Harika Guturu L, Sriram Krishnamachari
Center for Computational Biology, Department of Computational Biology, IIIT-Delhi, New Delhi, India.
PLoS One. 2025 Mar 21;20(3):e0319280. doi: 10.1371/journal.pone.0319280. eCollection 2025.
Protein synthesis involves translation initiation, elongation, termination, and ribosome recycling, and each step is controlled intricately by many signaling proteins. Translation initiation can be compactly categorized into two mechanisms: primary and secondary. The primary mechanism involves the recruitment of three important eukaryotic initiation factors, eIF2-GDP, eIF5, and eIF2B, and their interactions, followed by the GDP-GTP exchange by eIF2B to form an active dimer eIF2-GTP. The dimer binds with Met-tRNA to form a robust ternary complex (TC). The secondary mechanism closely mirrors the primary reaction mechanism, except that the interactions of eIF2B and eIF5 happen with the TC to form complexes. These interactions happen with high fidelity and precision, failing which fail-safe mechanisms are invoked instantaneously to delay the initiation process. In this work, we build a mathematical model to unravel how the transition between translation initiation and termination occurs at the initiation stage based on the elementary mechanisms we built from the network assembled from experimental observations. We focus only on the dynamics of primary and secondary mechanisms involved in the translation initiation process under normal and integrated stress response (ISR) conditions that act as a fail-safe mechanism by through phosphorylation-dephosphorylation (PdP) reactions. Since the network is huge and has many unknown kinetic parameters, we perform structural analysis using chemical reaction network theory (CRNT) and find hidden positive feedback loops that regulate the initiation mechanism. We apply bifurcation theory to show that the model exhibits ultrasensitivity and bistability under normal conditions, while under ISR, it exhibits both bistability and tristability for the choice of kinetic parameters. We attribute bistability to translation initiation and termination and tristability in ISR to translation recovery and attenuation. We conclude that the translation initiation process is a highly regulated process guided by the threshold and switching mechanisms to make quick decisions on the translation initiation, termination, recovery or attenuation under different conditions.
蛋白质合成涉及翻译起始、延伸、终止和核糖体循环，并且每一步都受到许多信号蛋白的复杂调控。翻译起始可简洁地分为两种机制：主要机制和次要机制。主要机制涉及三种重要的真核生物起始因子eIF2 - GDP、eIF5和eIF2B的募集及其相互作用，随后eIF2B进行GDP - GTP交换以形成活性二聚体eIF2 - GTP。该二聚体与甲硫氨酰 - tRNA结合形成稳定的三元复合物（TC）。次要机制与主要反应机制非常相似，只是eIF2B和eIF5的相互作用发生在TC上以形成复合物。这些相互作用以高保真度和精确性发生，一旦失败，会立即调用故障安全机制来延迟起始过程。在这项工作中，我们构建了一个数学模型，以根据我们从实验观察组装的网络所构建的基本机制，揭示在起始阶段翻译起始和终止之间的转变是如何发生的。我们仅关注正常和整合应激反应（ISR）条件下翻译起始过程中主要和次要机制的动力学，ISR通过磷酸化 - 去磷酸化（PdP）反应作为一种故障安全机制。由于该网络庞大且有许多未知的动力学参数，我们使用化学反应网络理论（CRNT）进行结构分析，并发现调节起始机制的隐藏正反馈回路。我们应用分岔理论表明，该模型在正常条件下表现出超敏感性和双稳态，而在ISR条件下，对于动力学参数的选择，它表现出双稳态和三稳态。我们将双稳态归因于翻译起始和终止，将ISR中的三稳态归因于翻译恢复和衰减。我们得出结论，翻译起始过程是一个高度受调控的过程，由阈值和切换机制引导，以便在不同条件下对翻译起始、终止、恢复或衰减做出快速决策。
