Genomic and proteomic approaches to understanding mitochondrial diversity in eukaryotic microbes

线粒体是真核亚细胞结构，起源于细菌内共生体与古生菌宿主的整合。尽管它们保留了一个残留的基因组，但几乎所有在线粒体内发挥功能的蛋白质--包括参与能量转换和细胞程序性死亡等关键过程的蛋白质--都编码在核基因组中。因此，为了充分了解线粒体的功能和进化，有必要系统地鉴定核编码的线粒体蛋白。线粒体蛋白质组研究已经在动物、植物和真菌中进行，然而，这种对多细胞生物的狭隘系统发育关注偏向于进化解释。因此，必须从真核微生物(原生生物)的广泛样本中确定线粒体的特征，因为它们构成了真核生物的大部分遗传多样性。对少数原生生物线粒体进行了深入的研究，揭示了不同谱系之间相当大的代谢差异，以及许多新的、功能未加注释的蛋白质。因此，还有很多事情需要了解：1)原生生物线粒体代谢的多样性，特别是其基因组完全未被探索的未培养群体；以及2)由于缺乏必要的遗传工具来剖析其功能，原生生物线粒体蛋白的功能尚不清楚。我们的研究目的就是要解决这两个问题。1)线粒体多样性：为了扩大我们对线粒体功能多样性的理解，我们将使用单细胞基因组学和转录组学来预测有孔虫中的线粒体蛋白质，有孔虫是一类丰富的海洋异养生物，众所周知很难培养。这项工作将研究生活在有氧和缺氧沉积物中的细胞的线粒体有何不同，为线粒体如何进化以在低氧中发挥作用提供重要线索。鉴于最近全球海洋最低含氧区的增加，这是一个重要的话题。2)线粒体功能：我的团队还将使用模型阿米巴动物，盘基网毛虫，作为研究原生动物线粒体进化和功能的工具。通过利用网柄菌易于培养、遗传工具箱和复杂的生命周期--包括单细胞和多细胞阶段--的优势，我们将使用蛋白质组学以及比较基因组学和功能基因组学来重建线粒体的祖先状态，阐明线粒体在从单细胞向多细胞转变中所起的作用，并询问新的线粒体蛋白的功能。这项工作对于对追踪基因组进化如何影响线粒体组成感兴趣的进化生物学家以及对建立蛋白质的假定功能感兴趣的功能生物学家来说将是重要的，这些蛋白质要么不存在于模型系统中，要么被多细胞系统的复杂生物学所掩盖。

Mitochondria are eukaryotic subcellular structures that originated from the integration of a bacterial endosymbiont into an archaeal host. Though they retain a relic genome, almost all proteins that function within mitochondria - including proteins involved in key processes like energy conversion and programmed cell death - are encoded in the nuclear genome. It is therefore necessary to systematically identify nucleus-encoded mitochondrial proteins in order to fully understand mitochondrial function and evolution. Mitochondrial proteome studies have been carried out in animals, plants, and fungi; however, such a narrow phylogenetic focus on multicellular organisms biases evolutionary interpretations. It is therefore imperative to characterize mitochondria from a broad sampling of eukaryotic microbes (protists), because they make up the bulk of genetic diversity within Eukarya. A small number of protist mitochondria have been intensively studied, revealing considerable metabolic variation between different lineages, and many novel, functionally unannotated proteins. As a result, much remains to be learned about: 1) the diversity of mitochondrial metabolism in protists, especially uncultured groups whose genomes are completely unexplored, and 2) the functions of protist mitochondrial proteins whose functions are not understood due to the scarcity of genetic tools necessary to dissect their function. Our research aim is to address these two problems. 1) Mitochondrial diversity: To expand our understanding of mitochondrial functional versatility, we will use single-cell genomics and transcriptomics to predict mitochondrial proteins in Foraminifera, an abundant group of marine heterotrophs that are notoriously difficult to culture. This work will examine how mitochondria from cells living in oxygenated and anoxic sediments differ, providing important clues to how mitochondria evolve to function in low oxygen. This is an important topic given recent global increases in oceanic oxygen minimum zones. 2) Mitochondrial function: My group will also employ the model amoebozoan, Dictyostelium discoideum, as a tool to investigate mitochondrial evolution and function in protists. By taking advantage of Dictyostelium's ease of cultivation, genetic toolkit, and complex life cycle - including unicellular and multicellular stages - we will use proteomics, along with comparative and functional genomics, to reconstruct mitochondrial ancestral states, elucidate the role that mitochondria play in the transition from unicellularity to multicellularity, and interrogate the functions of novel mitochondrial proteins. This work will be important to evolutionary biologists interested in tracing how genome evolution affects the composition of mitochondria, and to functional biologists interested in establishing putative functions for proteins that are either not present in model systems, or those whose function is obscured by the complex biology of multicellular systems.