S rRNA lacking the SRL confers a dominant lethal phenotype in <i>Escherichia coli</i> Isolated ΔSRL particles were found to be not only inactive in protein synthesis but also incompletely assembled. In particular, block 4 of the subunit, which includes the peptidyl transferase center, remained unfolded. Here, we explore the basis of this assembly defect. We find that 23S rRNA extracted from ΔSRL subunits can be efficiently reconstituted into 50S subunits, and these reconstituted ΔSRL particles exhibit full peptidyl transferase activity. We also further characterize ΔSRL particles purified from cells, using cryo-EM and proteomic methods. These particles lack density for rRNA and r-proteins of block 4, consistent with earlier chemical probing data. Incubation of these particles with excess total r-protein of the large subunit (TP50) fails to restore substantial peptidyl transferase activity. Interestingly, proteomic analysis of control and mutant particles shows an overrepresentation of multiple assembly factors in the ΔSRL case. We propose that one or more GTPases normally act to release assembly factors, and this activity is blocked in the absence of the SRL.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"585-599"},"PeriodicalIF":4.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143060505","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}