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Methods Mol Biol. 2018;1732:111-142. doi: 10.1007/978-1-4939-7598-3_8.

Studying AMPK in an Evolutionary Context.

Author information

1
Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.
2
Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
3
Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria.
4
Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany. ebersberger@bio.uni-frankfurt.de.
5
Senckenberg Biodiversity and Climate Research Centre (BIK-F), Frankfurt, Germany. ebersberger@bio.uni-frankfurt.de.

Abstract

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.

KEYWORDS:

AMPK evolution; Feature architecture; Functional equivalence; Phylogenetic profiles; Targeted ortholog search

PMID:
29480472
DOI:
10.1007/978-1-4939-7598-3_8
[Indexed for MEDLINE]

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