About: Polysomes Bypass a 50 Nucleotide Coding Gap less Efficiently than Monosomes Due to Attenuation of a 5’ mRNA Stem Loop and Enhanced Drop-off

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About: Polysomes Bypass a 50 Nucleotide Coding Gap less Efficiently than Monosomes Due to Attenuation of a 5’ mRNA Stem Loop and Enhanced Drop-off 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	Polysomes Bypass a 50 Nucleotide Coding Gap less Efficiently than Monosomes Due to Attenuation of a 5’ mRNA Stem Loop and Enhanced Drop-off
Creator	Samatova, Ekaterina Klimova, Mariia Loughran, Gary Atkins, John Baranov, Pavel Rodnina, Marina Weissman, Jonathan Wills, Norma Puglisi, Joseph Capece, Mark Coakley, Arthur O'connor, Patrick O'loughlin, Sinéad
source	Elsevier; Medline; PMC
abstract	Efficient translational bypassing of a 50 nt non-coding gap in a phage T4 topoisomerase subunit gene (gp60) requires several recoding signals. Here we investigate the function of the mRNA stem loop 5′ of the take-off codon, as well as the importance of ribosome loading density on the mRNA for efficient bypassing. We show that polysomes are less efficient at mediating bypassing than monosomes, both in vitro and in vivo, due to their preventing formation of a stem loop 5′ of the take-off codon and allowing greater peptidyl-tRNA drop off. A ribosome profiling analysis of phage T4 infected E. coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. However, ribosomes at this position also yielded some 53 nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5′ stem loop. NMR shows that the 5′ stem loop is highly dynamic. The importance of different nucleotides in the 5′ stem loop is revealed by mutagenesis studies. These data highlight the significance of the 5′ stem loop for the 50 nt bypassing, and further enhance appreciation of relevance of the extent of ribosome loading for recoding.
has issue date	2020-05-23(xsd:dateTime)
bibo:doi	10.1016/j.jmb.2020.05.010
bibo:pmid	32454154
has license	no-cc
sha1sum (hex)	3c643c7dfd1383dcb16e4ef5e98b208b58483ef7
schema:url	https://doi.org/10.1016/j.jmb.2020.05.010
resource representing a document's title	Polysomes Bypass a 50 Nucleotide Coding Gap less Efficiently than Monosomes Due to Attenuation of a 5’ mRNA Stem Loop and Enhanced Drop-off
has PubMed Central identifier	PMC7245268
has PubMed identifier	32454154
schema:publication	J Mol Biol
resource representing a document's body	covid:3c643c7dfd1383dcb16e4ef5e98b208b58483ef7#body_text
is schema:about of	named entity 'Bypass' named entity 'Enhanced' named entity 'Stem' named entity 'mRNA' named entity 'Polysomes' named entity 'Stem Loop' named entity 'structural analysis' named entity 'ribosomal subunits' named entity 'MNase' named entity 'nucleotide' named entity 'ribosome' named entity 'SHAPE' named entity 'NMR experiments' named entity 'S3C' named entity 'amino acids' named entity 'tetraloop' named entity 'RNase' named entity 'wild-type' named entity 'heterologous expression' named entity 'RNA' named entity 'Shine Dalgarno' named entity 'vector' named entity 'ribosome' named entity 'complete synthesis' named entity 'peptide signal' named entity 'leading edge' named entity 'vector' named entity 'cleavage' named entity 'mRNA' named entity 'fluorescent label' named entity 'mRNA' named entity 'compensatory mutations' named entity 'ribosomes' named entity 'E. coli' named entity 'translation initiation' named entity 'plasmid-borne' named entity 'Crick' named entity 'ribosome' named entity 'ribosome' named entity 'SHAPE analysis' named entity 'ribosome' named entity 'stop codons' named entity 'ribosome' named entity 'ribonuclease' named entity 'NMR' named entity 'codons' named entity 'protein' named entity 'codon' named entity '16S rRNA' named entity 'translational machinery' named entity 'ribosome' named entity 'gene' named entity 'KKYK' named entity 'vectors' named entity 'ribosome' named entity 'Cricket Paralysis virus' named entity 'A-site' named entity 'Arg' named entity 'ribosome' named entity 'initiation factors' named entity 'ribosome' named entity 'cryoEM' named entity 'codon' named entity 'codon' named entity 'translational machinery' named entity 'homing endonuclease gene' named entity 'cleavage' named entity 'ribosome' named entity 'oligonucleotide'

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