The Robustness of a Signaling Complex to Domain Rearrangements Facilitates Network Evolution

The rearrangement of protein domains is known to have key roles in the evolution of signaling networks and, consequently, is a major tool used to synthetically rewire networks. However, natural mutational events leading to the creation of proteins with novel domain combinations, such as in frame fusions followed by domain loss, retrotranspositions, or translocations, to name a few, often simultaneously replace pre-existing genes. Thus, while proteins with new domain combinations may establish novel network connections, it is not clear how the concomitant deletions are tolerated. We investigated the mechanisms that enable signaling networks to tolerate domain rearrangement-mediated gene replacements. Using as a model system the yeast mitogen activated protein kinase (MAPK)-mediated mating pathway, we analyzed 92 domain-rearrangement events affecting 11 genes. Our results indicate that, while domain rearrangement events that result in the loss of catalytic activities within the signaling complex are not tolerated, domain rearrangements can drastically alter protein interactions without impairing function. This suggests that signaling complexes can maintain function even when some components are recruited to alternative sites within the complex. Furthermore, we also found that the ability of the complex to tolerate changes in interaction partners does not depend on long disordered linkers that often connect domains. Taken together, our results suggest that some signaling complexes are dynamic ensembles with loose spatial constraints that could be easily re-shaped by evolution and, therefore, are ideal targets for cellular engineering.

蛋白质结构域重排已被证实对信号网络的演化具有关键作用，同时也是人工重构信号网络的核心手段之一。然而，诸如框内融合后伴随结构域丢失、逆转座或易位等（仅举数例）可产生带有全新结构域组合蛋白质的自然突变事件，往往会同时替换原有基因。因此，尽管带有全新结构域组合的蛋白质可建立新的网络连接，但伴随发生的基因缺失如何被细胞耐受，目前仍不明确。
本研究针对信号网络如何耐受结构域重排介导的基因替换这一问题展开了机制探索。本研究以酵母丝裂原活化蛋白激酶（mitogen activated protein kinase, MAPK）介导的交配通路作为模型系统，对涉及11个基因的92次结构域重排事件进行了分析。
研究结果显示：尽管会导致信号复合物内催化活性丧失的结构域重排事件无法被耐受，但在不损害功能的前提下，结构域重排可大幅改变蛋白质间的相互作用。这表明，即便部分复合物组分被招募至复合物内的其他结合位点，信号复合物仍可维持其正常功能。此外，本研究还发现，复合物耐受相互作用伴侣改变的能力，并不依赖于通常用于连接结构域的长无序连接肽段。
综合以上结果，本研究表明部分信号复合物属于具有松散空间约束的动态集合体，可被演化过程轻松重塑，因此是细胞工程的理想靶点。