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密切关系导致了高度共同进化和整合的基因集合，但一些系统表现出显著的易变性，本质上是将基因产物作为“可互换的部分”进行交换，或者重新连接整个分子相互作用网络。该项目将使用植物线粒体转移RNA(TRNAs)的多样性池和相关的tRNA处理酶网络作为模型，以了解当一个基因丢失并被另一个基因功能替代时，分子系统如何做出反应。这项研究将在本科生、研究生和博士后水平上提供生物信息学、分子遗传学和进化生物学方面的培训。在包括被子植物属Silene在内的一些植物谱系中，线粒体基因组中存在tRNA基因丢失的持续过程，并通过从细胞质中输入核编码的tRNA来进行功能替换。这些替换相当于将类似细菌的(线粒体)基因交换为类似古生菌的(核)基因，这些基因经过数十亿年的进化而分离。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tRNAs的成熟和充电依赖于与一些核编码酶(例如氨酰-tRNA合成酶)的特定相互作用。本项目将使用基因组学、转录学和实验方法来研究具有不同tRNA基因丢失/替换历史的Silene物种中tRNA加工酶如何在氨基酸序列和亚细胞靶向方面发生变化。这项工作将区分两种不同的假设：1)现有的线粒体酶已经进化成作为新的底物作用于细胞质tRNA，或者2)细胞质酶网络已经被重定向到线粒体，保持了它们与新进口的细胞质tRNA的功能关系。这一奖项反映了NSF的法定使命，并通过使用基金会的智力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.