Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases.
In spite of many efforts, the prediction of the location of proteins in eukaryotic cells (cytoplasm, mitochondrion or chloroplast) is still far from straightforward. In some cases (e.g. ribosomal proteins and aminoacyl-tRNA synthetases) both the cytoplasmic proteins and their organellar counterparts are encoded by the nuclear genome. A factorial correspondence analysis of the codon usage in yeast and Caenorhabditis elegans shows that the codon usage of those nuclear genes encoding ribosomal proteins or aminoacyl-tRNA synthetases is markedly different, depending on the final location of the proteins (cytoplasmic or mitochondrial). As a consequence, the location of such proteins-whose sequences are now frequently determined by systematic genomic sequencing-can be easily and quickly predicted. A WWW interface has been developed, aimed at providing a user-friendly tool for codon usage pattern analysis. It is available from http://www.genetique.uvsq.fr/afc.html
Chiapello
H
H
INRA, Biologie Cellulaire, Route de Saint Cyr, 78026 Versailles Cedex, France. chiapell@genetique.uvsq.fr
Ollivier
E
E
Landès-Devauchelle
C
C
Nitschké
P
P
Risler
J L
JL
D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics / Q000378:metabolism*; D000818:Animals; D017360:Arabidopsis / Q000166:cytology / Q000201:enzymology / Q000235:genetics; D001692:Biological Transport; D017173:Caenorhabditis elegans / Q000166:cytology / Q000201:enzymology / Q000235:genetics; D002467:Cell Nucleus / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D003062:Codon / Q000235:genetics*; D003593:Cytoplasm / Q000201:enzymology / Q000378:metabolism; D005057:Eukaryotic Cells / Q000166:cytology / Q000201:enzymology / Q000378:metabolism*; D005800:Genes, Fungal / Q000235:genetics; D017238:Genes, Helminth / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D016678:Genome; D020407:Internet; D008928:Mitochondria / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D012984:Software
D003062:Codon; D012269:Ribosomal Proteins; D000604:Amino Acyl-tRNA Synthetases