The Impact of Endosymbiosis on Genome Structure and Content

内共生是宿主细胞吸收并保留另一个细胞，导致长期细胞内缔合的过程。内共生现象被广泛认为对进化和细胞功能产生了重大影响，但我们对这一过程的实际运作方式，或者大多数内共生体的最终命运，却有着令人惊讶的肤浅理解。我们研究内共生体的获得或损失以及合作伙伴如何整合，以更好地解释这一过程及其对合作伙伴的影响。 亚细胞细胞器（线粒体和质体）是研究得最好的内共生体，但由于其极端的年龄和整合，也限制了其作为机制模型。事实上，最近对昆虫-细菌内共生的研究已经挑战了许多关于这一过程的长期假设，包括其互利性质。然而，昆虫代表了一个狭窄的内共生多样性谱：原生生物-细菌内共生要多样得多，但对于大多数昆虫，我们几乎没有功能或基因组方面的见解。使用单细胞基因组学来研究甚至未培养的微生物内共生体，我们可以更广泛地了解这一过程是如何展开的，使用两条研究路线来平衡深度和广度：1。游仆虫的内共生体替换。纤毛虫游仆虫拥有一个重要的内共生体，多核生物，我们已经表明，这是不断降解和重建的自由生活的菌株。但有些游仆虫缺乏多核小体，并具有不同的内共生体，而另一些游仆虫仍然有额外的“附属”内共生体。我们将测试，如果占主导地位的过程中重复更换延伸到这些内共生体，以及是否附件内共生体增加系统的功能复杂性。 2.研究原生生物-细菌内共生的多种系统。为了研究广泛的内共生环境，我们也将探讨内共生整合在不同的原生生物主机。一个经典的系统是白蚁后肠中的纤维素消化原生生物。我们将表征细菌内共生体从几个最近分歧的主机，以确定如何常见的收益，损失和更换，以及他们是否坚持通过主机物种形成。另一个系统是厌氧纤毛虫与产氢残体线粒体，“氢小体”。这些可以与产甲烷古细菌内共生体进行氢交换，我们发现内共生体的存在可能会加速氢化酶体的基因组还原。我们将通过检查广泛的纤毛虫宿主来测试这一点，有和没有内共生体。最后，我们将开展试点研究，探索系统，以确定进一步发展的候选人：自由生活的diplonemids与核和cepon-associated内共生体，和一个经典的实验室时间尺度系统变形虫。 这些研究将共同提供重要的见解，什么是在不同阶段和背景下的一个重要的进化过程的一般原则。

Endosymbiosis is the process where a host cell takes up and retains another cell, resulting in a long-term intracellular association. Endosymbiosis is widely accepted to have impacted evolution and cell function significantly, but we have a surprisingly superficial understanding of how the process actually works, or the ultimate fate of most endosymbionts. We study the gain or loss of endosymbionts and how partners integrate, to better explain the process and its impact on the partners.      Sub-cellular organelles (mitochondria and plastids) are are the best-studied endosymbionts, but are also limited as mechanistic models by their extreme age and integration. Indeed, work on more recent insect-bacterial endosymbioses has challenged many longstanding assumptions about the process, including its mutualistic nature. Insects, however, represent a narrow spectrum of endosymbiotic diversity: protist-bacterial endosymbioses are much more diverse, but for most we have few functional or genomic insights. Using single-cell genomics to study even uncultivated microbial endosymbioses, we can develop a broader understanding of how this process unfolds, using two lines of research to balance depth and breadth: 1. Endosymbiont replacement in Euplotes. The ciliate Euplotes harbours an essential endosymbiont, Polynucleobacter, which we have shown is constantly degraded and re-established from free-living strains. But some Euplotes lack Polynucleobacter, and possess different endosymbionts, while others still have extra "accessory" endosymbionts. We will test if the dominant process of repeated replacement extends to these endosymbionts, and whether accessory endosymbionts increase functional complexity of the system.  2. Diverse systems to study protist-bacterial endosymbiosis. To examine a wide breadth of endosymbiotic contexts, we will also explore endosymbiotic integration in diverse protist hosts. One classic system is cellulose-digesting protists in termite hindguts. We will characterize bacterial endosymbionts from several recently-diverged hosts to determine how common are gains, losses, and replacements, and whether they persist through host speciation. Another system is anaerobic ciliates with hydrogen-producing relict mitochondria, "hydrogenosomes". These can associate with methanogenic archaeal endosymbionts for hydrogen-exchange, and we find genomic reduction of hydrogenosomes may be accelerated by the presence of endosymbionts. We will test this by examining a wide range of ciliate hosts, with and without endosymbionts. Lastly, we will carry out pilot studies on under-explored systems to identify candidates for further development: free-living diplonemids with nucleus- and mitochondrion-associated endosymbionts, and a classic lab-timescale system in Amoeba.        These studies will collectively provided significant insights into what are general principles in diverse stages and contexts of an important evolutionary process.