Nature of selective constraints on synonymous codon usage of rice differs in GC-poor and GC-rich genes

Synonymous codon usage and cellular tRNA abundance are thought to be co-evolved in optimizing translational efficiencies in highly expressed genes. Here in this communication by taking the advantage of publicly available gene expression data of rice and Arabidopsis we demonstrated that tRNA gene cop...

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Bibliographic Details
Published in:Gene 2007-10, Vol.400 (1), p.71-81
Main Authors: Mukhopadhyay, Pamela, Basak, Surajit, Ghosh, Tapash Chandra
Format: Article
Language:English
Subjects:
Arabidopsis
Base Composition
Codon
Codon usage
Gene Dosage
Gene Expression Regulation, Plant
Genes, Plant
mRNA folding stability
Mutation
Oryza - genetics
Oryza sativa
Protein Biosynthesis
RNA, Transfer
Translational efficiencies
tRNA abundance
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Summary:Synonymous codon usage and cellular tRNA abundance are thought to be co-evolved in optimizing translational efficiencies in highly expressed genes. Here in this communication by taking the advantage of publicly available gene expression data of rice and Arabidopsis we demonstrated that tRNA gene copy number is not the only driving force favoring translational selection in all highly expressed genes of rice. We found that forces favoring translational selection differ between GC-rich and GC-poor classes of genes. Supporting our results we also showed that, in highly expressed genes of GC-poor class there is a perfect correspondence between majority of preferred codons and tRNA gene copy number that confers translational efficiencies to this group of genes. However, tRNA gene copy number is not fully consistent with models of translational selection in GC-rich group of genes, where constraints on mRNA secondary structure play a role to optimize codon usage in highly expressed genes.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2007.05.027