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Nucleic Acids Research 2005 33(Web Server Issue):W526-W531; doi:10.1093/nar/gki376
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host

Andreas Grote1,2, Karsten Hiller1, Maurice Scheer1,3, Richard Münch1, Bernd Nörtemann2, Dietmar C. Hempel2 and Dieter Jahn1,*

1Institut für Mikrobiologie, Spielmannstraße 7, Technische Universität Braunschweig D-38106 Braunschweig, Germany 2Institut für Bioverfahrenstechnik, Gaußstraße 17, Technische Universität Braunschweig D-38106 Braunschweig, Germany 3Fachbereich für Informatik, Am Exer 2, Fachhochschule Wolfenbüttel D-38302 Wolfenbüttel, Germany

*To whom correspondence should be addressed. Tel: +49 531 391 5801; Fax: +49 531 391 5854; Email: d.jahn{at}tu-bs.de

Received February 11, 2005. Revised March 7, 2005. Accepted March 7, 2005.

A novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production. In contrast to existing tools, JCat (Java Codon Adaptation Tool) does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method. Further options of JCat for codon adaptation include the avoidance of unwanted cleavage sites for restriction enzymes and Rho-independent transcription terminators. The output of JCat is both graphically and as Codon Adaptation Index (CAI) values given for the pasted sequence and the newly adapted sequence. Additionally, a list of genes in FASTA-format can be uploaded to calculate CAI values. In one example, all genes of the genome of Caenorhabditis elegans were adapted to Escherichia coli codon usage and further optimized to avoid commonly used restriction sites. In a second example, the Pseudomonas aeruginosa exbD gene codon usage was adapted to E.coli codon usage with parallel avoidance of the same restriction sites. For both, the degree of introduced changes was documented and evaluated. JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations. JCat is freely accessible at http://www.prodoric.de/JCat.


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