The Impact of Endosymbiosis on Genome Structure and Content

内共生是寄主细胞摄取并保留另一个细胞的过程，导致长期的细胞内结合。人们普遍认为，内共生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大多数内共生生物的最终命运的理解却令人惊讶地肤浅。我们研究了内共生菌的获得或损失以及伙伴如何整合，以更好地解释这一过程及其对伙伴的影响。亚细胞细胞器（线粒体和质体）是研究得最好的内共生体，但由于它们的极端年龄和整合，作为机制模型也受到限制。事实上，最近对昆虫-细菌内共生的研究挑战了许多长期存在的关于这一过程的假设，包括它的互惠性。然而，昆虫代表了一个狭窄的内共生多样性范围：原生生物-细菌内共生的多样性要多得多，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，我们可以更广泛地了解这个过程是如何展开的，使用两条研究线来平衡深度和广度：Euplotes的内共生替换。纤毛虫Euplotes拥有一种重要的内共生菌，多核杆菌，我们已经证明它不断地从自由生活的菌株中降解和重新建立。但有些整胞体缺乏多核杆菌，具有不同的内共生体，而另一些整胞体仍有额外的“附属”内共生体。我们将测试重复替换的主导过程是否延伸到这些内共生体，以及附属内共生体是否增加了系统的功能复杂性。2. 不同系统研究原生细菌内共生。为了研究广泛的内共生背景，我们还将探讨不同原生宿主的内共生整合。一个经典的系统是白蚁后肠中消化纤维素的原生生物。我们将从几个最近分化的宿主中描述细菌内共生体，以确定它们的获得、损失和替换有多普遍，以及它们是否在宿主物种形成中持续存在。另一个系统是厌氧纤毛虫，具有产生氢的残余线粒体，“氢基因体”。它们可以与产甲烷的古细菌内共生体进行氢交换，并且我们发现内共生体的存在可能会加速氢酶体的基因组减少。我们将通过检查广泛的纤毛虫宿主来验证这一点，有或没有内共生体。最后，我们将对尚未开发的系统进行试点研究，以确定进一步开发的候选系统：具有核和线粒体相关内共生生物的自由生活双尾虫，以及阿米巴原虫的经典实验室时间尺度系统。这些研究将共同为一个重要进化过程的不同阶段和背景下的一般原则提供重要的见解。

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.