National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Cell Cycle. 2012 Oct 15;11(20):3861-75. doi: 10.4161/cc.22068. Epub 2012 Sep 14.
In addition to their role in motility, eukaryotic cilia serve as a distinct compartment for signal transduction and regulatory sequestration of biomolecules. Recent genetic and biochemical studies have revealed an extraordinary diversity of protein complexes involved in the biogenesis of cilia during each cell cycle. Mutations in components of these complexes are at the heart of human ciliopathies such as Nephronophthisis (NPHP), Meckel-Gruber syndrome (MKS), Bardet-Biedl syndrome (BBS) and Joubert syndrome (JBTS). Despite intense studies, proteins in some of these complexes, such as the NPHP1-4-8 and the MKS, remain poorly understood. Using a combination of computational analyses we studied these complexes to identify novel domains in them which might throw new light on their functions and evolutionary origins. First, we identified both catalytically active and inactive versions of transglutaminase-like (TGL) peptidase domains in key ciliary/centrosomal proteins CC2D2A/MKS6, CC2D2B, CEP76 and CCDC135. These ciliary TGL domains appear to have originated from prokaryotic TGL domains that act as peptidases, either in a prokaryotic protein degradation system with the MoxR AAA+ ATPase, the precursor of eukaryotic dyneins and midasins, or in a peptide-ligase system with an ATP-grasp enzyme comparable to tubulin-modifying TTL proteins. We suggest that active ciliary TGL proteins are part of a cilia-specific peptidase system that might remove tubulin modifications or cleave cilia- localized proteins, while the inactive versions are likely to bind peptides and mediate key interactions during ciliogenesis. Second, we observe a vast radiation of C2 domains, which are key membrane-localization modules, in multiple ciliary proteins, including those from the NPHP1-4-8 and the MKS complexes, such as CC2D2A/MKS6, RPGRIP1, RPGRIP1L, NPHP1, NPHP4, C2CD3, AHI1/Jouberin and CEP76, most of which can be traced back to the last common eukaryotic ancestor. Identification of these TGL and C2 domains aid in the proper reconstruction of the Y-shaped linkers, which are key structures in the transitional zone of cilia, by allowing precise prediction of the multiple membrane-contacting and protein-protein interaction sites in these structures. These findings help decipher key events in the evolutionary separation of the ciliary and nuclear compartments in course of the emergence of the eukaryotic cell.
除了在运动中发挥作用外，真核纤毛还作为信号转导和生物分子调节隔离的独特隔室。最近的遗传和生化研究揭示了在每个细胞周期中参与纤毛发生的各种蛋白质复合物。这些复合物的组成部分的突变是人类纤毛病的核心，如肾单位纤毛症（NPHP）、Meckel-Gruber 综合征（MKS）、Bardet-Biedl 综合征（BBS）和 Joubert 综合征（JBTS）。尽管进行了深入研究，但这些复合物中的一些蛋白质，如 NPHP1-4-8 和 MKS，仍然知之甚少。我们使用计算分析的组合来研究这些复合物，以鉴定它们中的新型结构域，这些结构域可能为它们的功能和进化起源提供新的线索。首先，我们在关键的纤毛/中心体蛋白 CC2D2A/MKS6、CC2D2B、CEP76 和 CCDC135 中鉴定了催化活性和非活性形式的转谷氨酰胺酶样（TGL）肽酶结构域。这些纤毛 TGL 结构域似乎起源于原核 TGL 结构域，原核 TGL 结构域作为肽酶，要么在具有 MoxR AAA+ATP 酶（真核动蛋白和 midadin 的前体）的原核蛋白降解系统中，要么在具有与微管修饰 TTL 蛋白相当的 ATP 抓取酶的肽-连接酶系统中。我们认为，活性纤毛 TGL 蛋白是一种特异性纤毛蛋白酶系统的一部分，该系统可能去除微管修饰或切割位于纤毛的蛋白，而非活性版本可能结合肽并在纤毛发生过程中介导关键相互作用。其次，我们观察到大量 C2 结构域的辐射，这些结构域是关键的膜定位模块，存在于多种纤毛蛋白中，包括来自 NPHP1-4-8 和 MKS 复合物的蛋白，如 CC2D2A/MKS6、RPGRIP1、RPGRIP1L、NPHP1、NPHP4、C2CD3、AHI1/Jouberin 和 CEP76，其中大多数可以追溯到最后一个共同的真核祖先。这些 TGL 和 C2 结构域的鉴定有助于正确重建纤毛过渡区的 Y 形接头，这些接头是纤毛的关键结构，通过允许在这些结构中精确预测多个膜接触和蛋白质-蛋白质相互作用位点，从而实现这一目标。这些发现有助于阐明在真核细胞出现过程中纤毛和核隔室的进化分离的关键事件。
