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

TLDR

The study develops a novel method to adapt target gene codon usage for improved heterologous protein production in diverse prokaryotic and selected eukaryotic hosts. JCat, a Java Codon Adaptation Tool, automatically adapts codon usage—without requiring manual definition of highly expressed genes—while allowing avoidance of restriction sites and transcription terminators, and outputs graphical and CAI values, with support for FASTA lists and integration into the PRODORIC database. The tool successfully adapted the entire *C. elegans* genome and the *P.

Abstract

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.