{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T18:09:15Z","timestamp":1778350155450,"version":"3.51.4"},"reference-count":54,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T00:00:00Z","timestamp":1677456000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB-1411836"],"award-info":[{"award-number":["MCB-1411836"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB-1818229"],"award-info":[{"award-number":["MCB-1818229"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["308291-00001"],"award-info":[{"award-number":["308291-00001"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["308291-00001"],"award-info":[{"award-number":["308291-00001"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"United States Department of Agriculture","award":["MCB-1411836"],"award-info":[{"award-number":["MCB-1411836"]}]},{"name":"United States Department of Agriculture","award":["MCB-1818229"],"award-info":[{"award-number":["MCB-1818229"]}]},{"name":"United States Department of Agriculture","award":["308291-00001"],"award-info":[{"award-number":["308291-00001"]}]},{"name":"United States Department of Agriculture","award":["308291-00001"],"award-info":[{"award-number":["308291-00001"]}]},{"name":"USDA-NIFA","award":["MCB-1411836"],"award-info":[{"award-number":["MCB-1411836"]}]},{"name":"USDA-NIFA","award":["MCB-1818229"],"award-info":[{"award-number":["MCB-1818229"]}]},{"name":"USDA-NIFA","award":["308291-00001"],"award-info":[{"award-number":["308291-00001"]}]},{"name":"USDA-NIFA","award":["308291-00001"],"award-info":[{"award-number":["308291-00001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The cap-independent translation of plus-strand RNA plant viruses frequently depends on 3\u2032 structures to attract translation initiation factors that bind ribosomal subunits or bind directly to ribosomes. Umbraviruses are excellent models for studying 3\u2032 cap-independent translation enhancers (3\u2032CITEs), as umbraviruses can have different 3\u2032CITEs in the central region of their lengthy 3\u2032UTRs, and most also have a particular 3\u2032CITE (the T-shaped structure or 3\u2032TSS) near their 3\u2032 ends. We discovered a novel hairpin just upstream of the centrally located (known or putative) 3\u2032CITEs in all 14 umbraviruses. These CITE-associated structures (CASs) have conserved sequences in their apical loops and at the stem base and adjacent positions. In 11 umbraviruses, CASs are preceded by two small hairpins joined by a putative kissing loop interaction (KL). Converting the conserved 6-nt apical loop to a GNRA tetraloop in opium poppy mosaic virus (OPMV) and pea enation mosaic virus 2 (PEMV2) enhanced translation of genomic (g)RNA, but not subgenomic (sg)RNA reporter constructs, and significantly repressed virus accumulation in Nicotiana benthamiana. Other alterations throughout OPMV CAS also repressed virus accumulation and only enhanced sgRNA reporter translation, while mutations in the lower stem repressed gRNA reporter translation. Similar mutations in the PEMV2 CAS also repressed accumulation but did not significantly affect gRNA or sgRNA reporter translation, with the exception of deletion of the entire hairpin, which only reduced translation of the gRNA reporter. OPMV CAS mutations had little effect on the downstream BTE 3\u2032CITE or upstream KL element, while PEMV2 CAS mutations significantly altered KL structures. These results introduce an additional element associated with different 3\u2032CITEs that differentially affect the structure and translation of different umbraviruses.<\/jats:p>","DOI":"10.3390\/v15030638","type":"journal-article","created":{"date-parts":[[2023,2,28]],"date-time":"2023-02-28T03:29:46Z","timestamp":1677554986000},"page":"638","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Conserved Structure Associated with Different 3\u2032CITEs Is Important for Translation of Umbraviruses"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4610-3334","authenticated-orcid":false,"given":"Sayanta","family":"Bera","sequence":"first","affiliation":[{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20772, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muhammad","family":"Ilyas","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20772, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna A.","family":"Mikkelsen","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20772, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne E.","family":"Simon","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20772, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1099\/vir.0.042499-0","article-title":"Non-canonical translation in RNA viruses","volume":"93","author":"Firth","year":"2012","journal-title":"J. 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