In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations

Yoshiaki Ohashi, Akiko Yamashiro, Takanori Washio, Nobuyoshi Ishii, Hideyuki Ohshima, Tetsuko Michishita, Masaru Tomita, Mitsuhiro Itaya

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish
Pages (from-to)11-19
Number of pages9
JournalGene
Volume347
Issue number1
DOIs
Publication statusPublished - 2005 Feb 28

Fingerprint

Codon
Computer Simulation
Gene Expression
Escherichia coli
Genes
Dominant Genes
Initiator Codon
Green Fluorescent Proteins
Software
Proteins
red fluorescent protein

Keywords

  • DsRed
  • Escherichia coli
  • Genetic algorithm
  • Green fluorescent protein
  • Translation

ASJC Scopus subject areas

  • Genetics

Cite this

Ohashi, Y., Yamashiro, A., Washio, T., Ishii, N., Ohshima, H., Michishita, T., ... Itaya, M. (2005). In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations. Gene, 347(1), 11-19. https://doi.org/10.1016/j.gene.2004.11.027

In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations. / Ohashi, Yoshiaki; Yamashiro, Akiko; Washio, Takanori; Ishii, Nobuyoshi; Ohshima, Hideyuki; Michishita, Tetsuko; Tomita, Masaru; Itaya, Mitsuhiro.

In: Gene, Vol. 347, No. 1, 28.02.2005, p. 11-19.

Research output: Contribution to journalArticle

Ohashi, Y, Yamashiro, A, Washio, T, Ishii, N, Ohshima, H, Michishita, T, Tomita, M & Itaya, M 2005, 'In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations', Gene, vol. 347, no. 1, pp. 11-19. https://doi.org/10.1016/j.gene.2004.11.027
Ohashi Y, Yamashiro A, Washio T, Ishii N, Ohshima H, Michishita T et al. In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations. Gene. 2005 Feb 28;347(1):11-19. https://doi.org/10.1016/j.gene.2004.11.027
Ohashi, Yoshiaki ; Yamashiro, Akiko ; Washio, Takanori ; Ishii, Nobuyoshi ; Ohshima, Hideyuki ; Michishita, Tetsuko ; Tomita, Masaru ; Itaya, Mitsuhiro. / In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations. In: Gene. 2005 ; Vol. 347, No. 1. pp. 11-19.
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