Minimum free energy predicted base pairing in the 39 nt spliced leader and 5’ UTR of calmodulin mRNA from Trypanosoma cruzi: influence of the multiple trans-splicing sites

ABSTRACT We analyzed the compositional changes and the stable base pairs in the predicted secondary structure of the 5’ UTR calmodulin mRNA in T. cruzi. The three copies of calmodulin in T. cruzi genome display variable position of the trans splicing sites and give rise to several mRNA that differs slightly on 5’ UTR composition in the epimastigote stage. We show that the pattern of high probability base pairs in the minimum free energy predicted secondary structures of the calmodulin 5’ UTR remains unchanged despite the nucleotide composition variation. However, the 39 nt spliced leader (mini-exon, the 5’ exon sequence transferred to trypanosome mRNAs by the mechanism of trans splicing) shows a variable pattern of high and low probability base pairing as consequence of the altered composition of the 5’ UTR.

摘要：本研究分析了克氏锥虫（Trypanosoma cruzi）钙调蛋白（calmodulin）mRNA 5'非翻译区（5' Untranslated Region, 5' UTR）预测二级结构中的组成变化与稳定碱基对。克氏锥虫基因组中存在3个钙调蛋白拷贝，其反式剪接（trans splicing）位点位置存在差异，因此在上鞭毛体（epimastigote）阶段会产生若干5'非翻译区组成略有差异的mRNA。研究结果表明，尽管核苷酸组成存在差异，钙调蛋白5'非翻译区的最小自由能（minimum free energy）预测二级结构中高概率碱基对的模式始终保持稳定。然而，39 nt的剪接前导序列（spliced leader，又称微型外显子（mini-exon），即通过反式剪接（trans splicing）机制转移至锥虫mRNA的5'外显子序列），其高低概率碱基配对模式会因5'非翻译区组成的改变而发生变化。