Department of Biology, Colorado State University.
Department of Integrative Biology, University of Texas, Austin.
Genome Biol Evol. 2019 Aug 1;11(8):2194-2202. doi: 10.1093/gbe/evz144.
The function and evolution of eukaryotic cells depend upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins. However, the field lacks a consistent classification scheme for mitochondrial- and plastid-targeted proteins based on their molecular interactions with cytoplasmic genomes and gene products, which hinders efforts to standardize and compare results across studies. Here, we take advantage of detailed knowledge about the model angiosperm Arabidopsis thaliana to provide a curated database of plant cytonuclear interactions at the molecular level. CyMIRA (Cytonuclear Molecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/ and https://github.com/dbsloan/cymira and will serve as a resource to aid researchers in partitioning evolutionary genomic data into functional gene classes based on organelle targeting and direct molecular interaction with cytoplasmic genomes and gene products. It includes 11 categories (and 27 subcategories) of different cytonuclear complexes and types of molecular interactions, and it reports residue-level information for cytonuclear contact sites. We hope that this framework will make it easier to standardize, interpret, and compare studies testing the functional and evolutionary consequences of cytonuclear interactions.
真核细胞的功能和进化依赖于核基因组和细胞质基因组中编码的基因产物之间的直接分子相互作用。了解这些细胞质核相互作用如何驱动分子进化，并在隔离的群体和物种之间产生遗传不相容性，对真核生物学至关重要。植物是一个极好的系统，可以研究这些影响，因为它们的细胞质中存在两种不同的基因组区室（线粒体和质体），并且有详细的资源来详细描述核编码蛋白的亚细胞靶向。然而，该领域缺乏一种基于与细胞质基因组和基因产物的分子相互作用，对线粒体和质体靶向蛋白进行一致分类的方案，这阻碍了标准化和比较研究结果的努力。在这里，我们利用对模式被子植物拟南芥的详细了解，提供了一个植物细胞质核相互作用的分子水平的经校对的数据库。CyMIRA（拟南芥细胞质核分子相互作用参考）可在 http://cymira.colostate.edu/ 和 https://github.com/dbsloan/cymira 上获得，并将作为一个资源，帮助研究人员根据细胞器靶向和与细胞质基因组和基因产物的直接分子相互作用，将进化基因组数据划分为功能基因类。它包括 11 类（和 27 个子类）不同的细胞质核复合物和分子相互作用类型，并报告细胞质核接触位点的残基水平信息。我们希望这个框架将使标准化、解释和比较测试细胞质核相互作用的功能和进化后果的研究变得更加容易。
