About: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome

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About: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome
Creator	Butcher, Samuel Easterday, Preston Lang, Andrew Meulen, Kirk Mouzakis, Kathryn
topic	covid:c2ad458ccf62686e340e51ea95c439e7c4e2bc29#this
Source	Medline; PMC
abstract	The human immunodeficiency virus (HIV) requires a programmed −1 ribosomal frameshift for Pol gene expression. The HIV frameshift site consists of a heptanucleotide slippery sequence (UUUUUUA) followed by a spacer region and a downstream RNA stem–loop structure. Here we investigate the role of the RNA structure in promoting the −1 frameshift. The stem–loop was systematically altered to decouple the contributions of local and overall thermodynamic stability towards frameshift efficiency. No correlation between overall stability and frameshift efficiency is observed. In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Insertion or deletions in the spacer region appear to correspondingly change the identity of the base pairs encountered 8 nt downstream of the slippery site. Finally, the role of the surrounding genomic secondary structure was investigated and found to have a modest impact on frameshift efficiency, consistent with the hypothesis that the genomic secondary structure attenuates frameshifting by affecting the overall rate of translation.
has issue date	2012-12-15(xsd:dateTime)
bibo:doi	10.1093/nar/gks1254
bibo:pmid	23248007
has license	cc-by-nc
sha1sum (hex)	c2ad458ccf62686e340e51ea95c439e7c4e2bc29
schema:url	https://doi.org/10.1093/nar/gks1254
resource representing a document's title	HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome
has PubMed Central identifier	PMC3561942
has PubMed identifier	23248007
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:c2ad458ccf62686e340e51ea95c439e7c4e2bc29#body_text
is http://vocab.deri.ie/void#inDataset of	proxy:http/ns.inria.fr/covid19/c2ad458ccf62686e340e51ea95c439e7c4e2bc29
is schema:about of	named entity 'ENTRANCE' named entity 'PROMOTING' named entity 'FRAMESHIFT' named entity 'IMPACT' named entity 'GENE EXPRESSION' named entity 'RNA STRUCTURE' named entity 'CORRELATION' named entity 'APPEAR' named entity 'FOLLOWED BY' named entity 'GENOMIC' named entity 'FOUND' named entity 'stem-loop' named entity 'frameshift' named entity 'stability' named entity 'structure' named entity 'site' covid:arg/c2ad458ccf62686e340e51ea95c439e7c4e2bc29 named entity 'CHANNEL' named entity 'INVESTIGATE' named entity 'STRONG' named entity 'DECOUPLE' named entity 'CHANNEL' named entity 'SITE' named entity 'THERMODYNAMIC STABILITY' named entity 'STABILITY' named entity 'MRNA' named entity 'EFFICIENCY' named entity 'RNA STEM-LOOP STRUCTURE' named entity 'IS PAUSED' named entity 'STEM-LOOP' named entity 'ROLE' named entity 'STABILITY' named entity 'EFFICIENCY' named entity 'DETERMINED BY' named entity 'FRAMESHIFT' named entity 'RIBOSOME' named entity 'IS A' named entity 'ALTERED' named entity 'INSERTION' named entity 'MODEST' named entity 'BASE PAIRS' named entity 'SECONDARY STRUCTURE' named entity 'SEQUENCE' named entity 'RATE' named entity 'CHANGE' named entity 'HIV-1' named entity 'ENTRANCE' named entity 'MRNA' named entity 'HUMAN IMMUNODEFICIENCY VIRUS' named entity 'AFFECTING' named entity 'LOCAL' named entity 'SPACER REGION' named entity 'CONTRAST' named entity 'BASE PAIRS' named entity 'CONSISTENT WITH' named entity 'HYPOTHESIS' named entity '3-4' named entity 'HERE' named entity 'RIBOSOME' named entity 'SURROUNDING' named entity 'IDENTITY' named entity 'HIV' named entity 'TRANSLATION' named entity 'OBSERVED' named entity 'HAVE' named entity 'OPENING' named entity 'RIBOSOMAL FRAMESHIFT' named entity 'OVERALL' named entity 'DOWNSTREAM' named entity 'PREDICTED' named entity 'POL GENE' named entity 'RESIDE' named entity 'frameshifting' named entity 'secondary structure' named entity 'thermodynamic stability'

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