title: In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations.
abstract: The translation start site, immediately downstream from the start codon, is a dominant factor for gene expression in Escherichia coli. At present, no method exists to improve the expression level of cloned genes, since it remains difficult to find the best codon combination within the region. We determined the expression parameters that correspond to all sense codons within the first four codons using GFPuv which encodes a derivative of green fluorescent protein. Using a genetic algorithm (GA)-based computer program, these parameters were incorporated in a simple, static model for the prediction of translation efficiency, and optimized to the expression level for 137 randomly isolated GFPuv genes. The calculated initial translation index (ITI), also proven for the DsRed2 gene that encodes a red fluorescent protein, should provide a solution to overcome the gene expression problem in cloned genes whose expression is often inherently blocked at the translation process. The proposed method facilitates heterologous protein production in E. coli, the most commonly used host in biological and industrial fields.
authors.affiliation: Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Ohashi
authors.forename: Akiko
authors.initials: A
authors.lastname: Yamashiro
authors.forename: Takanori
authors.initials: T
authors.lastname: Washio
authors.forename: Nobuyoshi
authors.initials: N
authors.lastname: Ishii
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Ohshima
authors.forename: Tetsuko
authors.initials: T
authors.lastname: Michishita
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Itaya
mesh_terms: D003001:Cloning, Molecular; D003062:Codon / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D015870:Gene Expression / Q000235:genetics*; D049452:Green Fluorescent Proteins / Q000235:genetics; D008957:Models, Genetic; D014176:Protein Biosynthesis / Q000235:genetics*; D011994:Recombinant Proteins / Q000235:genetics
chemical_list: D003062:Codon; D011994:Recombinant Proteins; D049452:Green Fluorescent Proteins