Department of Chemical Engineering, Penn State University, University Park, PA 16802, USA and Department of Agricultural and Biological Engineering, Penn State University, University Park, PA 16802, USA.
Nucleic Acids Res. 2014 Feb;42(4):2646-59. doi: 10.1093/nar/gkt1139. Epub 2013 Nov 14.
The ribosome's interactions with mRNA govern its translation rate and the effects of post-transcriptional regulation. Long, structured 5' untranslated regions (5' UTRs) are commonly found in bacterial mRNAs, though the physical mechanisms that determine how the ribosome binds these upstream regions remain poorly defined. Here, we systematically investigate the ribosome's interactions with structured standby sites, upstream of Shine-Dalgarno sequences, and show that these interactions can modulate translation initiation rates by over 100-fold. We find that an mRNA's translation initiation rate is controlled by the amount of single-stranded surface area, the partial unfolding of RNA structures to minimize the ribosome's binding free energy penalty, the absence of cooperative binding and the potential for ribosomal sliding. We develop a biophysical model employing thermodynamic first principles and a four-parameter free energy model to accurately predict the ribosome's translation initiation rates for 136 synthetic 5' UTRs with large structures, diverse shapes and multiple standby site modules. The model predicts and experiments confirm that the ribosome can readily bind distant standby site modules that support high translation rates, providing a physical mechanism for observed context effects and long-range post-transcriptional regulation.
核糖体与 mRNA 的相互作用控制着翻译速度和转录后调控的效果。长而结构化的 5'非翻译区（5'UTR）在细菌 mRNA 中很常见，尽管决定核糖体如何结合这些上游区域的物理机制仍未得到明确界定。在这里，我们系统地研究了核糖体与 Shine-Dalgarno 序列上游的结构化备用位点的相互作用，并表明这些相互作用可以将翻译起始速率调节超过 100 倍。我们发现，mRNA 的翻译起始速率受单链表面积的大小、RNA 结构的部分展开以最小化核糖体结合自由能罚分、非协同结合和核糖体滑动的可能性控制。我们开发了一个生物物理模型，该模型采用热力学第一原理和一个四参数自由能模型，能够准确预测 136 个具有大结构、不同形状和多个备用位点模块的合成 5'UTR 的核糖体翻译起始速率。该模型预测并实验证实，核糖体可以轻易地结合支持高翻译速率的远距离备用位点模块，为观察到的上下文效应和远距离转录后调控提供了一种物理机制。
