Nucleic Acids Research, 2003, Vol. 31, No. 17 5195-5201
© 2003 Oxford University Press
Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan and 1 Proteios Research Inc., 1111, Tebiro, Kamakura, Kanagawa 248-8555, Japan
*To whom correspondence should be addressed at present address. Tel: +1 814 863 7334; Fax: +1 814 863 7336; Email: nxy10{at}psu.edu
Present address:
Yoshihito Niimura, Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802, USA
Adenine nucleotides have been found to appear preferentially in the regions after the initiation codons or before the termination codons of bacterial genes. Our previous experiments showed that AAA and AAT, the two most frequent second codons in Escherichia coli, significantly enhance translation efficiency. To determine whether such a characteristic feature of base frequencies exists in eukaryote genes, we performed a comparative analysis of the base biases at the gene terminal portions using the proteomes of seven eukaryotes. Here we show that the base appearance at the codon third positions of gene terminal regions is highly biased in eukaryote genomes, although the codon third positions are almost free from amino acid preference. The bias changes depending on its position in a gene, and is characteristic of each species. We also found that bias is most outstanding at the second codon, the codon after the initiation codon. NCN is preferred in every genome; in particular, GCG is strongly favored in human and plant genes. The presence of the bias implies that the base sequences at the second codon affect translation efficiency in eukaryotes as well as bacteria.
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