Evidence map›Paper›PMID 40133777›Full record

ArticleJournal of molecular biology2025

OPT: Codon optimize gene sequences for E. coli protein overexpression.

Daniel P H Wong, Kam-Ho Wong, Sunjae Park, Grégory Boël, John F Hunt, Daniel P Aalberts

Abstract read
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In one paragraph

Article in Journal of molecular biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Daniel P H WongPhysics Department, Williams College, Williamstown, MA 01267, USA.
Kam-Ho WongDepartment of Biological Sciences, Columbia University, New York, NY 10027, USA.
Sunjae ParkDepartment of Biological Sciences, Columbia University, New York, NY 10027, USA.
Grégory BoëlExpression Génétique Microbienne, CNRS, Universite Paris Cite, Institut de Biologie Physio-Chimique, F-75005 Paris, France. Electronic address: boel@ibpc.fr.
John F HuntDepartment of Biological Sciences, Columbia University, New York, NY 10027, USA. Electronic address: jfh21@columbia.edu.
Daniel P AalbertsPhysics Department, Williams College, Williamstown, MA 01267, USA. Electronic address: aalberts@williams.edu.

Funding

University of Georgia ProjectU54GM094597 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI MONTELIONE, GAETANO T · 2010 to 2014
$36.9M
AREA: Optimizing gene expression with mRNA free energy modeling and algorithmsR15GM106372 · NIGMS · WILLIAMS COLLEGE · PI AALBERTS, DANIEL PAUL · 2014 to 2014
$255k
NIGMS NIH HHS R15 GM106372NIGMS NIH HHS U54 GM094597
6 · The paper itself

Abstract

The ability to overexpress proteins is valuable for biotechnology, but not all sequences are compatible with high yield. We previously analyzed the sequence features and mRNA folding stability of a large data set of 6,384 distinct gene constructs, and developed a model for protein yield. Our OPT.williams.edu server (1) predicts the probability an input sequence will produce protein at a high level when overexpressed in E. coli, and (2) returns optimized synonymous sequences designed to boost protein expression. Here we also present experimental evidence of the high yields of our OPT constructs for eight commercially produced proteins.

Indexed as

CodonEscherichia coliEscherichia coli ProteinsGene ExpressionRNA, MessengerCodonEscherichia coli ProteinsRNA, Messengerprotein productionsynonymous codons

Identifiers

PMID40133777
PMCPMC12145263

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.