Codon influence on protein expression in E. coli correlates with mRNA levels (Q37319891)

19 August 2017

Codon influence on protein expression in E. coli correlates with mRNA levels (English)

1 reference

19 August 2017

0 references

Gaetano T. Montelione

12

object named as

Gaetano T Montelione

1 reference

19 August 2017

Grégory Boël

1

1 reference

19 August 2017

Reka Letso

2

1 reference

19 August 2017

Helen Neely

3

1 reference

19 August 2017

W Nicholson Price

4

1 reference

19 August 2017

Kam-Ho Wong

5

1 reference

19 August 2017

Min Su

6

1 reference

19 August 2017

Jon Luff

7

1 reference

19 August 2017

Mayank Valecha

8

1 reference

19 August 2017

John K Everett

9

1 reference

19 August 2017

Thomas B Acton

10

1 reference

19 August 2017

Rong Xiao

11

1 reference

19 August 2017

Daniel P Aalberts

13

1 reference

19 August 2017

John F Hunt

14

1 reference

19 August 2017

language of work or name

English

0 references

publication date

13 January 2016

1 reference

19 August 2017

1 reference

19 August 2017

529

1 reference

19 August 2017

7586

1 reference

19 August 2017

358-363

1 reference

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

The effect of tRNA levels on decoding times of mRNA codons

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Causes and effects of N-terminal codon bias in bacterial genes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Differential translation tunes uneven production of operon-encoded proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Efficient translation initiation dictates codon usage at gene start

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Estimating selection on synonymous codon usage from noisy experimental data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

EcoCyc: fusing model organism databases with systems biology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Large-scale experimental studies show unexpected amino acid effects on protein expression and solubility in vivo in E. coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Determinants of translation efficiency and accuracy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Preparation of protein samples for NMR structure, function, and small-molecule screening studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Differential arginylation of actin isoforms is regulated by coding sequence-dependent degradation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

A role for codon order in translation dynamics.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

An evolutionarily conserved mechanism for controlling the efficiency of protein translation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

RNAstructure: software for RNA secondary structure prediction and analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Translation efficiency is determined by both codon bias and folding energy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Coding-sequence determinants of gene expression in Escherichia coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Electrostatics in the ribosomal tunnel modulate chain elongation rates

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Quality control of bacterial mRNA decoding and decay

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Protein abundance profiling of the Escherichia coli cytosol

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

tmRNA-induced release of messenger RNA from stalled ribosomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Selective charging of tRNA isoacceptors induced by amino-acid starvation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Prediction of lipoprotein signal peptides in Gram-negative bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Synonymous codon selection controls in vivo turnover and amount of mRNA in Escherichia coli bla and ompA genes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

The selection-mutation-drift theory of synonymous codon usage

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Bacteriophage T7 RNA polymerase travels far ahead of ribosomes in vivo

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Codon optimality is a major determinant of mRNA stability

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Translation of CGA codon repeats in yeast involves quality control components and ribosomal protein L1.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Selective charging of tRNA isoacceptors explains patterns of codon usage.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

High-level production of uniformly ¹⁵N- and ¹³C-enriched fusion proteins in Escherichia coli.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

The use of lac-type promoters in control analysis.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

RNA codons and protein synthesis. 15. Dissimilar responses of mammalian and bacterial transfer RNA fractions to messenger RNA codons

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Low-usage codons in Escherichia coli, yeast, fruit fly and primates

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Silent substitutions predictably alter translation elongation rates and protein folding efficiencies

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Protein synthesis factors (RF1, RF2, RF3, RRF, and tmRNA) and peptidyl-tRNA hydrolase rescue stalled ribosomes at sense codons.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Adenine-containing codons enhance protein synthesis by promoting mRNA binding to ribosomal 30S subunits provided that specific tRNAs are not exhausted.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5054687

Exposing synonymous mutations

2 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNATURE16509

A new look at the statistical model identification

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNATURE16509

Influence of duplexes 3' to the mRNA initiation codon on the efficiency of monosome formation

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26760206

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Fine tuning of ribosomal accuracy

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26760206

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Role of the AGA/AGG codons, the rarest codons in global gene expression in Escherichia coli

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26760206

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NATURE16509

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

26760206

1 reference