Gene transfer in microbial eukaryotes

生命科学研究正处于一场革命之中，这场革命建立在我们对DNA的理解之上，DNA是生命的遗传物质。使用现代分子生物学的工具，以20年前无法想象的方式探索生活世界是可能的。取得重大进展的一个领域是我们对微生物生物圈的了解。数以千计的物种的基因组已经被破译，不仅是实验室培养的微生物，还有那些直接从它们的自然栖息地提取的微生物：从海洋和土壤样本到人类肠道的一切。对这些基因组序列的比较分析表明，横向基因转移(LGT)，即跨物种边界的DNA交换，是原核细胞进化的主要力量。LGT现在被广泛认为是细菌对抗生素产生抗药性、获得致病决定因素和适应新环境的重要机制。关于真核(含核)细胞参与LGT的程度尚不清楚。物种间LGT被用来解释在一些微生物真核生物以及植物、真菌甚至动物的基因组中存在意想不到的基因。然而，这种基因转移事件的潜在生物学机制在很大程度上尚不清楚。*我们研究的长期目标是阐明推动真核生物基因组进化的力量。在这里，我们将通过专注于三个相互关联的短期目标来努力实现这一目标：*(1)我们将从单细胞藻类和阿米巴物种集群中生成大型、强大的基因组序列数据集。*(2)我们将比较物种集群内和物种之间的基因组，以推断在较短的进化时间尺度上基因获得和丢失的模式；零星分布的基因的系统发育分析将使我们能够确定这些基因组的外来遗传物质的捐赠者。特别是，我们将寻找证据表明病毒可以在真核生物中充当LGT的介体，就像它们在原核生物中所做的那样。*(3)我们将比较我们的藻类和阿米巴密切相关菌株之间假定的LGT衍生基因的DNA序列，以寻找自然选择的证据，从而明确检验原核生物到真核生物和真核生物到真核生物的LGT可以适应受体生物的假设。当考虑微生物时，达尔文的生命之树开始看起来更像是一个生命网络，在地球上超过30亿年的生命中，生命在不同的生命形式之间垂直和水平地流动。该项目中产生的数据将有助于阐明真核生物树上LGT的节奏和模式，从而有助于了解微生物如何在自然界中适应和多样化。

Life science research is in the midst of a revolution built upon our understanding of DNA, the heredity material of life. Using the tools of modern molecular biology, it is possible to explore the living world in ways unimaginable 20 years ago. One area in which considerable advances have occurred is our understanding of the microbial biosphere. The genomes of thousands of species have been decoded, not only microbes cultured in the lab but those taken directly from their natural habitats: everything from ocean and soil samples to the human gut. Comparative analyses of these genome sequences have shown that lateral gene transfer (LGT)the exchange of DNA across species boundsis a major force in the evolution of prokaryotic cells. LGT is now widely accepted as an important mechanism by which bacteria develop resistance to antibiotics, acquire pathogenicity determinants, and adapt to new environments.******Much less is known about the extent to which eukaryotic (nucleus-containing) cells engage in LGT. Between-species LGT has been invoked to explain the presence of unexpected' genes in the genomes of some microbial eukaryotes, as well as those of plants, fungi and even animals. However, the underlying biological mechanisms of such gene transfer events are for the most part unclear. ******The long-term goal of our research is to elucidate the forces driving genome evolution in eukaryotes. Here we will work towards this goal by focusing on three inter-related short-term objectives: ******(1) We will generate large, robust genome sequence datasets from within species clusters of single-celled algae and amoebae. ******(2) We will compare genomes within and between species clusters in order to infer patterns of gene gain and loss over short evolutionary timescales; phylogenetic analyses of patchily distributed genes will allow us to determine the donors of foreign genetic material to these genomes. In particular, we will search for evidence that viruses can act of mediators of LGT in eukaryotes, as they do in prokaryotes.******(3) We will compare the DNA sequences of putative LGT-derived genes between closely related strains of our algae and amoebae to look for evidence of natural selection, thereby explicitly testing the hypothesis that prokaryote-to-eukaryote and eukaryote-to-eukaryote LGTs can be adaptive for the recipient organisms. ******When microbes are considered, Darwin's tree of life' has begun to look more like a web of lifegenes have flowed both vertically and horizontally between diverse life forms for more than three billion years of life on our planet. The data generated in this project will help elucidate the tempo and modes of LGT across the eukaryotic tree, thereby contributing to a robust picture of how microbes adapt and diversify in nature.*****