Global organization of a positive-strand RNA virus genome.

The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements...

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Autores principales:	Baodong Wu, Jörg Grigull, Moriam O Ore, Sylvie Morin, K Andrew White
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0741e321a8074e4e8eed6a9ff8729941
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spelling	oai:doaj.org-article:0741e321a8074e4e8eed6a9ff87299412021-11-18T06:05:36ZGlobal organization of a positive-strand RNA virus genome.1553-73661553-737410.1371/journal.ppat.1003363https://doaj.org/article/0741e321a8074e4e8eed6a9ff87299412013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23717202/?tool=EBIhttps://doaj.org/toc/1553-7366https://doaj.org/toc/1553-7374The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2'-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.Baodong WuJörg GrigullMoriam O OreSylvie MorinK Andrew WhitePublic Library of Science (PLoS)articleImmunologic diseases. AllergyRC581-607Biology (General)QH301-705.5ENPLoS Pathogens, Vol 9, Iss 5, p e1003363 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5
spellingShingle	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5 Baodong Wu Jörg Grigull Moriam O Ore Sylvie Morin K Andrew White Global organization of a positive-strand RNA virus genome.
description	The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes. The traditional view of these RNA elements are as local structures present in non-coding regions. However, this view is changing due to the discovery of regulatory elements in coding regions and functional long-range intra-genomic base pairing interactions. The ∼4.8 kb long RNA genome of the tombusvirus tomato bushy stunt virus (TBSV) contains these types of structural features, including six different functional long-distance interactions. We hypothesized that to achieve these multiple interactions this viral genome must utilize a large-scale organizational strategy and, accordingly, we sought to assess the global conformation of the entire TBSV genome. Atomic force micrographs of the genome indicated a mostly condensed structure composed of interconnected protrusions extending from a central hub. This configuration was consistent with the genomic secondary structure model generated using high-throughput selective 2'-hydroxyl acylation analysed by primer extension (i.e. SHAPE), which predicted different sized RNA domains originating from a central region. Known RNA elements were identified in both domain and inter-domain regions, and novel structural features were predicted and functionally confirmed. Interestingly, only two of the six long-range interactions known to form were present in the structural model. However, for those interactions that did not form, complementary partner sequences were positioned relatively close to each other in the structure, suggesting that the secondary structure level of viral genome structure could provide a basic scaffold for the formation of different long-range interactions. The higher-order structural model for the TBSV RNA genome provides a snapshot of the complex framework that allows multiple functional components to operate in concert within a confined context.
format	article
author	Baodong Wu Jörg Grigull Moriam O Ore Sylvie Morin K Andrew White
author_facet	Baodong Wu Jörg Grigull Moriam O Ore Sylvie Morin K Andrew White
author_sort	Baodong Wu
title	Global organization of a positive-strand RNA virus genome.
title_short	Global organization of a positive-strand RNA virus genome.
title_full	Global organization of a positive-strand RNA virus genome.
title_fullStr	Global organization of a positive-strand RNA virus genome.
title_full_unstemmed	Global organization of a positive-strand RNA virus genome.
title_sort	global organization of a positive-strand rna virus genome.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/0741e321a8074e4e8eed6a9ff8729941
work_keys_str_mv	AT baodongwu globalorganizationofapositivestrandrnavirusgenome AT jorggrigull globalorganizationofapositivestrandrnavirusgenome AT moriamoore globalorganizationofapositivestrandrnavirusgenome AT sylviemorin globalorganizationofapositivestrandrnavirusgenome AT kandrewwhite globalorganizationofapositivestrandrnavirusgenome
_version_	1718424581680660480

Global organization of a positive-strand RNA virus genome.

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