[论文解读] Modeling potent pathways for APC/C inhibition: pivotal roles for MCC and BubR1

Bashar Ibrahim|arXiv (Cornell University)|Nov 15, 2016

Microtubule and mitosis dynamics参考文献 37被引用 7

一句话总结

本研究采用系统生物学方法，对纺锤体组装检查点期间抑制后期促进复合物/细胞周期体（APC/C）的调控通路进行建模。通过测试五个模型变体，研究发现唯有同时包含纺锤体检查点复合物（MCC）和BubR1作为强效APC/C抑制剂的模型，才能准确再现野生型和突变型表型，凸显了二者在细胞周期调控中关键且协同的作用。

ABSTRACT

The highly conserved spindle assembly checkpoint (SAC) ensures that the sister chromatids of the duplicated genome are not separated and distributed to the spindle poles before all chromosomes have been properly linked to the microtubules of the mitotic spindle. Biochemically, the SAC delays cell cycle progression by preventing activation of the anaphase-promoting complex (APC/C) or cyclosome; whose activation by Cdc20 is required for sister-chromatid separation, which marks the transition into anaphase. In response to activation of the checkpoint, various species control the activity of both APC/C and Cdc20. However, the underlying regulatory pathways remain largely elusive. In this study, five possible model variants of APC/C regulation were constructed, namely BubR1, Mad2, MCC, MCF2 and an all-pathways model variant. These models are validated with experimental data from the literature. A wide range of parameter values have been tested to find critical values of the APC binding rate. The results show that all variants are able to capture the wild type behaviour of the APC. However, only one model variant, which included both MCC as well as BubR1 as potent inhibitors of the APC, was able to reproduce both wild type and mutant type behaviour of APC regulation. The presented work has successfully distinguished between five competing dynamical models of the same biological system using a systems biology approach. Furthermore, the results suggest that systems-level approach is vital for molecular biology and could also be used for compare the pathways of relevance with the objective to generate hypotheses and improve our understanding.

研究动机与目标

• 确定纺锤体组装检查点期间APC/C抑制的最准确分子模型。
• 解决控制APC/C活化的竞争性调控通路之间的模糊性。
• 确定MCC、BubR1或其组合是否是在体内APC/C的主要抑制剂。
• 将模型预测与文献中的实验数据进行验证。
• 展示系统生物学在区分生物上合理的调控机制方面的实用性。

提出的方法

• 构建了五个动力学模型变体：仅BubR1、仅Mad2、仅MCC、仅MCF2，以及全通路模型。
• 每个模型均使用常微分方程（ODEs）描述蛋白质相互作用，模拟APC/C抑制的动力学。
• 系统探索参数空间，以识别能再现实验行为的关键APC结合速率值。
• 利用已发表文献中的野生型和突变型表型数据对模型进行验证。
• 采用敏感性分析与鲁棒性分析比较模型性能，识别出最匹配的机制。
• 系统生物学框架使得在单一生物系统内对竞争性假说进行定量比较成为可能。

实验结果

研究问题

• RQ1 MCC、BubR1、Mad2或MCF2中哪一种抑制通路组合最能解释APC/C抑制的观测动力学？
• RQ2 是否包含MCC和BubR1的模型能够再现APC/C调控的野生型和突变型表型？
• RQ3 参数变化如何影响各模型变体的鲁棒性与准确性？
• RQ4 全通路模型与单一通路模型相比，在捕捉生物学行为方面有何区别？
• RQ5 系统层面的建模能否解决APC/C抑制分子机制中的模糊性？

主要发现

• 唯有同时将MCC和BubR1作为抑制剂的模型，才能成功再现APC/C调控的野生型和突变型表型。
• MCC-BubR1双抑制模型在广泛参数范围内均表现出更优的鲁棒性与一致性。
• 其他模型变体（如仅MCC或仅BubR1）无法捕捉突变表型，表明其机制表征不完整。
• 本研究识别出APC结合速率的关键参数阈值，可区分功能性与非功能性调控动力学。
• 系统生物学方法成功区分了五个竞争性模型，识别出最符合生物学实际的机制。
• 结果强调了在有丝分裂期间，整合多个抑制通路对于APC/C精确调控的必要性。