Carmel Ezra Stav, Tuller Tamir
Department of Biomedical Engineering, Tel Aviv University, Israel.
Comput Struct Biotechnol J. 2022 May 18;20:2521-2538. doi: 10.1016/j.csbj.2022.05.030. eCollection 2022.
The process of translation initiation in prokaryotes is mediated by the hybridization of the 16S rRNA of the small ribosomal subunit with the mRNA in a short region called the ribosomal binding site. However, translation initiation in chloroplasts, which have evolved from an ancestral bacterium, is not well understood. Some studies suggest that in many cases it differs from translation initiation in bacteria and involves various novel interactions of the mRNA structures with intracellular factors; however currently, there is no generic quantitative model related to these aspects in chloroplasts. We developed a novel computational pipeline and models that can be used for understanding and modeling translation regulation in chloroplasts. We demonstrate that local folding and co-folding energy of the rRNA and the mRNA correlates with codon usage estimators of expression levels (r = -0.63) and infer predictive models that connect these energies and codon usage to protein levels (with correlation up to 0.71). In addition, we demonstrate that the ends of the transcripts in chloroplasts are populated with various structural elements that may be functional. Furthermore, we report a database of 166 novel structures in the chloroplast transcripts that are predicted to be functional. We believe that the models reported here improve existing understandings of genomic evolution and the biophysics of translation in chloroplasts; as such, they can aid gene expression engineering in chloroplasts for various biotechnological objectives.
原核生物中的翻译起始过程是由小核糖体亚基的16S rRNA与mRNA在一个称为核糖体结合位点的短区域杂交介导的。然而，叶绿体起源于一种原始细菌，其翻译起始过程尚未得到充分理解。一些研究表明，在许多情况下，它与细菌中的翻译起始不同，涉及mRNA结构与细胞内因子的各种新型相互作用；然而目前，在叶绿体中还没有与这些方面相关的通用定量模型。我们开发了一种新颖的计算流程和模型，可用于理解和模拟叶绿体中的翻译调控。我们证明，rRNA和mRNA的局部折叠和共折叠能量与表达水平的密码子使用估计值相关（r = -0.63），并推断出将这些能量和密码子使用与蛋白质水平联系起来的预测模型（相关性高达0.71）。此外，我们证明叶绿体中转录本的末端充满了各种可能具有功能的结构元件。此外，我们报告了一个叶绿体转录本中166个预测具有功能的新结构的数据库。我们相信，这里报告的模型改进了对叶绿体基因组进化和翻译生物物理学的现有理解；因此，它们可以帮助实现叶绿体中针对各种生物技术目标的基因表达工程。
