Frequency Distribution And The Effect On Translation Initiation Of Triplet AUG In 5'UTR

When translation initiate, the ribosome will first combine to the ribosome-binding site in 5' untranslated region (5' UTR) of mRNA, so the compositional features of 5' UTR have strong effect on translation initiation. In this paper, the statistical method was used to study the effect on translation initiation of triplet AUGs in 5' UTR.The first part of the paper analyse the frequency distribution of triplet AUGs in the three reading frames respectively. There is a significant AUG depletion in reading frame 1 in both bacterial and archaeal genomes. Contrary to AUG depletion, the frequency of triplet UAAs in frame 1 increases obviously near the start codon compared with the distributions in frame 2 and 3. It is assumed that this special distribution of AUGs and UAAs is one of the mechanisms to keep protein coding genes away from incorrect translation initiation and improve the translation efficiency.In the second part of the paper, triplet AUGs were classified by the form of existence. 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 are upstream AUGs (uAUGs) which have no in-frame stop codon in the upstream sequences, especially in reading frame 1. In bacterial genomes, more uAUGs in reading frame 1 can be found in the genes having Shine-Dalgarno sequence. Further analyses show synonymous codon usage bias is weaker of the sequences leading by uAUGs than the codon sequences. This may be an indication that the synonymous codon usage bias is an important determinant of translation initiation in bacteria and archaea.