Rigoni Giovanni, Calvo Enrique, Glytsou Christina, Carro-Alvarellos Marta, Noguchi Masafumi, Semenzato Martina, Quirin Charlotte, Caicci Federico, Meneghetti Natascia, Sturlese Mattia, Ishihara Takaya, Moro Stefano, Rampazzo Chiara, Ishihara Naotada, Bezzo Fabrizio, Salviati Leonardo, Vazquez Jesùs, Sales Gabriele, Romualdi Chiara, Enriquez Jose Antonio, Scorrano Luca, Soriano Maria Eugenia
Department of Biology, University of Padova, Via U. Bassi 58B, 35121 Padova, Italy.
Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain; CIBER de Enfermedades Cardiovasculares, 28029 Madrid, Spain.
Cell Metab. 2025 Apr 1;37(4):1024-1038.e8. doi: 10.1016/j.cmet.2025.01.017. Epub 2025 Feb 24.
Mitochondrial proteins assemble dynamically in high molecular weight complexes essential for their functions. We generated and validated two searchable compendia of these mitochondrial complexes. Following identification by mass spectrometry of proteins in complexes separated using blue-native gel electrophoresis from unperturbed, cristae-remodeled, and outer membrane-permeabilized mitochondria, we created MARIGOLD, a mitochondrial apoptotic remodeling complexome database of 627 proteins. MARIGOLD elucidates how dynamically proteins distribute in complexes upon mitochondrial membrane remodeling. From MARIGOLD, we developed MitoCIAO, a mitochondrial complexes interactome tool that, by statistical correlation, calculates the likelihood of protein cooccurrence in complexes. MitoCIAO correctly predicted biologically validated interactions among components of the mitochondrial cristae organization system (MICOS) and optic atrophy 1 (OPA1) complexes. We used MitoCIAO to functionalize two ATPase family AAA domain-containing 3A (ATAD3A) complexes: one with OPA1 that regulates mitochondrial ultrastructure and the second containing ribosomal proteins that is essential for mitoribosome stability. These compendia reveal the dynamic nature of mitochondrial complexes and enable their functionalization.
线粒体蛋白动态组装成对其功能至关重要的高分子量复合物。我们生成并验证了两个关于这些线粒体复合物的可检索汇编。通过质谱鉴定从未受干扰、嵴重塑和外膜通透的线粒体中使用蓝色天然凝胶电泳分离的复合物中的蛋白质后，我们创建了MARIGOLD，一个包含627种蛋白质的线粒体凋亡重塑复合物组数据库。MARIGOLD阐明了线粒体膜重塑时蛋白质在复合物中如何动态分布。基于MARIGOLD，我们开发了MitoCIAO，一种线粒体复合物相互作用组工具，它通过统计相关性计算蛋白质在复合物中共出现的可能性。MitoCIAO正确预测了线粒体嵴组织系统（MICOS）和视神经萎缩1（OPA1）复合物各组分之间经生物学验证的相互作用。我们使用MitoCIAO对两个含ATP酶家族AAA结构域蛋白3A（ATAD3A）的复合物进行功能注释：一个与OPA1相互作用，调节线粒体超微结构，另一个包含对线粒体核糖体稳定性至关重要的核糖体蛋白。这些汇编揭示了线粒体复合物的动态性质，并使其功能得以注释。
