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A grey box indicates that the enzyme has been detected in that genome, black boxes indicate that it has not. For each clustergram, rows indicate individual enzymes and columns indicate individual genomes. (a) Clustergrams showing the phylogenetic profiles of individual enzymes in three metabolic pathways. Representative examples of pathways containing evolutionary submodules of enzymes. (c,d) As for (b) but showing the relationship of enzyme coverage between the nr dataset and the complete and partial genome datasets, respectively. Enzymes involved in secondary metabolism appear to be more highly represented in the partial genome datasets than the complete genome datasets. Each point indicates a discrete enzyme (color indicates superclass membership - see inset key in (d)). (b) Relationships of enzyme coverage between the partial and complete genome datasets.
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Compared to all the genes within the partial and complete genome datasets, the enzymes are more highly represented. Fifty percent of all enzymes are associated with approximately 15% of all partial genomes, approximately 60% of all complete genomes and approximately 75% of the nr categories used in this study. (a) Coverage of enzymes and genes provided by the three different datasets: the non-redundant protein database ( nr) partial genomes and complete genomes. Representation of enzymes within three large-scale datasets. However, the precise complement of enzymes associated within this core for each species is flexible. These findings point to an emerging picture in which a core of enzyme activities involving amino acid, energy, carbohydrate and lipid metabolism have evolved to provide the basic functions required for life.
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Enzymes and pathways associated with the periphery of this network were less well conserved and associated with taxon-specific innovations. Expanding analyses to a global metabolic network revealed a highly conserved, but nonetheless flexible, 'core' of enzymes largely involved in multiple reactions across different pathways. Instead, such modularity appears restricted to smaller subsets of enzymes. Applying a novel co-conservation analysis, KEGG defined pathways did not generally display evolutionary coherence. However, organizing these enzymes within the context of functional pathways revealed a spectrum of conservation from those that are highly conserved (for example, carbohydrate, energy, amino acid and nucleotide metabolism enzymes) to those specific to individual taxa (for example, those involved in glycan metabolism and secondary metabolite pathways). In general, metabolic enzymes are highly conserved. Here we supplement existing genome and protein resources with partial genome datasets derived from 193 eukaryotes to present a comprehensive survey of the conservation of metabolism across 26 taxa representing the three domains of life. The recent availability of vast amounts of sequence data from diverse sets of organisms provides an opportunity to systematically examine metabolism from a comparative perspective.
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Cellular metabolism is a fundamental biological system consisting of myriads of enzymatic reactions that together fulfill the basic requirements of life.