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。虽然这种相互作用的密切性导致了高度共同进化和整合的基因组，但有些系统表现出显著的不稳定性，基本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（tRNA）的多样性池和相关的tRNA加工酶网络作为模型，以了解当一个基因丢失并在功能上被另一个基因取代时，分子系统如何反应。该研究将提供生物信息学、分子遗传学和进化生物学的本科生、研究生和博士后培训。它还将与一年级本科生的外展工作和计划相结合，以扩大获得计算生物学的就业机会。在一些植物谱系中，包括被子植物属Silene，存在一个正在进行的过程，即从线粒体基因组中丢失tRNA基因，并通过从细胞质中输入核编码的tRNA进行功能替换。这些替换相当于将类细菌（线粒体）基因交换为类古细菌（核）基因，这些基因在数十亿年的进化中被分离。目前尚不清楚这些变化如何发生而不破坏线粒体翻译系统的基本功能，因为tRNA的成熟和充电取决于与许多核编码酶的特异性相互作用（例如，氨酰-tRNA合成酶）。该项目将使用基因组学，转录组学和实验方法来研究tRNA加工酶如何在具有不同历史的最近tRNA基因丢失/替换的Silene物种中改变氨基酸序列和亚细胞靶向。这项工作将区分两种备选假设：1）现有的线粒体酶已经进化为作用于作为新底物的胞质tRNA，或2）胞质酶网络已经重新靶向线粒体，该奖项反映了NSF的法定使命，并通过使用基金会的知识产权进行评估，被认为值得支持。优点和更广泛的影响审查标准。

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.