Abstract
Approaches for systematizing information of relatedness between organisms is important in biology. Phylogenetic analyses based on sets of highly conserved genes are currently the basis for the Tree of Life. Genome-scale metabolic reconstructions contain high-quality information regarding the metabolic capability of an organism and are typically restricted to metabolically active enzyme-encoding genes. While there are many tools available to generate draft reconstructions, expert-level knowledge is still required to generate and manually curate high-quality genome-scale metabolic models and to fill gaps in their reaction networks. Here, we use the tool AutoKEGGRec to construct 975 genome-scale metabolic draft reconstructions encoded in the KEGG database without further curation. The organisms are selected across all three domains, and their metabolic networks serve as basis for generating phylogenetic trees. We find that using all reactions encoded, these metabolism-based comparisons give rise to a phylogenetic tree with close similarity to the Tree of Life. While this tree is quite robust to reasonable levels of noise in the metabolic reaction content of an organism, we find a significant heterogeneity in how much noise an organism may tolerate before it is incorrectly placed in the tree. Furthermore, by using the protein sequences for particular metabolic functions and pathway sets, such as central carbon-, nitrogen-, and sulfur-metabolism, as basis for the organism comparisons, we generate highly specific phylogenetic trees. We believe the generation of phylogenetic trees based on metabolic reaction content, in particular when focused on specific functions and pathways, could aid the identification of functionally important metabolic enzymes and be of value for genome-scale metabolic modellers and enzyme-engineers.
Highlights
Phylogenetic trees have been important in systematizing information in biology for several centuries [1]
Starting from a set of 975 organisms selected from the KEGG database currently consisting of 6, 758 organisms, we investigate the penetration of metabolic reactions, i.e. how is the metabolic reaction-set of an organism comprised of reactions that are unique to that organism or reactions that are used by many organisms
Defining a reaction present in less than 10% of the organisms as low penetration (LP), more than 90% as high penetration (HP), and presence in 35 − 65% as medium penetration (MP), we find that an average organism is composed of 7±7% LP, 25±5% MP, and 14±6% HP reactions
Summary
Phylogenetic trees have been important in systematizing information in biology for several centuries [1]. Genome-scale reconstructions to assess metabolic phylogeny and organism clustering from using 16/18 S rDNA to a selection of conserved (ribosomal) proteins/genes still a topic for research [2,3,4]. Whole genome and genome-scale data approaches allowed by the rapid development in computational methods and computation hardware are broadening the species tree among all taxa [5,6,7], for example by gaining an increased resolution by reducing statistical errors due to too few comparisons [8]. There exists several approaches to integrate more sequencing data into phylogeny determinations, as for example the use of whole-genome-scale phylogeny [10]. We will focus on using genome-scale metabolic reconstructions as the foundation for determining phylogenetic trees based on metabolic capability
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