Corradi Nicolas, Sanders Ian R
Department of Ecology and Evolution, Biology building, University of Lausanne, 1015 Lausanne, Switzerland.
BMC Evol Biol. 2006 Mar 10;6:21. doi: 10.1186/1471-2148-6-21.
The P-type II ATPase gene family encodes proteins with an important role in adaptation of the cell to variation in external K+, Ca2+ and Na2+ concentrations. The presence of P-type II gene subfamilies that are specific for certain kingdoms has been reported but was sometimes contradicted by discovery of previously unknown homologous sequences in newly sequenced genomes. Members of this gene family have been sampled in all of the fungal phyla except the arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota), which are known to play a key-role in terrestrial ecosystems and to be genetically highly variable within populations. Here we used highly degenerate primers on AMF genomic DNA to increase the sampling of fungal P-Type II ATPases and to test previous predictions about their evolution. In parallel, homologous sequences of the P-type II ATPases have been used to determine the nature and amount of polymorphism that is present at these loci among isolates of Glomus intraradices harvested from the same field.
In this study, four P-type II ATPase sub-families have been isolated from three AMF species. We show that, contrary to previous predictions, P-type IIC ATPases are present in all basal fungal taxa. Additionally, P-Type IIE ATPases should no longer be considered as exclusive to the Ascomycota and the Basidiomycota, since we also demonstrate their presence in the Zygomycota. Finally, a comparison of homologous sequences encoding P-type IID ATPases showed unexpectedly that indel mutations among coding regions, as well as specific gene duplications occur among AMF individuals within the same field.
On the basis of these results we suggest that the diversification of P-Type IIC and E ATPases followed the diversification of the extant fungal phyla with independent events of gene gains and losses. Consistent with recent findings on the human genome, but at a much smaller geographic scale, we provided evidence that structural genomic changes, such as exonic indel mutations and gene duplications are less rare than previously thought and that these also occur within fungal populations.
P型II ATP酶基因家族编码的蛋白质在细胞适应外部钾离子、钙离子和钠离子浓度变化中发挥重要作用。已有报道称存在特定于某些界的P型II基因亚家族，但新测序基因组中发现的先前未知同源序列有时与之相矛盾。除丛枝菌根真菌（AMF；球囊霉门）外，该基因家族的成员已在所有真菌门中进行了采样，已知AMF在陆地生态系统中起关键作用，且在种群内遗传高度可变。在此，我们对AMF基因组DNA使用高度简并引物，以增加真菌P型II ATP酶的采样，并检验先前关于其进化的预测。同时，P型II ATP酶的同源序列已用于确定从同一田地采集的Glomus intraradices分离株中这些位点存在的多态性的性质和数量。
在本研究中，从三种AMF物种中分离出四个P型II ATP酶亚家族。我们表明，与先前预测相反，P型IIC ATP酶存在于所有基础真菌类群中。此外，P型IIE ATP酶不应再被视为子囊菌门和担子菌门所特有，因为我们也证明了它们在接合菌门中的存在。最后，对编码P型IID ATP酶的同源序列的比较意外地表明，同一田地内的AMF个体之间，编码区存在插入缺失突变以及特定的基因重复。
基于这些结果，我们认为P型IIC和E ATP酶的多样化遵循现存真菌门的多样化，伴随着基因得失的独立事件。与最近关于人类基因组的发现一致，但在更小的地理尺度上，我们提供了证据表明，结构基因组变化，如外显子插入缺失突变和基因重复比以前认为的更不罕见，并且这些变化也发生在真菌种群内。
