Department of Statistical Sciences, University of Bologna, Bologna, 40126, Italy.
Institute for Microelectronics and Microsystems - Bologna Unit, CNR, Bologna, 40129, Italy.
Sci Rep. 2021 Apr 28;11(1):9218. doi: 10.1038/s41598-021-87534-y.
Circular codes represent a form of coding allowing detection/correction of frame-shift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein synthesis levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results can lead to defining new universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.
环形码是一种编码方式，可以检测/纠正移码错误。基于环形码的最新理论进展，我们发现蛋白质编码序列存在无间隔的环形码标记，而这些标记在内含子中不存在，并且与密码子碱基的酮-氨基转化密切相关。这些特性与翻译速度、密码子影响和蛋白质合成水平强烈相关。引人注目的是，环形码标记在编码序列的起始处不存在，但在起始密码子后稳定地出现 40 个密码子，暗示了翻译延伸过程。最后，我们使用环形码的视角表明，密码子对翻译的影响与密码子前两个碱基的强弱二分法相关。这些结果可以为生物信息学和生物技术应用中的序列指标和序列优化定义新的通用工具，并为解码过程背后的分子机制提供启示。
