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Nature. 2016 Jan 21;529(7586):358-363. doi: 10.1038/nature16509. Epub 2016 Jan 13.

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

Boël G1,2,3, Letso R#1,2, Neely H#1,2, Price WN#1,2, Wong KH1,2, Su M1,2, Luff J1,2, Valecha M1,2, Everett JK2,4, Acton TB2,4, Xiao R2,4, Montelione GT2,4,5, Aalberts DP6, Hunt JF1,2.

Author information

1
Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.
2
Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
3
CNRS FRE3630, Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
4
Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
5
Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
6
Department of Physics, Williams College, Williamstown, MA 01267, USA.
#
Contributed equally

Abstract

Degeneracy in the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, has an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyse the sequence features influencing protein expression levels in 6,348 experiments using bacteriophage T7 polymerase to synthesize messenger RNA in Escherichia coli. Logistic regression yields a new codon-influence metric that correlates only weakly with genomic codon-usage frequency, but strongly with global physiological protein concentrations and also mRNA concentrations and lifetimes in vivo. Overall, the codon content influences protein expression more strongly than mRNA-folding parameters, although the latter dominate in the initial ~16 codons. Genes redesigned based on our analyses are transcribed with unaltered efficiency but translated with higher efficiency in vitro. The less efficiently translated native sequences show greatly reduced mRNA levels in vivo. Our results suggest that codon content modulates a kinetic competition between protein elongation and mRNA degradation that is a central feature of the physiology and also possibly the regulation of translation in E. coli.

PMID:
26760206
PMCID:
PMC5054687
DOI:
10.1038/nature16509
[Indexed for MEDLINE]
Free PMC Article

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