Comparative genome analysis in social amoebas

生物学家试图了解复杂的多细胞生物是如何从简单的单细胞祖先进化而来的。从理论上讲，我们知道这是如何发生的：早期生物体基因的自发突变在其后代的发育程序中引起了微小的变化。这有时会导致一个更成功地繁殖的改进的成年体，从而逐渐取代早期的形式。然而，要真正理解这个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，以及这种突变如何改变基因功能，从而改变发育程序。因为像我们这样的复杂生物很难获得如此详细的信息，所以我们在社会性变形虫中研究了这个问题。群居变形虫以单细胞形式以森林土壤中的细菌为食。然而，在饥饿的时候，它们聚集在一起，形成一个果实结构，其中一部分细胞被保存为孢子。其他细胞被牺牲，形成有助于孢子扩散的茎。这种生活方式依赖于细胞的相互协作和专业化。在进化过程中，社会性变形虫从具有10-100个细胞和两种细胞类型的基础物种发展到具有超过100,000个细胞和多达五种细胞类型的高级物种。一种先进的物种盘基骨柱（Dictyostelium disideum）被广泛用作模型系统，以了解细胞如何移动、喂养和繁殖，以及它们如何相互沟通以实现多细胞化。盘状棘球蚴的基因组已经被完全测序，这意味着我们有了控制这些过程的所有基因的完整清单。盘状草以环AMP （cAMP）作为细胞间通讯的主要信号分子。它作为一种化学引诱剂，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还能诱导孢子分化，调控孢子萌发过程。在之前bbsrc资助的研究中，我们构建了一个社会变形虫的家谱，显示它们被细分为四个主要群体。disideum属进化程度最高的第4类群。从所有四组的物种中，我们通过基因扩增获得了cAMP信号传导所必需的基因片段。这表明cAMP的许多作用是保守的。然而，在两组之间，我们观察到这些基因活跃的发育阶段的变化。一个这样的变化导致了在第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。出于许多原因，在整个基因组的水平上比较物种进化会好得多。因此，在这个项目中，我们建议完成对白桦多香的基因组测序。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苍白孢粉基因组测序草案的资助。P.pallidum特别适合于进化研究，因为它在家谱中处于基础位置，而且它是少数几个易于进行基因操作的盘形骨类之一。完整的苍白假单胞菌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，而且非常重要的是，还将告诉我们哪些基因缺失。通过识别基因的损失和获得，并通过比较盘状棘球蚴和苍白棘球蚴之间的保守基因，我们可以发现在进化过程中发生的遗传变化。完整的苍白假单胞菌基因组也将对盘基骨门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，这些区域迄今尚未得到很好的表征。

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.