Jain Arpit, Roustan Valentin, Weckwerth Wolfram, Ebersberger Ingo
Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
Methods Mol Biol. 2018;1732:111-142. doi: 10.1007/978-1-4939-7598-3_8.
The AMPK protein kinase forms the heart of a complex network controlling the metabolic activities in a eukaryotic cell. Unraveling the steps by which this pathway evolved from its primordial roots in the last eukaryotic common ancestor to its present status in contemporary species has the potential to shed light on the evolution of eukaryotes. A homolog search for the proteins interacting in this pathway is considerably straightforward. However, interpreting the results, when reconstructing the evolutionary history of the pathway over larger evolutionary distances, bears a number of pitfalls. With this in mind, we present a protocol to trace a metabolic pathway across contemporary species and backward in evolutionary time. Alongside the individual analysis steps, we provide guidelines for data interpretation generalizing beyond the analysis of AMPK.
AMPK蛋白激酶构成了控制真核细胞代谢活动的复杂网络的核心。阐明该途径从最后一个真核生物共同祖先的原始根源进化到当代物种中当前状态的步骤，有可能为真核生物的进化提供线索。在该途径中相互作用的蛋白质的同源物搜索相当简单。然而，在跨越更大进化距离重建该途径的进化历史时，解释结果存在许多陷阱。考虑到这一点，我们提出了一种在当代物种中追踪代谢途径并在进化时间上向后追溯的方案。除了各个分析步骤外，我们还提供了数据解释指南，这些指南可推广到AMPK分析之外。
