{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T18:03:09Z","timestamp":1790877789543,"version":"4.1.0"},"reference-count":99,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007397","name":"Univerzita Karlova v Praze","doi-asserted-by":"publisher","award":["PROGRES Q43"],"award-info":[{"award-number":["PROGRES Q43"]}],"id":[{"id":"10.13039\/100007397","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007397","name":"Univerzita Karlova v Praze","doi-asserted-by":"publisher","award":["UNCE204013"],"award-info":[{"award-number":["UNCE204013"]}],"id":[{"id":"10.13039\/100007397","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Ribosomal proteins, because of their RNA-binding capacity, may engage various cellular RNAs and fulfill non-ribosomal roles. Previously, we and others described the intergenic regulation mediated by splicing of\n                    <jats:italic>RPL22<\/jats:italic>\n                    paralogs in\n                    <jats:italic>Saccharomyces cerevisiae<\/jats:italic>\n                    . Here, we prepared a panel of\n                    <jats:italic>RPL22A\/B<\/jats:italic>\n                    intronic mutants with respect to their RNAfold-predicted features and analyzed their properties. We tested splicing efficiency and Rpl22-intron binding using an intron-containing reporter and a yeast three-hybrid system, respectively. We found that the splicing of\n                    <jats:italic>RPL22<\/jats:italic>\n                    introns can be inhibited by stabilizing a predicted stem as part of a particular type of conformation (I structure). Stabilizing the formation of an alternate stem (P structure) permitted splicing. Binding of the Rpl22 protein to the intron led to enhanced splicing inhibition in WT and several of the mutants, which we interpret as stabilization of the I structure. Mutagenesis identified both the main and alternative 5\u2019ss and additional stem loops as part of the regulatory mechanism. The inhibitory conformation of the intron did not prevent recognition of the 5\u2019ss and branch point, but rather stalled splicing at a later stage, before the first catalytic step. We conclude that the structural ensemble of the\n                    <jats:italic>RPL22<\/jats:italic>\n                    pre-mRNA behaves as an allosteric switch that responds to Rpl22 concentration.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0359197","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T17:26:15Z","timestamp":1790875575000},"page":"e0359197","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Intronic RNA of yeast RPL22 paralogs acts as an allosteric switch"],"prefix":"10.1371","volume":"21","author":[{"given":"Kate\u0159ina","family":"Abrh\u00e1mov\u00e1","sequence":"first","affiliation":[{"name":"Charles University","place":["Praha, Czech Republic"],"department":["Department of Cell Biology, Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Gredov\u00e1","sequence":"additional","affiliation":[{"name":"Charles University","place":["Praha, Czech Republic"],"department":["Department of Cell Biology, Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karol\u00edna","family":"Navr\u00e1tilov\u00e1","sequence":"additional","affiliation":[{"name":"Charles University","place":["Praha, Czech Republic"],"department":["Department of Cell Biology, Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"Boumaiza","sequence":"additional","affiliation":[{"name":"Charles University","place":["Praha, Czech Republic"],"department":["Department of Cell Biology, Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3813-7777","authenticated-orcid":true,"given":"Petr","family":"Folk","sequence":"additional","affiliation":[{"name":"Charles University","place":["Praha, Czech Republic"],"department":["Department of Cell Biology, Faculty of Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"key":"pone.0359197.ref001","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.molcel.2009.03.006","article-title":"How common are extraribosomal functions of ribosomal proteins?","volume":"34","author":"JR Warner","year":"2009","journal-title":"Mol Cell"},{"issue":"1","key":"pone.0359197.ref002","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.cell.2005.07.034","article-title":"Regulation of p53 translation and induction after DNA damage by ribosomal protein L26 and 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proteins","volume":"6","author":"S Ramalho","year":"2024","journal-title":"NAR Cancer"},{"issue":"3","key":"pone.0359197.ref019","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/j.cell.2007.08.037","article-title":"Functional specificity among ribosomal proteins regulates gene expression","volume":"131","author":"S Komili","year":"2007","journal-title":"Cell"},{"issue":"7","key":"pone.0359197.ref020","doi-asserted-by":"crossref","first-page":"2701","DOI":"10.1093\/nar\/gkq1218","article-title":"Expression of ribosomal protein L22e family members in Drosophila melanogaster: rpL22-like is differentially expressed and alternatively spliced","volume":"39","author":"MG Kearse","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"pone.0359197.ref021","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1080\/19336934.2018.1549419","article-title":"Functional interplay between ribosomal protein paralogues in the eRpL22 family in Drosophila 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Fok","year":"2006","journal-title":"RNA"},{"issue":"19","key":"pone.0359197.ref028","doi-asserted-by":"crossref","first-page":"9844","DOI":"10.1128\/JVI.01014-09","article-title":"Growth-promoting properties of Epstein-Barr virus EBER-1 RNA correlate with ribosomal protein L22 binding","volume":"83","author":"JL Houmani","year":"2009","journal-title":"J Virol"},{"key":"pone.0359197.ref029","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/ncomms1938","article-title":"Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins","volume":"3","author":"CTY Chan","year":"2012","journal-title":"Nat Commun"},{"key":"pone.0359197.ref030","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s13008-016-0024-3","article-title":"Rpl22 is required for IME1 mRNA translation and meiotic induction in S. cerevisiae","volume":"11","author":"SJ Kim","year":"2016","journal-title":"Cell 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basis for an RNA-based enhancer","volume":"1","author":"D Libri","year":"1995","journal-title":"RNA"},{"issue":"22","key":"pone.0359197.ref038","doi-asserted-by":"crossref","first-page":"9759","DOI":"10.1093\/nar\/gkr662","article-title":"Secondary structure is required for 3\u2019 splice site recognition in yeast","volume":"39","author":"O Gahura","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"14","key":"pone.0359197.ref039","doi-asserted-by":"crossref","first-page":"4533","DOI":"10.1093\/nar\/gkp407","article-title":"Modulation of alternative splicing by long-range RNA structures in Drosophila","volume":"37","author":"VA Raker","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0359197.ref040","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.cell.2005.07.028","article-title":"Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures","volume":"123","author":"BR Graveley","year":"2005","journal-title":"Cell"},{"issue":"4","key":"pone.0359197.ref041","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/j.gde.2011.04.001","article-title":"RNA structure and the mechanisms of alternative splicing","volume":"21","author":"CJ McManus","year":"2011","journal-title":"Curr Opin Genet Dev"},{"issue":"7","key":"pone.0359197.ref042","doi-asserted-by":"crossref","first-page":"356","DOI":"10.3390\/genes9070356","article-title":"An Evolutionary mechanism for the generation of competing RNA structures associated with mutually exclusive exons","volume":"9","author":"TM Ivanov","year":"2018","journal-title":"Genes (Basel)"},{"issue":"1","key":"pone.0359197.ref043","article-title":"BRD2 and BRD3 genes independently evolved RNA structures to control unproductive splicing","volume":"6","author":"M Petrova","year":"2024","journal-title":"NAR Genom 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Rep"},{"issue":"8","key":"pone.0359197.ref047","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.1016\/j.molcel.2021.01.040","article-title":"Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing","volume":"81","author":"T Saldi","year":"2021","journal-title":"Mol Cell"},{"issue":"4","key":"pone.0359197.ref048","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1080\/21541264.2021.1985931","article-title":"Transcription complexes as RNA chaperones","volume":"12","author":"N Said","year":"2021","journal-title":"Transcription"},{"key":"pone.0359197.ref049","doi-asserted-by":"crossref","first-page":"2871","DOI":"10.1016\/j.csbj.2022.05.041","article-title":"Secondary structures in RNA synthesis, splicing and translation","volume":"20","author":"I Georgakopoulos-Soares","year":"2022","journal-title":"Comput Struct Biotechnol 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Gruber","year":"2015","journal-title":"RNA Bioinformatics. 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Steffen","year":"2006","journal-title":"Bioinformatics"},{"issue":"24","key":"pone.0359197.ref057","doi-asserted-by":"crossref","first-page":"7280","DOI":"10.1093\/nar\/gkg938","article-title":"A statistical sampling algorithm for RNA secondary structure prediction","volume":"31","author":"Y Ding","year":"2003","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"pone.0359197.ref058","doi-asserted-by":"crossref","first-page":"3377","DOI":"10.1093\/bioinformatics\/btv372","article-title":"Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams","volume":"31","author":"P Kerpedjiev","year":"2015","journal-title":"Bioinformatics"},{"issue":"4","key":"pone.0359197.ref059","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004249","article-title":"Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae","volume":"10","author":"T Kawashima","year":"2014","journal-title":"PLoS 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Genomics"},{"issue":"18","key":"pone.0359197.ref072","doi-asserted-by":"crossref","first-page":"2425","DOI":"10.1101\/gad.13.18.2425","article-title":"Luc7p, a novel yeast U1 snRNP protein with a role in 5\u2019 splice site recognition","volume":"13","author":"P Fortes","year":"1999","journal-title":"Genes Dev"},{"issue":"10","key":"pone.0359197.ref073","doi-asserted-by":"crossref","first-page":"6543","DOI":"10.1128\/MCB.19.10.6543","article-title":"Genetic and physical interactions involving the yeast nuclear cap-binding complex","volume":"19","author":"P Fortes","year":"1999","journal-title":"Mol Cell Biol"},{"issue":"1","key":"pone.0359197.ref074","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.molcel.2005.05.007","article-title":"Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex","volume":"19","author":"J G\u00f6rnemann","year":"2005","journal-title":"Mol 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Biol"},{"issue":"7774","key":"pone.0359197.ref078","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/s41586-019-1523-6","article-title":"A unified mechanism for intron and exon definition and back-splicing","volume":"573","author":"X Li","year":"2019","journal-title":"Nature"},{"issue":"10","key":"pone.0359197.ref079","doi-asserted-by":"crossref","first-page":"4539","DOI":"10.1093\/nar\/gks049","article-title":"Structure-function analysis and genetic interactions of the yeast branchpoint binding protein Msl5","volume":"40","author":"J Chang","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pone.0359197.ref080","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1038\/s41586-018-0323-8","article-title":"Prespliceosome structure provides insights into spliceosome assembly and regulation","volume":"559","author":"C Plaschka","year":"2018","journal-title":"Nature"},{"issue":"11","key":"pone.0359197.ref081","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a032417","article-title":"Structural insights into nuclear pre-mRNA Splicing in higher eukaryotes","volume":"11","author":"B Kastner","year":"2019","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"2","key":"pone.0359197.ref082","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1101\/gad.8.2.211","article-title":"Regulation of splicing at an intermediate step in the formation of the spliceosome","volume":"8","author":"J Vilardell","year":"1994","journal-title":"Genes Dev"},{"issue":"6","key":"pone.0359197.ref083","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1016\/j.molcel.2008.05.002","article-title":"L30 binds the nascent RPL30 transcript to repress U2 snRNP recruitment","volume":"30","author":"S Mac\u00edas","year":"2008","journal-title":"Mol 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Res"},{"issue":"7871","key":"pone.0359197.ref087","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1038\/s41586-021-03789-5","article-title":"Structural insights into how Prp5 proofreads the pre-mRNA branch site","volume":"596","author":"Z Zhang","year":"2021","journal-title":"Nature"},{"key":"pone.0359197.ref088","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.73888","article-title":"Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing","volume":"11","author":"J Kumar","year":"2022","journal-title":"Elife"},{"issue":"1","key":"pone.0359197.ref089","article-title":"Alternate RNA structures","volume":"12","author":"MT-P Wu","year":"2020","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"5","key":"pone.0359197.ref090","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1038\/s41594-024-01480-7","article-title":"Structures of aberrant spliceosome intermediates on their way to disassembly","volume":"32","author":"K Soni","year":"2025","journal-title":"Nat Struct Mol Biol"},{"issue":"5","key":"pone.0359197.ref091","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1038\/s41594-025-01536-2","article-title":"Finding and recycling stalled spliceosomes","volume":"32","author":"CC Query","year":"2025","journal-title":"Nat Struct Mol Biol"},{"issue":"1","key":"pone.0359197.ref092","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.chembiol.2023.12.010","article-title":"Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states","volume":"31","author":"R Bose","year":"2024","journal-title":"Cell Chem Biol"},{"issue":"2","key":"pone.0359197.ref093","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1261\/rna.052233.115","article-title":"Conformational dynamics of stem II of the U2 snRNA","volume":"22","author":"ML Rodgers","year":"2016","journal-title":"RNA"},{"key":"pone.0359197.ref094","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.RWR-0028-2018","article-title":"The T-Box Riboswitch: tRNA as an effector to modulate gene regulation","volume":"6","author":"KD Kreuzer","year":"2018","journal-title":"Microbiol Spectrum"},{"issue":"8","key":"pone.0359197.ref095","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1002\/iub.2098","article-title":"An evolving tale of two interacting RNAs-themes and variations of the T-box riboswitch mechanism","volume":"71","author":"KC Suddala","year":"2019","journal-title":"IUBMB Life"},{"issue":"7231","key":"pone.0359197.ref096","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/nature07598","article-title":"A stress-responsive RNA switch regulates VEGFA expression","volume":"457","author":"PS Ray","year":"2009","journal-title":"Nature"},{"key":"pone.0359197.ref097","doi-asserted-by":"crossref","first-page":"1326","DOI":"10.1016\/j.csbj.2019.10.001","article-title":"Mammalian RNA switches: Molecular rheostats in gene regulation, disease, and medicine","volume":"17","author":"KC Venkata Subbaiah","year":"2019","journal-title":"Comput Struct Biotechnol J"},{"issue":"3","key":"pone.0359197.ref098","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1016\/j.bbrc.2019.06.106","article-title":"hnRNP L-mediated RNA switches function as a hypoxia-induced translational regulon","volume":"516","author":"KC Venkata Subbaiah","year":"2019","journal-title":"Biochem Biophys Res Commun"},{"issue":"1","key":"pone.0359197.ref099","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/nprot.2007.13","article-title":"High-efficiency yeast transformation using the LiAc\/SS carrier DNA\/PEG method","volume":"2","author":"RD Gietz","year":"2007","journal-title":"Nat 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