Endosymbiosis and genome evolution in eukaryotic microbes

真核微生物的内共生和基因组进化

• 批准号: RGPIN-2014-05871
• 负责人: Archibald, John
• 金额: $ 6.19万
• 依托单位: Dalhousie University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=588667
• 关键词: Endosymbiosis; genome; evolution; eukaryotic; microbes

We are in the midst of a scientific revolution built on our understanding of DNA, the hereditary molecule of life. Using the tools of molecular biology, we are exploring the world around us in ways unimaginable just a decade ago. One area in which truly remarkable advances have taken place is our understanding of the microbial biosphere. The genomes (genetic ‘blueprints’) of thousands of species have been decoded, not only organisms cultured in the lab but microbes taken directly from their natural habitats: the human gut, the oceans, soil, even the air we breathe. Comparative analyses of this wealth of genetic data have revealed that horizontal gene transfer—the exchange of genetic material across species boundaries—is a potent evolutionary force. There is increasing support for the notion that when microbes are considered, Darwin’s ‘tree of life’ is in fact a web of life—a complex net through which genes have flowed both vertically and horizontally between diverse life forms for more than three billion years. The Archibald Laboratory studies the role of symbiosis in the evolution of complex life forms. The process of endosymbiosis, in which one cell takes up residence inside another, involves the ‘mixing and matching’ not just of genes but entire organisms. The mitochondria that produce energy inside complex cells such as our own are, in essence, domesticated bacteria: they descend from free-living bacterial cells by endosymbiosis. Plastids (chloroplasts), the light gathering compartments of plants and algae, are also of endosymbiotic origin. In this proposal we will apply molecular and computer-based research approaches to the study of DNA in single-celled algae. The goal is to develop a detailed understanding of the pattern and process of endosymbiosis and its role in the origin of complex photosynthetic eukaryotes. The particular microbes we study are the cellular equivalent of ‘Russian nesting dolls’: they evolved as a result of repeated rounds of endosymbiosis in which cells come to reside within other cells, which are themselves nested within larger cells. These serial endosymbiosis events have generated some of the most abundant and ecologically important primary producers on Earth, including diatoms (the ‘jewels’ of the ocean), giant kelp, and dinoflagellate algae, which cause ‘red tides’ and are also essential components of coral reefs. Despite its obvious biological significance, relatively little is known about the mechanistic details of secondary endosymbiosis. We will analyze the genomes of certain algal groups to gain insight into (i) how and how often genes move from one sub-cellular compartment to another in different species and (ii) the extent to which these anciently-evolved chimaeric cells are the product of ‘mix and match’ biochemistry. Next to the origin of life itself, the endosymbiotic origins of mitochondria and plastids were arguably the most important events in the history of our planet. Yet until quite recently symbiosis was dismissed as an evolutionary oddity. The reality is that photosynthetic marine microbes carry out half of the primary production on Earth and form the foundation of oceanic food webs. It is important for us to understand where these organisms came from; how they interact with one another; and how they are likely to adapt to human-induced environmental change.

我们正处于一场以我们对生命遗传分子 DNA 的理解为基础的科学革命之中。利用分子生物学工具，我们正在以十年前难以想象的方式探索周围的世界。真正取得显着进展的领域之一是我们对微生物生物圈的理解。数千个物种的基因组（遗传“蓝图”）已被破译，不仅包括实验室培养的生物体，还有直接取自自然栖息地的微生物：人类肠道、海洋、土壤，甚至我们呼吸的空气。对大量遗传数据的比较分析表明，水平基因转移（跨物种边界的遗传物质交换）是一种强大的进化力量。 人们越来越多地支持这样一种观点，即当考虑微生物时，达尔文的“生命之树”实际上是一个生命之网——一个复杂的网络，基因在超过三十亿年的时间里在不同生命形式之间垂直和水平地流动。 阿奇博尔德实验室研究共生在复杂生命形式进化中的作用。内共生过程中，一个细胞占据另一个细胞的内部，不仅涉及基因的“混合和匹配”，还涉及整个生物体的“混合和匹配”。在像我们这样的复杂细胞内产生能量的线粒体本质上是驯化的细菌：它们通过内共生从自由生活的细菌细胞中分离出来。质体（叶绿体）是植物和藻类的光收集区室，也是内共生起源的。 在本提案中，我们将应用基于分子和计算机的研究方法来研究单细胞藻类的 DNA。目标是详细了解内共生的模式和过程及其在复杂光合真核生物起源中的作用。我们研究的特定微生物相当于“俄罗斯嵌套娃娃”的细胞：它们是反复循环内共生的结果，其中细胞驻留在其他细胞内，而其他细胞本身又嵌套在更大的细胞内。这些一系列的内共生事件产生了地球上一些最丰富、对生态最重要的初级生产者，包括硅藻（海洋的“宝石”）、巨型海带和甲藻，它们会引起“赤潮”，也是珊瑚礁的重要组成部分。尽管其具有明显的生物学意义，但人们对次生内共生的机制细节知之甚少。我们将分析某些藻类的基因组，以深入了解（i）不同物种中基因从一个亚细胞区室移动到另一个亚细胞区室的方式和频率，以及（ii）这些古老进化的嵌合细胞在多大程度上是“混合和匹配”生物化学的产物。 除了生命本身的起源之外，线粒体和质体的内共生起源可以说是地球历史上最重要的事件。然而直到最近，共生还被视为一种进化上的奇怪现象而被忽视。现实情况是，光合海洋微生物承担了地球上一半的初级生产，并构成了海洋食物网的基础。了解这些生物体的来源对我们来说非常重要。他们如何彼此互动；以及它们如何适应人类引起的环境变化。