Codon adaptation–based control of protein expression in C. elegans

We present a method to control protein levels under native genetic regulation in Caenorhabditis elegans by using synthetic genes with adapted codons. We found that the force acting on the spindle in C. elegans embryos was related to the amount of the G-protein regulator GPR-1/2. Codon-adapted versions of any C. elegans gene can be designed using our web tool, C. elegans codon adapter.

[1]  Elizabeth Casey,et al.  Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. , 2001, Genetics.

[2]  R. Waterston,et al.  Cloning, sequencing, and mapping of an α-actinin gene from the nematode Caenorhabditis elegans , 1991 .

[3]  Alessandra Carbone,et al.  Codon adaptation index as a measure of dominating codon bias , 2003, Bioinform..

[4]  S. Brenner The genetics of Caenorhabditis elegans. , 1974, Genetics.

[5]  Anthony A. Hyman,et al.  Polarity controls forces governing asymmetric spindle positioning in the Caenorhabditis elegans embryo , 2001, Nature.

[6]  S. Knudsen,et al.  Prediction of human mRNA donor and acceptor sites from the DNA sequence. , 1991, Journal of molecular biology.

[7]  Pierre Gönczy,et al.  Translation of Polarity Cues into Asymmetric Spindle Positioning in Caenorhabditis elegans Embryos , 2003, Science.

[8]  P. Sharp,et al.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. , 1987, Nucleic acids research.

[9]  P. Zipperlen,et al.  Functional genomic analysis of C. elegans chromosome I by systematic RNA interference , 2000, Nature.

[10]  Gang Wu,et al.  The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression. , 2006, Protein expression and purification.

[11]  S. van den Heuvel,et al.  A complex of LIN-5 and GPR proteins regulates G protein signaling and spindle function in C elegans. , 2003, Genes & development.

[12]  Peter G. Korning,et al.  Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. , 1996, Nucleic acids research.

[13]  J. Ahringer,et al.  Asymmetrically Distributed C. elegans Homologs of AGS3/PINS Control Spindle Position in the Early Embryo , 2003, Current Biology.

[14]  Jonathon Howard,et al.  The Distribution of Active Force Generators Controls Mitotic Spindle Position , 2003, Science.

[15]  Andreas Henschel,et al.  DEQOR: a web-based tool for the design and quality control of siRNAs , 2004, Nucleic Acids Res..

[16]  L. Duret,et al.  tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. , 2000, Trends in genetics : TIG.

[17]  Anthony A. Hyman,et al.  Spindle Oscillations during Asymmetric Cell Division Require a Threshold Number of Active Cortical Force Generators , 2006, Current Biology.

[18]  A. Hyman,et al.  LET-99, GOA-1/GPA-16, and GPR-1/2 Are Required for Aster-Positioned Cytokinesis , 2007, Current Biology.

[19]  C. Kurland,et al.  Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. , 1996, Journal of molecular biology.

[20]  David Tollervey,et al.  Coding-Sequence Determinants of Gene Expression in Escherichia coli , 2009, Science.

[21]  Y. Dong,et al.  Systematic functional analysis of the Caenorhabditis elegans genome using RNAi , 2003, Nature.

[22]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[23]  David E Hill,et al.  Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. , 2004, Genome research.