The effect of tRNA levels on decoding times of mRNA codons (Q34044490)

30 July 2017

The effect of tRNA levels on decoding times of mRNA codons (English)

1 reference

30 July 2017

Tamir Tuller

2

0 references

author name string

Alexandra Dana

series ordinal

1

1 reference

PubMed ID

25056313

30 July 2017

language of work or name

English

0 references

publication date

23 July 2014

1 reference

30 July 2017

Nucleic Acids Research

1 reference

30 July 2017

42

1 reference

30 July 2017

14

1 reference

30 July 2017

9171-9181

1 reference

Creative Commons Attribution-NonCommercial 4.0 International

30 July 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Modelling the efficiency of codon-tRNA interactions based on codon usage bias

1 reference

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Translation elongation can control translation initiation on eukaryotic mRNAs

5 July 2018

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New universal rules of eukaryotic translation initiation fidelity

5 July 2018

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rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

5 July 2018

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Positively charged residues are the major determinants of ribosomal velocity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

5 July 2018

1 reference

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Non-optimal codon usage is a mechanism to achieve circadian clock conditionality.

5 July 2018

1 reference

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Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

5 July 2018

1 reference

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The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Speeding with control: codon usage, tRNAs, and ribosomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Balanced codon usage optimizes eukaryotic translational efficiency

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

A role for tRNA modifications in genome structure and codon usage

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Characterization of exponentially modified Gaussian peaks in chromatography

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Strong association between mRNA folding strength and protein abundance in S. cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Composite effects of gene determinants on the translation speed and density of ribosomes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Understanding the contribution of synonymous mutations to human disease

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Global quantification of mammalian gene expression control

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Folding at the birth of the nascent chain: coordinating translation with co-translational folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Synonymous but not the same: the causes and consequences of codon bias

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Genome-wide translational profiling by ribosome footprinting

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

On relevance of codon usage to expression of synthetic and natural genes in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

A role for codon order in translation dynamics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Translation efficiency is determined by both codon bias and folding energy

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

The mechanism of eukaryotic translation initiation and principles of its regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Coding-sequence determinants of gene expression in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

A pause for thought along the co-translational folding pathway

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Electrostatics in the ribosomal tunnel modulate chain elongation rates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Tissue-specific differences in human transfer RNA expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

A "silent" polymorphism in the MDR1 gene changes substrate specificity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Using annotated peptide mass spectrum libraries for protein identification

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Hearing silence: non-neutral evolution at synonymous sites in mammals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Solving the riddle of codon usage preferences: a test for translational selection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Codon bias and heterologous protein expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Hierarchy of sequence-dependent features associated with prokaryotic translation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Global analysis of protein expression in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Precision and functional specificity in mRNA decay

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Cotranslational protein folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Translational efficiency is regulated by the length of the 3' untranslated region

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Quantities of individual aminoacyl-tRNA families and their turnover in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Codon usage and tRNA content in unicellular and multicellular organisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Coevolution of codon usage and transfer RNA abundance

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Ribosome motions modulate electrostatic properties

5 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU646

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU646

A new look at the statistical model identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU646

Totally asymmetric exclusion process with extended objects: A model for protein synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU646

Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU646

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU646

Prediction of variable translation rate effects on cotranslational protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU646

Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4132755

Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting tran

28 October 2018

1 reference

12 December 2020

Study of faecal shedding of Clostridium difficile in horses treated with penicillin

1 reference

12 December 2020

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes

1 reference

12 December 2020

Concerted action of the ribosome and the associated chaperone trigger factor confines nascent polypeptide folding

1 reference

12 December 2020

Kinetics of translation of gamma B crystallin and its circularly permutated variant in an in vitro cell-free system: possible relations to codon distribution and protein folding

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKU646

1 reference

30 July 2017

1 reference

30 July 2017

1 reference

PubMed ID

25056313