Endosymbiosis and genome evolution in eukaryotic microbes

我们正处于一场科学革命之中，这场革命建立在我们对DNA的理解之上，DNA是生命的遗传分子。利用分子生物学的工具，我们正在以十年前无法想象的方式探索我们周围的世界。一个真正取得显著进步的领域是我们对微生物生物圈的理解。数以千计物种的基因组（遗传“蓝图”）已经被解码，不仅是实验室培养的生物，还有直接从自然栖息地获取的微生物：人类肠道，海洋，土壤，甚至我们呼吸的空气。对这些丰富的遗传数据进行比较分析后发现，水平基因转移（跨越物种边界的遗传物质交换）是一种强大的进化力量。越来越多的人支持这样一种观点，即当考虑微生物时，达尔文的“生命之树”实际上是一张生命之网--一张复杂的网，基因在不同的生命形式之间垂直和水平地流动了30多亿年。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。内共生的过程，即一个细胞在另一个细胞内居住，不仅涉及基因的“混合和匹配”，而且涉及整个生物体。在复杂的细胞（如我们自己的细胞）中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进化而来。质体（叶绿体），植物和藻类的集光室，也是内共生起源的。在这个建议中，我们将应用分子和计算机为基础的研究方法，在单细胞藻类的DNA的研究。目标是发展一个详细的了解模式和过程的内共生及其作用的起源复杂的光合真核生物。我们研究的特定微生物相当于“俄罗斯嵌套娃娃”的细胞：它们是由于反复的内共生而进化的，在这种内共生中，细胞居住在其他细胞中，而其他细胞本身又嵌套在更大的细胞中。这些一系列的内共生事件产生了地球上一些最丰富和生态上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，它们引起“赤潮”，也是珊瑚礁的重要组成部分。尽管其明显的生物学意义，相对知之甚少的机制细节次生内共生。我们将分析某些藻类群体的基因组，以深入了解（i）基因如何以及如何经常从一个亚细胞区室移动到不同物种的另一个亚细胞区室，以及（ii）这些古代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，线粒体和质体的内共生起源可以说是我们星球历史上最重要的事件。然而直到最近，共生现象还被认为是进化论中的一个古怪现象。事实上，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。对我们来说，重要的是要了解这些生物来自哪里;它们如何相互作用;以及它们如何适应人类引起的环境变化。

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.