Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.
Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda s/n, Rosario S2000FHQ, Argentina.
PLoS Genet. 2019 Feb 21;15(2):e1007986. doi: 10.1371/journal.pgen.1007986. eCollection 2019 Feb.
Genes and genomes can evolve through interchanging genetic material, this leading to reticular evolutionary patterns. However, the importance of reticulate evolution in eukaryotes, and in particular of horizontal gene transfer (HGT), remains controversial. Given that metabolic pathways with taxonomically-patchy distributions can be indicative of HGT events, the eukaryotic nitrate assimilation pathway is an ideal object of investigation, as previous results revealed a patchy distribution and suggested that the nitrate assimilation cluster of dikaryotic fungi (Opisthokonta) could have been originated and transferred from a lineage leading to Oomycota (Stramenopiles). We studied the origin and evolution of this pathway through both multi-scale bioinformatic and experimental approaches. Our taxon-rich genomic screening shows that nitrate assimilation is present in more lineages than previously reported, although being restricted to autotrophs and osmotrophs. The phylogenies indicate a pervasive role of HGT, with three bacterial transfers contributing to the pathway origin, and at least seven well-supported transfers between eukaryotes. In particular, we propose a distinct and more complex HGT path between Opisthokonta and Stramenopiles than the one previously suggested, involving at least two transfers of a nitrate assimilation gene cluster. We also found that gene fusion played an essential role in this evolutionary history, underlying the origin of the canonical eukaryotic nitrate reductase, and of a chimeric nitrate reductase in Ichthyosporea (Opisthokonta). We show that the ichthyosporean pathway, including this novel nitrate reductase, is physiologically active and transcriptionally co-regulated, responding to different nitrogen sources; similarly to distant eukaryotes with independent HGT-acquisitions of the pathway. This indicates that this pattern of transcriptional control evolved convergently in eukaryotes, favoring the proper integration of the pathway in the metabolic landscape. Our results highlight the importance of reticulate evolution in eukaryotes, by showing the crucial contribution of HGT and gene fusion in the evolutionary history of the nitrate assimilation pathway.
基因和基因组可以通过交换遗传物质进行进化，从而导致网状进化模式。然而，在真核生物中，特别是在水平基因转移（HGT）方面，网状进化的重要性仍然存在争议。由于具有分类学上斑驳分布的代谢途径可能表明发生了 HGT 事件，因此真核硝酸盐同化途径是一个理想的研究对象，因为先前的研究结果显示出斑驳的分布，并表明二核真菌（后生动物）的硝酸盐同化簇可能是从导致卵菌（Stramenopiles）的谱系中起源和转移而来的。我们通过多尺度生物信息学和实验方法研究了该途径的起源和进化。我们丰富的分类群基因组筛选表明，硝酸盐同化存在于比以前报道的更多的谱系中，尽管仅限于自养生物和渗透营养生物。系统发育分析表明 HGT 具有普遍作用，有三个细菌转移对途径起源有贡献，至少有七个在真核生物之间得到很好支持的转移。特别是，我们提出了一个与以前提出的不同且更复杂的 HGT 路径，涉及到 Opisthokonta 和 Stramenopiles 之间至少两次硝酸盐同化基因簇的转移。我们还发现，基因融合在这一进化历史中起着至关重要的作用，它是经典真核硝酸盐还原酶和 Ichthyosporea（后生动物）中嵌合硝酸盐还原酶的起源。我们表明，包括这种新型硝酸盐还原酶在内的ichthyosporean 途径在生理上是活跃的，并且转录上是共调控的，对不同的氮源有反应；与具有独立途径 HGT 获取的遥远真核生物相似。这表明这种转录调控模式在真核生物中趋同进化，有利于途径在代谢景观中的适当整合。我们的研究结果强调了网状进化在真核生物中的重要性，表明 HGT 和基因融合在硝酸盐同化途径的进化历史中起着至关重要的作用。
