Engineering genes for predictable protein expression (Q34198748)

31 July 2017

title

Engineering genes for predictable protein expression (English)

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31 July 2017

Claes Gustafsson

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31 July 2017

Jeremy Minshull

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31 July 2017

Sridhar Govindarajan

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31 July 2017

Jon Ness

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31 July 2017

Alan Villalobos

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31 July 2017

Mark Welch

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31 July 2017

publication date

8 March 2012

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Protein Expression and Purification

31 July 2017

published in

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31 July 2017

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31 July 2017

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31 July 2017

page(s)

37-46

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TAL effectors: customizable proteins for DNA targeting

31 July 2017

cites work

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RNA interference of cofilin in Chinese hamster ovary cells improves recombinant protein productivity

5 July 2018

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Ending the message: poly(A) signals then and now

5 July 2018

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Designing genes for successful protein expression

5 July 2018

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Codon usage: Nature's roadmap to expression and folding of proteins

5 July 2018

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MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

5 July 2018

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Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology

5 July 2018

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

5 July 2018

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Tagging recombinant proteins to enhance solubility and aid purification.

5 July 2018

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Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

5 July 2018

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Beyond directed evolution—semi-rational protein engineering and design

5 July 2018

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Creation of a bacterial cell controlled by a chemically synthesized genome

5 July 2018

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A role for codon order in translation dynamics.

5 July 2018

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Slowing bacterial translation speed enhances eukaryotic protein folding 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=3746766

Design parameters to control synthetic 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=3746766

Programming cells by multiplex genome engineering and accelerated evolution

5 July 2018

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Genome sequence of the recombinant protein production host Pichia pastoris

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

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=3746766

You're one in a googol: optimizing genes for 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=3746766

RNA interference technology to improve recombinant protein production in Chinese hamster ovary 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=3746766

Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

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=3746766

Preferred and avoided codon pairs in three domains of life

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

A high-throughput screen for hyaluronic acid accumulation in recombinant Escherichia coli transformed by libraries of engineered sigma factors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Analysis of the distribution of functionally relevant rare codons

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Following translation by single ribosomes one codon at a time.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Engineering proteinase K using machine learning and synthetic 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=3746766

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=3746766

Genetics. SNPs, silent but not invisible.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

The frequency of translational misreading errors in E. coli is largely determined by tRNA competition.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

SGDB: a database of synthetic genes re-designed for optimizing protein over-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=3746766

Gene Designer: a synthetic biology tool for constructing artificial DNA segments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Overexpression of tnaC of Escherichia coli inhibits growth by depleting tRNA2Pro availability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Phenotypic alteration and target gene identification using combinatorial libraries of zinc finger proteins in prokaryotic 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=3746766

Selective charging of tRNA isoacceptors induced by amino-acid starvation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

mRNA helicase activity of the ribosome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

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=3746766

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Putting engineering back into protein engineering: bioinformatic approaches to catalyst design.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Selective charging of tRNA isoacceptors explains patterns of 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=3746766

Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging 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=3746766

Simple and efficient method for heterologous expression of clostridial 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=3746766

Effects of a minor isoleucyl tRNA on heterologous protein translation 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=3746766

Quantitative sequence-activity models (QSAM)--tools for sequence design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Effects of rare codon clusters on high-level expression of heterologous proteins 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=3746766

Codon pair utilization biases influence translational elongation step times

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

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=3746766

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=3746766

Influences of mRNA secondary structure on initiation by eukaryotic 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=3746766

Translation of the sequence AGG-AGG yields 50% ribosomal frameshift

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Codon contexts from weakly expressed genes reduce expression 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=3746766

Relationship between protein synthesis and concentrations of charged and uncharged tRNATrp 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=3746766

RNA editing by cytidine insertion in mitochondria of Physarum polycephalum

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth 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=3746766

Rare codons play a positive role in the expression of the stationary phase sigma factor RpoS (σ(S)) 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=3746766

Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Unfolding of mRNA secondary structure by the bacterial translation initiation complex

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Amino acid content of recombinant proteins influences the metabolic burden response

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Limitations of codon adaptation index and other coding DNA-based features for prediction of protein expression in Saccharomyces cerevisiae.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squares

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

The pair of arginine codons AGA AGG close to the initiation codon of the lambda int gene inhibits cell growth and protein synthesis by accumulating peptidyl-tRNAArg4.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Codon pairs in the genome of Escherichia coli

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Exploring relationships in gene expressions: a partial least squares approach.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Structured model to predict intracellular amino acid shortages during recombinant protein overexpression in E. coli

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Absence of effect of varying Thr-Leu codon pairs on protein synthesis in a T7 system

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3746766

Increased levels of recombinant human proteins with the Escherichia coli strain Rosetta(DE3)

28 October 2018

1 reference

12 December 2020

Enhancing the protein production levels in Escherichia coli with a strong promoter

1 reference

12 December 2020

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

1 reference

12 December 2020

Codon usage determines translation rate in Escherichia coli

1 reference

12 December 2020

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

1 reference

12 December 2020

10.1016/J.PEP.2012.02.013

Identifiers

DOI

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31 July 2017

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31 July 2017

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