FREQUENCY DISTRIBUTION AND THE EFFECT ON TRANSLATION INITIATION OF TRIPLET AUG IN 5′UTR

Set three reading frames artificially in 5′ untranslated region (5′ UTR) of bacterial and archaeal genomes and analyse the frequencies distribution of triplet AUG in the three reading frames respectively. There is an obviously AUG depletion in reading frame 1 in both bacterial and archaeal genomes. AUG depletion may be an indication that upstream AUG can probably disturb the translation initiation of bacteria and archaea. The authors found that majority of AUGs in the upstream sequences have in-frame stop codons in the upstream sequences and form upstream open reading frame (uORF), only a fraction of AUGs in the upstream have no in-frame stop codon in the upstream sequences, especially in reading frame 1. The authors call them upstream AUGs (uAUGs). In bacterial genomes, more uAUGs in reading frame 1 can be found in the genes having a Shine-Dalgarno sequence. Further analyses show synonymous codon usage bias is weaker of the sequences leading by uAUGs than the codon sequences. It may be an indication that the synonymous codon usage bias is an important determinant of translation initiation accurately in bacteria and archaea.