About: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus

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About: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus
Creator	Baric, Ralph Sims, Amy Yount, Boyd Hennig, Mirko Ishimaru, Daniella Taylor, Deborah Dinman, Jonathan Plant, Ewan Armbruster, David Eldho, Nadukkudy Pé Rez-Alvarado, Gabriela Roth, Braden
topic	covid:fa021bfcf95acdbde556098bfd84e8a84c7948c9#this
Source	Medline; PMC
abstract	Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.
has issue date	2012-12-26(xsd:dateTime)
bibo:doi	10.1093/nar/gks1361
bibo:pmid	23275571
has license	cc-by-nc
sha1sum (hex)	fa021bfcf95acdbde556098bfd84e8a84c7948c9
schema:url	https://doi.org/10.1093/nar/gks1361
resource representing a document's title	RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus
has PubMed Central identifier	PMC3575852
has PubMed identifier	23275571
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:fa021bfcf95acdbde556098bfd84e8a84c7948c9#body_text
is http://vocab.deri.ie/void#inDataset of	proxy:http/ns.inria.fr/covid19/fa021bfcf95acdbde556098bfd84e8a84c7948c9
is schema:about of	named entity 'EFFICIENT' named entity 'MAGNESIUM' named entity 'KISSING' named entity 'ANALYSIS' named entity 'IN VITRO' named entity 'THESE' named entity 'ENVIRONMENT' named entity 'PRF' named entity 'COMPLEX FORMATION' named entity 'ABOLISHED' named entity 'VIRAL' named entity 'PLAY' named entity 'IMPORTANT' named entity 'SIGNALS' named entity 'CHANGED' named entity 'INVOLVED' named entity 'DESCRIBING' named entity 'REDUCED' named entity 'COMPLEX' named entity 'REVEALED' named entity 'CORONAVIRUS' named entity 'CODON CHANGE' named entity 'RESULTS' named entity 'INVOLVING' named entity 'CAUSED BY' named entity 'INABILITY' named entity 'AFFECTED' named entity 'EMBEDDED' named entity 'RNA' named entity 'CELLULAR' named entity 'RNA SYNTHESIS' named entity 'MESSENGER RNA' named entity 'STIMULATED' named entity 'PREVIOUSLY' named entity 'DESCRIBED' named entity 'RIBOSOMAL' named entity 'DIMERIZATION' named entity 'SEQUENCE' named entity 'DIMERS' named entity 'PSEUDOKNOT' named entity 'ROLE' named entity 'RNA' named entity 'SARS CORONAVIRUS' named entity 'INTERACTIONS' named entity 'TEMPERATURE' named entity 'FORMED' named entity 'FUNCTION' named entity 'ROLE' named entity 'SARS-COV' named entity 'NEW INFORMATION' named entity 'PSEUDOKNOTS' named entity 'LEVELS' named entity 'STEM-LOOP' named entity 'STEM' named entity 'STRUCTURE' named entity 'UNUSUAL' named entity 'TYPE' named entity 'ASSEMBLE' named entity 'UNKNOWN' named entity '5.7' named entity 'ENCODED' named entity 'HERE' named entity 'PRESENT' named entity 'LOOP' named entity '28H' named entity 'DIMERIZATION' named entity 'LENGTH' named entity 'CHANGE IN'

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