ABSTRACT

Shine-Dalgarno (SD) sequences, the core element of prokaryotic ribosome-binding sites, facilitate mRNA translation by base-pair interaction with the anti-SD (aSD) sequence of 16S rRNA. In contrast to this paradigm, an inspection of thousands of prokaryotic species unravels tremendous SD sequence diversity both within and between genomes, whereas aSD sequences remain largely static. The pattern has led many to suggest unidentified mechanisms for translation initiation. Here we review known translation-initiation pathways in prokaryotes. Moreover, we seek to understand the cause and consequence of SD diversity through surveying recent advances in biochemistry, genomics, and high-throughput genetics. These findings collectively show: (1) SD:aSD base pairing is beneficial but nonessential to translation initiation. (2) The 5ʹ untranslated region of mRNA evolves dynamically and correlates with organismal phylogeny and ecological niches. (3) Ribosomes have evolved distinct usage of translation-initiation pathways in different species. We propose a model portraying the SD diversity shaped by optimization of gene expression, adaptation to environments and growth demands, and the species-specific prerequisite of ribosomes to initiate translation. The model highlights the coevolution of ribosomes and mRNA features, leading to functional customization of the translation apparatus in each organism.

摘要

Shine-Dalgarno (SD) 序列是原核生物核糖体结合位点的核心元件，通过与 16S rRNA 的抗 SD (aSD) 序列的碱基对相互作用促进 mRNA 翻译。与这种范式相反，对数千种原核物种的检查揭示了基因组内部和基因组之间巨大的 SD 序列多样性，而 aSD 序列基本上保持不变。这种模式导致许多人提出了翻译启动的未知机制。在这里，我们回顾了原核生物中已知的翻译起始途径。此外，我们试图通过调查生物化学、基因组学和高通量遗传学的最新进展来了解 SD 多样性的原因和后果。这些发现共同表明：(1) SD:aSD 碱基配对对翻译起始有益但不是必需的。(2) mRNA的5′非翻译区是动态进化的，与有机体系统发育和生态位相关。(3) 核糖体在不同物种中进化出了翻译起始途径的不同用途。我们提出了一个模型，该模型描述了由基因表达优化、对环境和生长需求的适应以及核糖体启动翻译的物种特异性先决条件所形成的 SD 多样性。该模型突出了核糖体和 mRNA 特征的共同进化，导致每个生物体中翻译装置的功能定制。我们提出了一个模型，该模型描述了由基因表达优化、对环境和生长需求的适应以及核糖体启动翻译的物种特异性先决条件所形成的 SD 多样性。该模型突出了核糖体和 mRNA 特征的共同进化，导致每个生物体中翻译装置的功能定制。我们提出了一个模型，该模型描述了由基因表达优化、对环境和生长需求的适应以及核糖体启动翻译的物种特异性先决条件所形成的 SD 多样性。该模型突出了核糖体和 mRNA 特征的共同进化，导致每个生物体中翻译装置的功能定制。