The molecular basis of phenotypic evolution in social amoebas

生物学家想要了解复杂的多细胞生物体是如何从简单的单细胞祖先进化而来的。我们从理论上知道发生了什么：早期生物体基因的自发突变导致其后代的发育程序发生微小变化。这有时会导致改良的成虫更成功地繁殖，并因此逐渐取代早期的形式。然而，为了真正了解这一过程并证明它确实发生了，我们必须追溯哪些基因发生了突变，以及这种突变是如何改变基因功能的。我们还需要知道哪些发育机制是由突变的基因调控的，以及改变的发育机制最终是如何产生改良的成人形态的。因为不可能获得像我们这样高度进化的动物的如此详细的信息，我们在社会变形虫中调查了这个问题。这些生物在取食时以单细胞的形式生活，但在饥饿时聚集形成多细胞子实体，其中一定比例的细胞被保存为孢子。其他细胞形成柄和其他结构来支持孢子体。这种生活方式有赖于细胞的相互协作和专业化。一种名为盘藻的物种被许多实验室用作模型系统，以了解细胞如何移动、进食、繁殖和相互交流。在之前的研究中，我们构建了所有100个已知社会阿米巴物种的系统树，结果表明，社会阿米巴有四个主要群体。对于这100个物种中的每一个，我们都测量了30种属性(特征)，这些属性描述了它们的行为，它们组成部分的大小和形状，以及它们可以分化的细胞类型的数量。通过将这些信息与家谱相结合，我们获得了这些特征进化的顺序以及哪些特征总是一起出现的信息。最早的社会变形虫直接从聚集体中形成非常小的子实体。所有的细胞都先分化成前孢子细胞，然后一些细胞又发生变化，形成柄。这些早期物种可能使用一种名为Glorin的化合物进行聚集，就像他们的祖先孤独的阿米巴变形虫一样，他们仍然可以从单细胞形成包囊以生存饥饿。形成大型子实体的能力与一个中间的迁徙“鼻涕虫”阶段一起出现，这个阶段可以将聚集体带到土壤表面。在鼻涕虫内，前柄和前孢子细胞的分化比例与子实体所需的比例相同。细胞也形成了新的结构来支持茎，并使用cAMP脉冲聚集。然而，它们失去了形成包囊的能力。在这个新项目中，我们想要了解这些特征是如何进化的，以及它们为什么一起进化。它们之间有什么联系，需要什么新的机制来获得更多的细胞类型和建立更大的结构。其次，我们想要了解更高级物种的基因是如何改变的，从而使这些变化成为可能。我们最近与一个德国团队合作，对代表社会变形虫第1、2和3组的物种的基因组进行了测序。组4中的盘状螺旋体基因组已经测序完毕。从理论上讲，我们现在可以识别进化过程中发生的所有基因的变化。然而，由于每个生物体中有大量的基因(约12.000个)，这首先需要一种计算方法来确定最有可能参与我们想要研究的机制的基因。一旦选择了候选基因，我们就可以用更早形式的基因来替换进化程度更高的物种的基因，看看这是否会导致更高级的特性的丧失。相反的情况也是可能的。通过这种方式，我们将能够确定进化用来产生我们今天所看到的种类繁多的多细胞生物体的遗传机制。

Biologists want to understand how complex multicellular organisms have evolved from simple single-celled ancestors. We know in theory what happened: Spontaneous mutations in the genes of earlier organisms caused small changes in the developmental program of their offspring. This sometimes resulted in an improved adult that more successfully reproduced, and therefore gradually replaced the earlier form. However, to really understand this process and prove that it actually occurred, we have to trace back which genes were mutated and how this mutation changed gene function. We also need to know which developmental mechanisms were regulated by the mutated genes and how the altered developmental mechanism eventually produced the improved adult form. Because it is not possible to obtain such detailed information for highly evolved animals like ourselves, we investigate this problem in the social amoebas. These organisms live as single cells when they are feeding, but aggregate when starved to form a multicellular fruiting body, in which a proportion of cells is preserved as spores. The other cells form a stalk and other structures to support the spore mass. This life style depends on mutual collaboration and specialization of cells. One species, D.discoideum, is used by many laboratories as a model system to understand how cells move, eat, propagate and communicate with each other. In previous research, we constructed a family tree of all 100 known social amoeba species, which showed that there are four major groups of social amoebas. For each of the 100 species, we have measured 30 properties (traits), which describe their behaviours, the size and shape of their component parts and the number of cell types in which they can differentiate. By combining this information with the family tree, we have gained information in what order these traits evolved and which traits are always seen together. The earliest social amoeba formed very small fruiting bodies directly from aggregates. All cells first differentiated into prespore cells and then some changed again to form the stalk. These early species probably used a compound called glorin to aggregate and, like their ancestors the solitary amoebas, they could still form cysts from single cells to survive starvation.The ability to form large fruiting bodies appeared together with an intermediate migratory "slug" stage that could bring the aggregates to the soil surface. Inside the slug prestalk and prespore cells differentiated in the same proportions as needed in the fruiting body. Cells also formed new structures to support the stalk and used cAMP pulses to aggregate. However, they lost the ability to form cysts. In the new project we want to understand how these traits evolved and why they evolved together. What is the connection between them and what novel mechanisms were needed to obtain more cell types and build larger structures. Secondly, we want to understand how the genes of the more advanced species were altered to make these changes possible.In collaboration with a German team, we have recently sequenced the genomes of species that represent groups 1,2 and 3 of social amoebas. The genome of D.discoideum in group 4 was already sequenced before. We can now, in theory, identify changes in all the genes that occurred during evolution. However, due to the large number of genes in each organism (~12.000) this requires at first a computational approach to identify the most likely genes to be involved in the mechanisms that we want to study. Once candidate genes have been selected, we can replace the gene of a more evolved species with that of an earlier form and see whether this results in the loss of the more advanced property. The reverse is also possible. In this manner we will be able to determine the genetic mechanisms that have been used by evolution to generate the enormous variety of multicellular organisms that we see today.