蛋白质折叠用法的分析,类似于密码子使用,对生物系统的进化和现代蛋白质组的起源提供了深刻的见解。虽然以前的研究已经检查了现代基因组中的折叠分布,我们的研究重点是细菌核糖体中蛋白质折叠的比较分布和使用,古细菌,和真核生物。我们确定了某些超核糖体折叠的患病率,如细菌中的OB折叠和古细菌和真核生物中的SH3结构域。观察到的核糖体中的蛋白质折叠分布宣布了未来的幂律分布,其中只有少数折叠非常普遍,大多数是罕见的。此外,我们强调了在所有王国的核糖体中存在三个原始Rossmann折叠,显示其在核糖体结构和功能中的古老和基本作用。我们的研究还探讨了分子趋同的早期机制,不同的蛋白质折叠在不同王国的核糖体中结合等价的核糖体RNA结构。这种比较分析增强了我们对核糖体进化的理解,特别是大小亚基的不同进化路径,并强调了从RNA世界到现代细胞生命的过渡过程中RNA和蛋白质成分之间复杂的相互作用。超越折叠的概念还可以将大量核糖体蛋白分为五类urfolds或metafold,这可以证明他们的祖先性格和共同起源。这项工作还表明,通过简单但有序的折叠逐渐获得扩展构成了不可阻挡的进化机制。这一观察结果支持这样的观点,即简单但结构化的核糖体蛋白先于其无序延伸的发展。
The analysis of protein fold usage, similar to codon usage, offers profound insights into the evolution of biological systems and the origins of modern proteomes. While previous studies have examined fold distribution in modern genomes, our study focuses on the comparative distribution and usage of protein folds in
ribosomes across bacteria, archaea, and eukaryotes. We identify the prevalence of certain \'super-ribosome folds,\' such as the OB fold in bacteria and the SH3 domain in archaea and eukaryotes. The observed protein fold distribution in the
ribosomes announces the future power-law distribution where only a few folds are highly prevalent, and most are rare. Additionally, we highlight the presence of three copies of proto-Rossmann folds in
ribosomes across all kingdoms, showing its ancient and fundamental role in ribosomal structure and function. Our study also explores early mechanisms of molecular convergence, where different protein folds bind equivalent ribosomal RNA structures in
ribosomes across different kingdoms. This comparative analysis enhances our understanding of ribosomal evolution, particularly the distinct evolutionary paths of the large and small subunits, and underscores the complex interplay between RNA and protein components in the transition from the RNA world to modern cellular life. Transcending the concept of folds also makes it possible to group a large number of ribosomal proteins into five categories of urfolds or metafolds, which could attest to their ancestral character and common origins. This work also demonstrates that the gradual acquisition of extensions by simple but ordered folds constitutes an inexorable evolutionary mechanism. This observation supports the idea that simple but structured ribosomal proteins preceded the development of their disordered extensions.