Comparative genome analysis in social amoebas

生物学家试图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。我们从理论上知道这是如何发生的：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，为了真正理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，从而改变了发育程序。由于很难获得像我们这样的复杂生物体的如此详细的信息，我们在社会变形虫中研究了这个问题。社会变形虫以森林土壤中的细菌为单一细胞。然而，当饥饿时，它们聚集在一起形成一个果实结构，其中一定比例的细胞被保存为孢子。其他细胞被牺牲以形成有助于孢子散布的柄。这种生活方式有赖于细胞的相互协作和专业化。在进化过程中，社会阿米巴已经从只有10-100个细胞和两种细胞类型的基础物种，发展到形成100.000多个细胞和多达五种细胞类型的结构的高级物种。盘基网柄菌是一种高级物种，被广泛用作了解细胞如何运动、喂养和繁殖以及它们如何相互通信以实现多细胞的模式系统。盘状芽孢杆菌的基因组已经完全测序，这意味着我们有一个控制这些过程的所有基因的完整清单。盘状芽孢杆菌以环磷酸腺苷(CAMP)作为细胞间通讯的主要信号分子。它起到了化学吸引剂的作用，将饥饿的细胞聚集在一起，然后继续引导细胞建立子实体。CAMP还诱导孢子分化，调节孢子萌发过程。在之前BBSRC资助的研究中，我们构建了社会性阿米巴的系谱，结果表明，他们被细分为四大类群。盘形藻属于进化程度最高的类群4。从这四个类群的物种中，我们通过基因扩增获得了cAMP信号转导所必需的基因片段。这表明，cAMP的许多角色是保守的。然而，在不同的组之间，我们观察到这些基因活跃的发育阶段的变化。其中一种变化导致在第4组物种中使用cAMP作为化学引诱剂。基因扩增只能用于非常保守的基因，并且只能提供DNA小区域的信息。由于许多原因，在整个基因组水平上比较物种进化要好得多。因此，通过这项计划，我们建议完成对梅花聚伞菌基因组的测序。这项工作将与一个德国团队合作进行，该团队已经获得了对梅毒螺旋体基因组测序草案的资助。梅毒螺旋体特别适合于进化研究，因为它在家谱中占有基础地位，是少数几个易于进行基因操作的硬柄类动物之一。完整的梅毒螺旋体基因组序列将为我们提供所有cAMP信号基因的完整清单和序列，非常重要的是，还将告诉我们哪些基因缺失。通过识别基因的丢失和获得，以及通过比较盘状螺旋体和梅毒螺旋体之间保守的基因，我们可以检测到进化过程中发生的遗传变化。完成的梅毒螺旋体基因组也将对盘基菌和更广泛的研究界有很大的好处。例如，它可以用来识别蛋白质中具有重要作用的保守区域，这些区域到目前为止还没有得到很好的表征。

Biologists try to understand how complex multicellular organisms have evolved from simple single-celled ancestors. We know in theory how this happened: spontaneous mutations in the genes of earlier organisms caused small changes in the developmental program of their off-spring. 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 and consequently the developmental program. Because it is difficult to obtain such detailed information for complex organisms like ourselves, we investigate this problem in the social amoebas. Social amoebas feed as single cells on bacteria in forest soil. However, when starving, they come together and form a fruiting structure, in which a proportion of cells is preserved as spores. The other cells are sacrificed to form a stalk that aids in spore dispersal. This life style depends on mutual collaboration and specialization of cells. In the course of evolution the social amoebae have progressed from basal species that form structures with 10-100 cells and only two cell-types, to advanced species that form structures with over 100.000 cells and up to five cell types. One advanced species, Dictyostelium discoideum, is used widely as a model system to understand how cells move, feed and propagate and how they communicate with each other to achieve multicellularity. The D.discoideum genome has been completely sequenced, which means that we have a complete inventory of all the genes that control these processes. D.discoideum uses cyclic AMP (cAMP) as the major signal molecule for cell-cell communication. It acts as a chemoattractant to bring starving cells together, and then continues to guide cells to build a fruiting body. cAMP also induces the differentiation of the spores and regulates the process of spore germination. In previous BBSRC-funded research we constructed a family tree of the social amoebas, which shows that they are subdivided into four major groups. D.discoideum belongs to the most evolved group 4. From species in all four groups, we obtained fragments of the genes that are necessary for cAMP signalling by gene amplification. This suggests that many roles of cAMP are conserved. However, between groups, we observed changes in the stage of development at which these genes are active. One such as change gave rise to the use of cAMP as chemoattractant in the group 4 species. Gene amplification can only be used for very deeply conserved genes and only provides information on small regions of DNA. For many reasons it would be much better to compare species evolution at the level of the entire genome. With this project we therefore propose to sequence the genome of Polysphondylium pallidum to completion. This work will be performed in collaboration with a German team, who already obtained funding for draft sequencing of the P.pallidum genome. P.pallidum is particularly suitable for evolutionary studies because it occupies a basal position in the family tree and it is one of the few Dictyostelids that is readily accessible for gene manipulation. The complete P.pallidum genome sequence will give us the complete inventory and sequences of all cAMP signalling genes, and very importantly, will also tell us which genes are missing. By identifying gene losses and gains, and by comparing genes that are conserved between D.discoideum and P.pallidum, we can detect the genetic changes that occurred in the course of evolution. The completed P.pallidum genome will also be of great benefit for the Dictyostelium and broader research community. For instance, it can be used to identify conserved regions in proteins with important roles, that are thus far not well characterized.