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“Big Loser” codon pairs in E. coli have normal usage in other genomes
Author(s) -
Menninger John R
Publication year - 2006
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.20.4.a502-b
Subject(s) - open reading frame , biology , codon usage bias , transfer rna , genetics , start codon , ribosome , genome , genetic code , reading frame , base pair , stop codon , ribosomal rna , sequence (biology) , amino acid , dna , messenger rna , gene , rna , peptide sequence
The frequency of pairs of adjacent codons in the open reading frames of E. coli were compared with the number expected on the basis of the frequencies of the constituent codons. Seven pairs (“Big Losers”) that encode typical amino acids had minimum values, less than 0.07, of Observed/Expected ratios. The ratios of these pairs in three other microbial genomes ( B. subtilis , S. aureus , H. influenzae ) were generally closer to unity. The number of pairs with the reversed codon sequence was generally higher than the number of big loser pairs in E. coli open reading frames, as was the normalized numbers both of codon pairs with five‐out‐of‐six bases and of amino acid pairs that resulted from translating the big losers. The low Observed/Expected ratio of big losers cannot be explained by tRNA abundance nor by base sequence. Instead, the data suggested selection against these codon pairs during translation. When DNA sequences that specify the 16S rRNA and ribosomal proteins for the four species were aligned, there were eleven differences in residues that occur within 15 Å of the codon‐anticodon sites. These observations could be explained by the co‐evolution of mRNA sequences and ribosome structure.