About: Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication

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About: Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication 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
title	Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication
Creator	Leibowitz, Julian Liu, Pinghua Li, Lichun Kang, Hyojeung Giedroc, David Makkinje, Nick Williamson, Shawn
source	Elsevier; Medline; PMC
abstract	The leader RNA of the 5' untranslated region (UTR) of coronaviral genomes contains two stem-loop structures denoted SL1 and SL2. Herein, we show that SL1 is functionally and structurally bipartite. While the upper region of SL1 is required to be paired, we observe strong genetic selection against viruses that contain a deletion of A35, an extrahelical nucleotide that destabilizes SL1, in favor of genomes that contain a diverse panel of destabilizing second-site mutations, due to introduction of a non-canonical base pair near A35. Viruses containing destabilizing SL1-ΔA35 mutations also contain one of two specific mutations in the 3' UTR. Thermal denaturation and imino proton solvent exchange experiments reveal that the lower half of SL1 is unstable and that second-site SL1-ΔA35 substitutions are characterized by one or more features of the wild-type SL1. We propose a %22dynamic SL1%22 model, in which the base of SL1 has an optimized lability required to mediate a physical interaction between the 5' and 3' UTRs that stimulates subgenomic RNA synthesis. Although not conserved at the nucleotide sequence level, these general structural characteristics of SL1 appear to be conserved in other coronaviral genomes.
has issue date	2008-03-01(xsd:dateTime)
bibo:doi	10.1016/j.jmb.2008.01.068
bibo:pmid	18289557
has license	bronze-oa
sha1sum (hex)	d8a4109ac8947b1e80df71baa59c1689e801a2d5
schema:url	https://doi.org/10.1016/j.jmb.2008.01.068
resource representing a document's title	Structural lability in stem-loop 1 drives a 5' UTR-3' UTR interaction in coronavirus replication
has PubMed Central identifier	PMC2652258
has PubMed identifier	18289557
schema:publication	Journal of Molecular Biology
resource representing a document's body	covid:d8a4109ac8947b1e80df71baa59c1689e801a2d5#body_text
is schema:about of	named entity 'INTERACTION' named entity 'DRIVES' named entity 'While' named entity 'Although' named entity 'A35' named entity 'nucleotide sequence' named entity 'A35' named entity 'DUE TO' named entity 'PROTON' named entity 'SPECIFIC' named entity 'UPPER REGION' named entity 'MODEL' named entity 'CONTAIN' named entity 'INTRODUCTION' named entity 'STRONG' named entity 'HALF' named entity 'EXPERIMENTS' named entity 'IMINO' named entity 'LEVEL' named entity 'RNA' named entity 'THERMAL' named entity 'CANONICAL BASE PAIR' named entity 'SL1' named entity 'APPEAR' named entity 'OBSERVE' named entity 'FEATURES' named entity 'EXCHANGE' named entity 'BASE' named entity 'A35' named entity 'STEM-LOOP' named entity 'GENOMES' named entity 'FAVOR' named entity 'WILD-TYPE' named entity 'UTR' named entity 'PANEL' named entity 'SOLVENT' named entity 'RNA SYNTHESIS' named entity 'GENERAL' named entity 'UNSTABLE' named entity 'CHARACTERIZED' named entity 'MEDIATE' named entity 'LOWER' named entity 'NUCLEOTIDE SEQUENCE' named entity 'CHARACTERISTICS' named entity 'ONE OF' named entity 'STRUCTURAL' named entity 'DELETION' named entity 'SL2' named entity 'STRUCTURES' named entity 'NEAR' named entity 'GENETIC SELECTION' named entity 'SECOND' named entity 'CONTAINS' named entity 'STRUCTURAL' named entity 'NON-' named entity 'CONSERVED' named entity 'DIVERSE' named entity 'SITE' named entity 'DENATURATION' named entity 'UNTRANSLATED REGION' named entity 'NUCLEOTIDE' named entity 'VIRUSES' named entity 'PAIRED' named entity 'CONTAINING' named entity 'PHYSICAL INTERACTION' named entity 'REVEAL' named entity 'REQUIRED' named entity 'THESE' named entity 'BIPARTITE' named entity 'MUTATIONS' named entity 'UTR' named entity 'STEM-LOOP' covid:arg/d8a4109ac8947b1e80df71baa59c1689e801a2d5 named entity 'Viruses' named entity 'conserved'

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