AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site

Abstract

Background: The translation start site plays an important role in the control of translation efficiency of eukaryotic mRNAs. The recognition of the start AUG codon by eukaryotic ribosomes is considered to depend on its nucleotide context. However, the fraction of eukaryotic mRNAs with the start codon in a suboptimal context is relatively large. It may be expected that mRNA should possess some features providing efficient translation, including the proper recognition of a translation start site. It has been experimentally shown that a downstream hairpin located in certain positions with respect to start codon can compensate in part for the suboptimal AUG context and also increases translation from non-AUG initiation codons. Prediction of such a compensatory hairpin may be useful in the evaluation of eukaryotic mRNA translation properties.

Results: We evaluated interdependency between the start codon context and mRNA secondary structure at the CDS beginning: it was found that a suboptimal start codon context significantly correlated with higher base pairing probabilities at positions 13 - 17 of CDS of human and mouse mRNAs. It is likely that the downstream hairpins are used to enhance translation of some mammalian mRNAs in vivo. Thus, we have developed a tool, AUG_hairpin, to predict local stem-loop structures located within the defined region at the beginning of mRNA coding part. The implemented algorithm is based on the available published experimental data on the CDS-located stem-loop structures influencing the recognition of upstream start codons.

Conclusion: An occurrence of a potential secondary structure downstream of start AUG codon in a suboptimal context (or downstream of a potential non-AUG start codon) may provide researchers with a testable assumption on the presence of additional regulatory signal influencing mRNA translation initiation rate and the start codon choice. AUG_hairpin, which has a convenient Web-interface with adjustable parameters, will make such an evaluation easy and efficient.

Figure 1

Description of experiment reported by Kozak ([8]): The hairpin (inverted repeats are marked with bold type and yellow boxes) was placed at the distances of 5, 11, 17, and 35 nucleotides from the CDS beginning (marked with blue boxes).

Figure 2

Predicted local secondary structure at the CDS beginning of Agamous mRNA (printscreen of AUG_hairpin output www-page; nucleotide sequence of 5'-UTR-CDS fragment was taken from [15]). Borders of the critical region (12^th and 30^th pos.) are marked with green colour; stem region of the eligible hairpin is marked with blue colour; start codon is marked with red colour.

Figure 3

Predicted local secondary structure at the CDS beginning of NsRpoT-C mRNA (printscreen of AUG_hairpin output www-page; nucleotide sequence of 5'-UTR-CDS fragment was taken from AB084950 GenBank entry and [20]). Borders of the critical region (12^th and 30^th pos.) are marked with green colour; stem region of the eligible hairpin is marked with blue colour; start codon is marked with red colour.