title: Comprehensive sequence analysis of translation termination sites in various eukaryotes.
abstract: Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation efficiency, as predicted according to Codon Adaptation Index (CAI) value. We used RIKEN full-length mouse cDNA sequences and ten other eukaryotic UniGene datasets from NCBI for the analyses. First, we conducted sequence profile analyses following translation termination sites. We found base G and A at position +1 as a strong consensus for mouse cDNA. A similar consensus was found for other mammals, such as Homo sapiens, Rattus norvegicus and Bos taurus. However, some plants had different consensus sequences. We then analysed the correlation between the strength of consensus at each position and the codon biases of whole coding regions, using information content and CAI value. The results showed that in mouse cDNA, CAI value had a positive correlation with information content at positions +1. We also found that, for positions with strong consensus, the strength of the consensus is likely to have a positive correlation with CAI value in some other eukaryotes. Along with these observations, biological insights into the relationship between gene expression level, codon biases and consensus sequence around stop codons will be discussed.
authors.affiliation: Institute for Advanced Biosciences, Keio University, 5322 Endo, Fujisawa, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Ozawa
authors.forename: S
authors.initials: S
authors.lastname: Hanaoka
authors.forename: R
authors.initials: R
authors.lastname: Saito
authors.forename: T
authors.initials: T
authors.lastname: Washio
authors.forename: S
authors.initials: S
authors.lastname: Nakano
authors.forename: A
authors.initials: A
authors.lastname: Shinagawa
authors.forename: M
authors.initials: M
authors.lastname: Itoh
authors.forename: K
authors.initials: K
authors.lastname: Shibata
authors.forename: P
authors.initials: P
authors.lastname: Carninci
authors.forename: H
authors.initials: H
authors.lastname: Konno
authors.forename: J
authors.initials: J
authors.lastname: Kawai
authors.forename: Y
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: M
authors.initials: M
authors.lastname: Tomita
mesh_terms: D020413:3' Untranslated Regions / Q000737:chemistry / Q000235:genetics; D000818:Animals; D001482:Base Composition; D005057:Eukaryotic Cells / Q000378:metabolism*; D006801:Humans; D010944:Plants / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D051381:Rats; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D020413:3' Untranslated Regions