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| Status |
Public on Apr 01, 2009 |
| Title |
Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe. |
| Organism |
Schizosaccharomyces pombe |
| Experiment type |
Genome variation profiling by array
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| Summary |
Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon
usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans, but was
not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution.
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| Overall design |
Relative amounts of mRNA for each ORF were measured by DNA microarray using genomic DNA as a reference, and the copy number of mRNA was calculated using an estimate of the total mRNA number in the cell as 100,000 copies.
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| Contributor(s) |
Hiraoka Y, Kawamata K, Haraguchi T, Chikashige Y |
| Citation(s) |
19335619 |
| |
| Submission date |
Nov 11, 2008 |
| Last update date |
Jan 23, 2023 |
| Contact name |
Atsushi Matsuda |
| Organization name |
National Institute of Information and Communications Technology
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| Street address |
588-2, Iwaoka, Iwaoka-cho, Nishi-ku
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| City |
Kobe |
| ZIP/Postal code |
651-2492 |
| Country |
Japan |
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| Platforms (1) |
| GPL5577 |
KARC Schizosaccharomyces pombe 5K Ver. D2 ORF array |
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| Samples (1) |
| GSM341452 |
Relative amounts of mRNA for each ORF |
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| Relations |
| BioProject |
PRJNA110739 |
