Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study

Abstract

Phylogenetic trees are typically constructed using genetic and genomic data, and provide robust evolutionary relationships of species from the genomic point of view. We present an application of network motif mining and analysis of metabolic pathways that when used in combination with phylogenetic trees can provide a more complete picture of evolution. By using distributions of three-node motifs as a proxy for metabolic similarity, we analyze the ancestral origin of Eukaryotic organelles from the metabolic point of view to illustrate the application of our motif mining and analysis network approach. Our analysis suggests that the hypothesis of an early proto-Eukaryote could be valid. It also suggests that a δ- or ε-Proteobacteria may have been the endosymbiotic partner that gave rise to modern mitochondria. Our evolutionary analysis needs to be extended by building metabolic network reconstructions of species from the phylum Crenarchaeota, which is considered to be a possible archaeal ancestor of the eukaryotic cell. In this paper, we also propose a methodology for constructing phylogenetic trees that incorporates metabolic network signatures to identify regions of genomically-estimated phylogenies that may be spurious. We find that results generated from our approach are consistent with a parallel phylogenetic analysis using the method of feature frequency profiles.

Revealing the metabolic characteristics of human embryonic stem cells by genome‐scale metabolic modeling

“…Motifs are patterns with significant higher occurrences in complex networks than in randomized networks . Recent studies have demonstrated that metabolic network motif abundance is related to biochemical functions and able to capture inter‐species differences .…”

On the origin of non-membrane-bound organelles, and their physiological function

“…Although the proposition of an endosymbiotic origin of eukaryotes initially met stiff resistance, and several details of the theory presented by Margulis turned out to be incorrect, 1 it has come to be generally accepted. The endosymbiotic theory explains the origin of double-membrane-bound organelles in eukaryotes, and has spurred continued debate about the evolution of other membrane-bound organelles including the nucleus (Embley and Martin, 2006; Devos et al, 2014; Shellman et al, 2014). Interestingly, the third organelles mentioned by Sagan (1967) were the (9+2) basal bodies – assemblies of microtubules found at the base of flagellum and cilium that are essential for mitosis.…”

DORMAN: Database of Reconstructed MetAbolic Networks

“…For instance, [19] shows that genes that are related to highly connected reactions in metabolic networks are subject to stricter evolutionary constraints. Another example is [20] that uses motifs in a metabolic network to study the evolutionary origin of six Eukaryotic organelles. Finally, Reporter Algorithm [3] detects biomarker metabolites, which have the highest dysregulation of gene expression in their direct neighborhood with respect to a phenotype.…”