AMPK Methods and Protocols

Chapter 8

Studying AMPK in an Evolutionary Context

Arpit Jain, Valentin Roustan, Wolfram Weckwerth, and Ingo Ebersberger

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.

Key wordsAMPK evolution, Targeted ortholog search, Feature architecture, Functional equivalence,

Phylogenetic profiles

1 Introduction

Technological advances and continuing drop in prices [1] have

rendered genome sequencing a routine task in biological research.

The ultimate goal of any sequencing project is to characterize

structural and functional components in a genome shedding light

on the metabolic characteristics of the corresponding species. Com-

prehensive experimental characterization of protein function is

however limited to only few model organisms. In the case of

“non-model” organisms, for which protocols for experimental

research are often not established, or which are even uncultivable

under lab conditions, analyses rely on bioinformatics approaches to

transfer annotations of protein functions from model organisms.

Phylogenetic profiling is the current state-of-the-art bioinformatics

technique to reconstruct the evolutionary history of genes and

pathways [2], to predict protein–protein interactions [3], and to

infer functional similarities between proteins [4]. The phylogenetic

profile for a gene is constructed as a {1,0} vector representing the

presence (1) or absence (0) of homologs in contemporary species.

Dietbert Neumann and Benoit Viollet (eds.),AMPK: Methods and Protocols, Methods in Molecular Biology, vol. 1732,
https://doi.org/10.1007/978-1-4939-7598-3_8,©Springer Science+Business Media, LLC 2018

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