RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.
European Virus Bioinformatics Center (EVBC), Jena, Germany.
Bioinformatics. 2019 Feb 15;35(4):579-583. doi: 10.1093/bioinformatics/bty678.
The protein-coding sequences of messenger RNAs are the linear template for translation of the gene sequence into protein. Nevertheless, the RNA can also form secondary structures by intramolecular base-pairing.
We show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base-pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under-represented. We conclude that this bias may result from the co-evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein-coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1.
Supplementary data are available at Bioinformatics online.
信使 RNA 的编码序列是将基因序列翻译成蛋白质的线性模板。然而，RNA 也可以通过分子内碱基配对形成二级结构。
我们表明，在全球范围内，所有生命形式的密码子内核苷酸分布都存在偏倚。因此，需要在一个密码子的第 1 位与另一个密码子的第 1 位之间进行碱基配对的 RNA 二级结构（此处命名为 RNA 二级结构类 c1）的出现频率较低。我们得出结论，这种偏差可能是由于密码子序列和 mRNA 二级结构的共同进化所致，这表明 RNA 二级结构在 mRNA 的编码区通常很重要。上述结果还表明，密码子的第 2 位对氨基酸选择的影响比第 1 位小。
补充数据可在“生物信息学”在线获取。
