The evolution of signaling pathways is complex and well-studied. In particular, the emergence of animal multicellularity had a major impact on protein-protein interactions and signaling systems in eukaryotic cells. However, choanoflagellates, our closest non-metazoan ancestor, contain a number of closely related signaling and trafficking proteins and domains. In addition, because choanoflagellates can adopt a rosette-/multicellular-like state, a lot can be gained by comparing proteins involved in choanoflagellate and human signaling pathways. Here, we look at how selectivity determinants evolved in the PDZ domain. There are over 250 PDZ domains in the human proteome, which are involved in critical protein-protein interactions that result in large multimolecular complexes, e.g., in the postsynaptic density of neuronal synapses. Binding of C-terminal sequences by PDZ domains is often transient and recognition typically involves 6 residues or less, with only 2 residues specifying the binding motif. We solved high resolution crystal structures of Monosiga brevicollis PDZ domains homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains to investigate if the non-motif preferences are conserved, despite hundreds of millions of years of evolution. We also calculated binding affinities for GIPC, SHANK1, and SNX27 PDZ domains from M. brevicollis. Overall, we found that peptide selectivity is conserved between these two disparate organisms, with one exception, mbDLG-3. In addition, we identify 178 PDZ domains in the M. brevicollis proteome, including 11 new sequences, which we verified using Rosetta and homology modeling. Overall, our results provide novel insight into signaling pathways in the choanoflagellate organism.

中文翻译：

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Monosiga brevicollis PDZ域中非基序选择性决定因素的演变

信号转导途径的进化是复杂的，并且已经被充分研究。特别是，动物多细胞性的出现对真核细胞中的蛋白质相互作用和信号系统产生了重大影响。然而，我们最接近的非亚甲基偶氮类祖先鞭毛藻含有许多密切相关的信号传导和运输蛋白和结构域。另外，由于鞭毛鞭毛虫可以采取玫瑰花状/多细胞样状态，因此通过比较参与鞭毛鞭毛虫和人类信号传导途径的蛋白质可以获得很多益处。在这里，我们看一下选择性决定因素在PDZ域中的演变。人类蛋白质组中有超过250个PDZ域，这些域与关键的蛋白质-蛋白质相互作用有关，从而导致大型的多分子复合物，例如神经突触的突触后密度。PDZ域与C端序列的结合通常是瞬时的，识别通常涉及6个或更少的残基，只有2个残基指定结合基序。我们解决了高分辨晶体结构与人Dlg1，PDZ2，Dlg1，PDZ3，GIPC和SHANK1 PDZ域同源的Monosiga brevicollis PDZ域，尽管经历了数亿年的进化，但仍研究了非基序偏好是否得到保留。我们还计算了GIPC，SHANK1和SNX27 PDZ结构域的结合亲和力从M. brevicollis。总的来说，我们发现在这两种不同的生物之间，肽的选择性是保守的，只有一个例外是mbDLG-3。此外，我们在短枝杆菌蛋白质组中鉴定了178个PDZ域，包括11个新序列，我们使用Rosetta和同源性建模对其进行了验证。总体而言，我们的研究结果提供了对鞭毛鞭毛虫生物体内信号通路的新颖见解。