CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis
CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis
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DOI：
10.1093/gbe/evz144
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发表时间：
2019-08-01
影响因子：
3.3
通讯作者：
Sloan, Daniel B.
中科院分区：
文献类型：
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作者：
Forsythe, Evan S.;Sharbrough, Joel;Sloan, Daniel B.
真核细胞的功能和进化取决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。了解这些细胞核相互作用如何驱动分子进化并在孤立的种群和物种之间产生遗传不相容性对于真核生物学至关重要。植物是研究此类效应的杰出系统，因为它们的细胞质（线粒体和质体）中存在两种不同的基因组区室，并且拥有详细描述核编码蛋白质的亚细胞靶向的广泛资源。然而，该领域缺乏基于线粒体和质体靶向蛋白与细胞质基因组和基因产物的分子相互作用的一致分类方案，这阻碍了标准化和比较研究结果的努力。在这里，我们利用有关被子植物拟南芥模型的详细知识，在分子水平上提供植物细胞核相互作用的精选数据库。 CyMIRA（拟南芥细胞核分子相互作用参考）可在http://cymira.colostate.edu/和https://github.com/dbsloan/cymira获取，将作为一种资源，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别。它包括 11 个类别（和 27 个子类别）不同的细胞核复合物和分子相互作用类型，并报告细胞核接触位点的残基水平信息。我们希望这个框架能够更容易地标准化、解释和比较测试细胞核相互作用的功能和进化后果的研究。
The function and evolution of eukaryotic cells depend upon direct molecular interactions between geneproducts 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 systemto investigate such effects becauseof 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 (CytonuclearMolecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/andhttps://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.