title: Codon influence on protein expression in E. coli correlates with mRNA levels.
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.
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.|CNRS FRE3630, Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Grégory
authors.initials: G
authors.lastname: Boël
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Reka
authors.initials: R
authors.lastname: Letso
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Helen
authors.initials: H
authors.lastname: Neely
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: W Nicholson
authors.initials: WN
authors.lastname: Price
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Kam-Ho
authors.initials: KH
authors.lastname: Wong
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Min
authors.initials: M
authors.lastname: Su
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Jon
authors.initials: J
authors.lastname: Luff
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Mayank
authors.initials: M
authors.lastname: Valecha
authors.affiliation: Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.|Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: John K
authors.initials: JK
authors.lastname: Everett
authors.affiliation: Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.|Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Acton
authors.affiliation: Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.|Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Rong
authors.initials: R
authors.lastname: Xiao
authors.affiliation: Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.|Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.|Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: Gaetano T
authors.initials: GT
authors.lastname: Montelione
authors.affiliation: Department of Physics, Williams College, Williamstown, MA 01267, USA.
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Aalberts
authors.affiliation: Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA.|Northeast Structural Genomics Consortium; Institut de Biologie Physico-Chimique, 13-rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: John F
authors.initials: JF
authors.lastname: Hunt
mesh_terms: D003062:Codon / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D005813:Genes, Synthetic / Q000235:genetics; D006207:Half-Life; D007700:Kinetics; D016015:Logistic Models; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016017:Odds Ratio; D010441:Peptide Chain Elongation, Translational; D014176:Protein Biosynthesis / Q000235:genetics*; D059370:RNA Folding; D020871:RNA Stability; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000235:genetics; D014764:Viral Proteins / Q000378:metabolism
chemical_list: D003062:Codon; D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger; D014764:Viral Proteins; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases