Mitonuclear interactions and coevolution in the dynamic plant mitochondrial tRNA pool

基本的生物学功能依赖于基因产物之间的直接分子相互作用。尽管这种相互作用的亲密性导致了高度共同进化和整合的基因集，但一些系统表现出显著的不稳定性，本质上是交换基因产物作为“可互换部件”或重新连接整个分子相互作用网络。该项目将利用植物线粒体转移rna （trna）的多样性和trna加工酶的相关网络作为模型，以了解当一个基因丢失并被另一个基因功能取代时分子系统的反应。该研究将为本科生、研究生和博士后提供生物信息学、分子遗传学和进化生物学方面的培训。它还将与面向一年级本科生的拓展工作和项目相结合，以拓宽计算生物学领域的就业机会。在一些植物谱系中，包括被子植物Silene属，线粒体基因组中存在tRNA基因丢失和通过从细胞质中输入核编码tRNA来进行功能替代的持续过程。这些替换相当于将细菌样（线粒体）基因交换为古细菌样（核）基因，这些基因在数十亿年的进化中分离开来。目前尚不清楚这些变化是如何在不破坏线粒体翻译系统基本功能的情况下发生的，因为trna的成熟和充电取决于与许多核编码酶（例如，氨基酰基trna合成酶）的特定相互作用。该项目将使用基因组学、转录组学和实验方法来研究tRNA加工酶在具有不同tRNA基因丢失/替换历史的硅烯物种中氨基酸序列和亚细胞靶向方面的变化。这项工作将区分两种可能的假设：1)现有的线粒体酶已经进化到作为新的底物作用于细胞质trna，或者2)细胞质酶网络已经重新定位到线粒体，维持它们与新输入的细胞质trna的功能关系。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Basic biological functions depend on direct molecular interactions between gene products. Although the intimacy of such interactions has led to highly coevolved and integrated sets of genes, some systems demonstrate remarkable lability, essentially swapping gene products as “interchangeable parts” or rewiring entire networks of molecular interactions. This project will use the diverse pool of plant mitochondrial transfer RNAs (tRNAs) and the associated network of tRNA-processing enzymes as a model to understand how molecular systems respond when one gene is lost and functionally replaced by another. The research will provide training at the undergraduate, graduate, and postdoctoral levels in bioinformatics, molecular genetics, and evolutionary biology. It will also be coupled with outreach efforts and programs for first-year undergraduates to broaden access to career opportunities in computational biology.In some plant lineages, including the angiosperm genus Silene, there is an ongoing process of tRNA gene loss from the mitochondrial genome and functional replacement by import of nuclear-encoded tRNAs from the cytosol. These replacements amount to exchanging bacterial-like (mitochondrial) genes for archaeal-like (nuclear) genes that are separated by billions of years of evolution. It is not clear how these changes occur without disrupting the essential functions of mitochondrial translation systems because the maturation and charging of tRNAs depends on specific interactions with a number of nuclear-encoded enzymes (e.g., aminoacyl-tRNA synthetases). This project will use genomic, transcriptomic, and experimental approaches to investigate how tRNA-processing enzymes change in amino acid sequence and subcellular targeting in Silene species with different histories of recent tRNA gene loss/replacement. The work will distinguish between two alternative hypotheses: 1) that existing mitochondrial enzymes have evolved to act on cytosolic tRNAs as new substrates, or 2) that cytosolic enzyme networks have been retargeted to the mitochondria, maintaining their functional relationship with the newly imported cytosolic tRNAs.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.