{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T07:20:08Z","timestamp":1768634408912,"version":"3.49.0"},"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2021,8,24]],"date-time":"2021-08-24T00:00:00Z","timestamp":1629763200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/R023204\/1"],"award-info":[{"award-number":["EP\/R023204\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Royal Society Wolfson Fellowship","award":["RSWF\/R1\/180009"],"award-info":[{"award-number":["RSWF\/R1\/180009"]}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["110145, 110146"],"award-info":[{"award-number":["110145, 110146"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The vast majority of viruses consist of a nucleic acid surrounded by a protective icosahedral protein shell called the capsid. During viral infection of a host cell, the timing and efficiency of the assembly process is important for ensuring the production of infectious new progeny virus particles. In the class of single-stranded RNA (ssRNA) viruses, the assembly of the capsid takes place in tandem with packaging of the ssRNA genome in a highly cooperative co-assembly process. In simple ssRNA viruses such as the bacteriophage MS2 and small RNA plant viruses such as STNV, this cooperative process results from multiple interactions between the protein shell and sites in the RNA genome which have been termed packaging signals. Using a stochastic assembly algorithm which includes cooperative interactions between the protein shell and packaging signals in the RNA genome, we demonstrate that highly efficient assembly of STNV capsids arises from a set of simple local rules. Altering the local assembly rules results in different nucleation scenarios with varying assembly efficiencies, which in some cases depend strongly on interactions with RNA packaging signals. Our results provide a potential simple explanation based on local assembly rules for the ability of some ssRNA viruses to spontaneously assemble around charged polymers and other non-viral RNAs <jats:italic>in vitro<\/jats:italic>.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009306","type":"journal-article","created":{"date-parts":[[2021,8,24]],"date-time":"2021-08-24T17:24:33Z","timestamp":1629825873000},"page":"e1009306","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5288-6171","authenticated-orcid":true,"given":"Sam R.","family":"Hill","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1824-2003","authenticated-orcid":true,"given":"Reidun","family":"Twarock","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8344-8446","authenticated-orcid":true,"given":"Eric C.","family":"Dykeman","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2021,8,24]]},"reference":[{"issue":"14","key":"pcbi.1009306.ref001","doi-asserted-by":"crossref","first-page":"5361","DOI":"10.1073\/pnas.1319479111","article-title":"Solving a Levinthal\u2019s paradox for virus assembly identifies a unique antiviral strategy","volume":"111","author":"EC Dykeman","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"7","key":"pcbi.1009306.ref002","doi-asserted-by":"crossref","first-page":"2227","DOI":"10.1073\/pnas.1420812112","article-title":"Revealing the density of encoded functions in a viral RNA","volume":"112","author":"N Patel","year":"2015","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"pcbi.1009306.ref003","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms12524","article-title":"Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ","volume":"7","author":"RI Koning","year":"2016","journal-title":"Nature communications"},{"issue":"20","key":"pcbi.1009306.ref004","doi-asserted-by":"crossref","first-page":"10673","DOI":"10.1073\/pnas.1915078117","article-title":"Genome organization and interaction with capsid protein in a multipartite RNA virus","volume":"117","author":"C Beren","year":"2020","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"pcbi.1009306.ref005","first-page":"1","article-title":"Genomic RNA folding mediates assembly of human parechovirus","volume":"8","author":"S Shakeel","year":"2017","journal-title":"Nature communications"},{"issue":"19","key":"pcbi.1009306.ref006","doi-asserted-by":"crossref","first-page":"4621","DOI":"10.1093\/nar\/21.19.4621","article-title":"Encapsidation of heterologous RNAs by bacteriophage MS2 coat protein","volume":"21","author":"GG Pickett","year":"1993","journal-title":"Nucleic acids research"},{"issue":"10","key":"pcbi.1009306.ref007","doi-asserted-by":"crossref","first-page":"5684","DOI":"10.1016\/S0021-9258(19)39417-7","article-title":"Translational repression by bacteriophage MS2 coat protein expressed from a plasmid. 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