{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T11:17:45Z","timestamp":1767179865547,"version":"build-2238731810"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005367","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,2,23]],"date-time":"2017-02-23T00:00:00Z","timestamp":1487808000000}}],"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2017,2,8]],"date-time":"2017-02-08T00:00:00Z","timestamp":1486512000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001869","name":"Academia Sinica","doi-asserted-by":"publisher","award":["101-CDA-L05"],"award-info":[{"award-number":["101-CDA-L05"]}],"id":[{"id":"10.13039\/501100001869","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["103-2311-B-001-034-MY3"],"award-info":[{"award-number":["103-2311-B-001-034-MY3"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001869","name":"Academia Sinica","doi-asserted-by":"publisher","award":["104-CDA-M04"],"award-info":[{"award-number":["104-CDA-M04"]}],"id":[{"id":"10.13039\/501100001869","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["103-2118-M-001-011-MY2"],"award-info":[{"award-number":["103-2118-M-001-011-MY2"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005367","type":"journal-article","created":{"date-parts":[[2017,2,8]],"date-time":"2017-02-08T13:38:57Z","timestamp":1486561137000},"page":"e1005367","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons"],"prefix":"10.1371","volume":"13","author":[{"given":"Yen-Fu","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hsiu-Chuan","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai-Neng","family":"Chuang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4034-8960","authenticated-orcid":true,"given":"Chih-Hsu","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hsueh-Chi S.","family":"Yen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9224-5800","authenticated-orcid":true,"given":"Chen-Hsiang","family":"Yeang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2017,2,8]]},"reference":[{"issue":"17","key":"ref1","doi-asserted-by":"crossref","first-page":"9724","DOI":"10.1016\/S0021-9258(18)81714-8","article-title":"Identification of a selenocysteyl-tRNA(Ser) in mammalian cells that recognizes the nonsense codon, UGA","volume":"264","author":"BJ Lee","year":"1989","journal-title":"The Journal of biological chemistry"},{"issue":"5572","key":"ref2","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1126\/science.1069588","article-title":"Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA","volume":"296","author":"G Srinivasan","year":"2002","journal-title":"Science"},{"issue":"6243","key":"ref3","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1126\/science.aab0515","article-title":"CRL2 aids elimination of truncated selenoproteins produced by failed UGA\/Sec decoding","volume":"349","author":"H-C Lin","year":"2015","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1146\/annurev.nutr.23.011702.073318","article-title":"Mechanism and regulation of selenoprotein synthesis","volume":"23","author":"DM Driscoll","year":"2003","journal-title":"Annual review of nutrition"},{"issue":"11","key":"ref5","doi-asserted-by":"crossref","first-page":"3565","DOI":"10.1128\/MCB.22.11.3565-3576.2002","article-title":"How Selenium Has Altered Our Understanding of the Genetic Code","volume":"22","author":"DL Hatfield","year":"2002","journal-title":"Molecular and Cellular Biology"},{"issue":"7","key":"ref6","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1089\/ars.2007.1528","article-title":"From selenium to selenoproteins: synthesis, identity, and their role in human health","volume":"9","author":"LV Papp","year":"2007","journal-title":"Antioxidants & redox signaling"},{"issue":"11","key":"ref7","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1016\/j.biochi.2006.04.015","article-title":"Selenoprotein synthesis: UGA does not end the story","volume":"88","author":"C Allmang","year":"2006","journal-title":"Biochimie"},{"issue":"24","key":"ref8","doi-asserted-by":"crossref","first-page":"6882","DOI":"10.1093\/emboj\/19.24.6882","article-title":"SECIS-SBP2 interactions dictate selenocysteine incorporation efficiency and selenoprotein hierarchy","volume":"19","author":"SC Low","year":"2000","journal-title":"The EMBO journal"},{"issue":"36","key":"ref9","doi-asserted-by":"crossref","first-page":"25447","DOI":"10.1074\/jbc.274.36.25447","article-title":"Purification, redox sensitivity, and RNA binding properties of SECIS-binding protein 2, a protein involved in selenoprotein biosynthesis","volume":"274","author":"PR Copeland","year":"1999","journal-title":"The Journal of biological chemistry"},{"issue":"2","key":"ref10","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1093\/emboj\/19.2.306","article-title":"A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs","volume":"19","author":"PR Copeland","year":"2000","journal-title":"The EMBO journal"},{"issue":"2","key":"ref11","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1093\/embo-reports\/kvd033","article-title":"Decoding apparatus for eukaryotic selenocysteine insertion","volume":"1","author":"RM Tujebajeva","year":"2000","journal-title":"EMBO Rep"},{"issue":"1\u20134","key":"ref12","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1002\/biof.5520140104","article-title":"Selenocysteine incorporation directed from the 3'UTR: characterization of eukaryotic EFsec and mechanistic implications","volume":"14","author":"MJ Berry","year":"2001","journal-title":"Biofactors"},{"issue":"2","key":"ref13","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/S0092-8674(00)81331-8","article-title":"Emerging understanding of translation termination","volume":"87","author":"Y Nakamura","year":"1996","journal-title":"Cell"},{"issue":"2","key":"ref14","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1093\/emboj\/cdg017","article-title":"Termination of translation: interplay of mRNA, rRNAs and release factors?","volume":"22","author":"L Kisselev","year":"2003","journal-title":"The EMBO journal"},{"issue":"8","key":"ref15","doi-asserted-by":"crossref","first-page":"2284","DOI":"10.1093\/emboj\/18.8.2284","article-title":"Dynamics and efficiency in vivo of UGA-directed selenocysteine insertion at the ribosome","volume":"18","author":"S Suppmann","year":"1999","journal-title":"The EMBO journal"},{"issue":"7","key":"ref16","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1093\/nar\/24.7.1195","article-title":"Analysis of eukaryotic mRNA structures directing cotranslational incorporation of selenocysteine","volume":"24","author":"H Kollmus","year":"1996","journal-title":"Nucleic acids research"},{"issue":"36","key":"ref17","doi-asserted-by":"crossref","first-page":"37852","DOI":"10.1074\/jbc.M404639200","article-title":"Efficiency of mammalian selenocysteine incorporation","volume":"279","author":"A Mehta","year":"2004","journal-title":"The Journal of biological chemistry"},{"issue":"18","key":"ref18","doi-asserted-by":"crossref","first-page":"3753","DOI":"10.1093\/nar\/22.18.3753","article-title":"Selenocysteine insertion or termination: factors affecting UGA codon fate and complementary anticodon:codon mutations","volume":"22","author":"MJ Berry","year":"1994","journal-title":"Nucleic acids research"},{"issue":"27","key":"ref19","doi-asserted-by":"crossref","first-page":"19401","DOI":"10.1074\/jbc.M113.481051","article-title":"Translational redefinition of UGA codons is regulated by selenium availability","volume":"288","author":"MT Howard","year":"2013","journal-title":"The Journal of biological chemistry"},{"issue":"7","key":"ref20","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1261\/rna.7370104","article-title":"A regulatory role for Sec tRNA[Ser]Sec in selenoprotein synthesis","volume":"10","author":"RR Jameson","year":"2004","journal-title":"RNA"},{"issue":"17","key":"ref21","doi-asserted-by":"crossref","first-page":"5868","DOI":"10.1093\/nar\/gkp635","article-title":"Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine","volume":"37","author":"L Latreche","year":"2009","journal-title":"Nucleic acids research"},{"issue":"37","key":"ref22","doi-asserted-by":"crossref","first-page":"21659","DOI":"10.1074\/jbc.270.37.21659","article-title":"Cloning and functional characterization of human selenophosphate synthetase, an essential component of selenoprotein synthesis","volume":"270","author":"SC Low","year":"1995","journal-title":"The Journal of biological chemistry"},{"issue":"11","key":"ref23","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1016\/j.bbagen.2009.03.015","article-title":"Hierarchical regulation of selenoprotein expression and sex-specific effects of selenium","volume":"1790","author":"L Schomburg","year":"2009","journal-title":"Biochimica et biophysica acta"},{"issue":"5624","key":"ref24","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1126\/science.1083516","article-title":"Characterization of mammalian selenoproteomes","volume":"300","author":"GV Kryukov","year":"2003","journal-title":"Science"},{"issue":"5903","key":"ref25","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1126\/science.1160489","article-title":"Global protein stability profiling in mammalian cells","volume":"322","author":"HC Yen","year":"2008","journal-title":"Science"},{"issue":"24","key":"ref26","doi-asserted-by":"crossref","first-page":"7284","DOI":"10.1093\/emboj\/20.24.7284","article-title":"A dynamic competition between release factor 2 and the tRNA(Sec) decoding UGA at the recoding site of Escherichia coli formate dehydrogenase H","volume":"20","author":"JB Mansell","year":"2001","journal-title":"The EMBO journal"},{"issue":"3","key":"ref27","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.ceb.2004.03.003","article-title":"Nonsense-mediated mRNA decay: terminating erroneous gene expression","volume":"16","author":"KE Baker","year":"2004","journal-title":"Curr Opin Cell Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1146\/annurev.biochem.76.050106.093909","article-title":"The nonsense-mediated decay RNA surveillance pathway","volume":"76","author":"YF Chang","year":"2007","journal-title":"Annual review of biochemistry"},{"issue":"7347","key":"ref29","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature10098","article-title":"Global quantification of mammalian gene expression control","volume":"473","author":"B Schwanhausser","year":"2011","journal-title":"Nature"},{"issue":"11","key":"ref30","doi-asserted-by":"crossref","first-page":"R130","DOI":"10.1186\/gb-2009-10-11-r130","article-title":"BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources","volume":"10","author":"C Wu","year":"2009","journal-title":"Genome biology"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"D1093","DOI":"10.1093\/nar\/gkr1177","article-title":"MOPED: Model Organism Protein Expression Database","volume":"40","author":"E Kolker","year":"2012","journal-title":"Nucleic acids research"},{"issue":"10","key":"ref32","first-page":"1442","article-title":"The selenocysteine incorporation machinery: interactions between the SECIS RNA and the SECIS-binding protein SBP2","volume":"7","author":"JE Fletcher","year":"2001","journal-title":"RNA"},{"issue":"12","key":"ref33","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1017\/S1355838299991598","article-title":"Identification of a protein component of a mammalian tRNA(Sec) complex implicated in the decoding of UGA as selenocysteine","volume":"5","author":"F Ding","year":"1999","journal-title":"RNA"},{"issue":"50","key":"ref34","doi-asserted-by":"crossref","first-page":"41568","DOI":"10.1074\/jbc.M506696200","article-title":"Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery","volume":"280","author":"XM Xu","year":"2005","journal-title":"The Journal of biological chemistry"},{"issue":"7","key":"ref35","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1016\/j.cell.2010.06.019","article-title":"SnapShot: key numbers in biology","volume":"141","author":"U Moran","year":"2010","journal-title":"Cell"},{"issue":"1","key":"ref36","first-page":"e4","article-title":"Biosynthesis of selenocysteine on its tRNA in eukaryotes","volume":"5","author":"XM Xu","year":"2007","journal-title":"PLoS biology"},{"issue":"11","key":"ref37","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1093\/jn\/137.11.2333","article-title":"Total aminoacyl-transfer RNA pool is greater in liver than muscle in rabbits","volume":"137","author":"RR Wolfe","year":"2007","journal-title":"The Journal of nutrition"},{"issue":"2","key":"ref38","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1016\/j.gene.2013.11.049","article-title":"tRNA gene copy number variation in humans","volume":"536","author":"JR Iben","year":"2014","journal-title":"Gene"},{"issue":"12","key":"ref39","doi-asserted-by":"crossref","first-page":"e221","DOI":"10.1371\/journal.pgen.0020221","article-title":"Tissue-specific differences in human transfer RNA expression","volume":"2","author":"KA Dittmar","year":"2006","journal-title":"PLoS genetics"},{"issue":"14","key":"ref40","doi-asserted-by":"crossref","first-page":"10228","DOI":"10.1016\/S0021-9258(18)82194-9","article-title":"Post-transcriptional regulation of the steady-state levels of mitochondrial tRNAs in HeLa cells","volume":"268","author":"MP King","year":"1993","journal-title":"The Journal of biological chemistry"},{"issue":"10","key":"ref41","doi-asserted-by":"crossref","first-page":"2045","DOI":"10.1038\/nprot.2013.116","article-title":"Real-time single-molecule coimmunoprecipitation of weak protein-protein interactions","volume":"8","author":"HW Lee","year":"2013","journal-title":"Nature protocols"},{"issue":"3","key":"ref42","article-title":"A quantitative spatial proteomics analysis of proteome turnover in human cells. Molecular & cellular proteomics","volume":"11","author":"FM Boisvert","year":"2012","journal-title":"MCP"},{"issue":"4","key":"ref43","doi-asserted-by":"crossref","first-page":"e35581","DOI":"10.1371\/journal.pone.0035581","article-title":"Selenocysteine insertion sequence binding protein 2L is implicated as a novel post-transcriptional regulator of selenoprotein expression","volume":"7","author":"J Donovan","year":"2012","journal-title":"PLoS One"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005367","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,2,23]],"date-time":"2017-02-23T00:00:00Z","timestamp":1487808000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005367","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,23]],"date-time":"2022-07-23T16:59:34Z","timestamp":1658595574000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005367"}},"subtitle":[],"editor":[{"given":"Joshua B.","family":"Plotkin","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,2,8]]},"references-count":43,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2017,2,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005367","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,2,8]]}}}