Mapping Metabolic Evolution–Hints for the RNA World

June 1st, 2007 Placozoan Posted in News |

IT IS KNOWN that proteins can be broken down into various domains, often with a characteristic fold, and new proteins can be generated by splicing new domains onto an existing protein. The first ancestral domains probably evolved from the combination of genes for shorter peptides called antecedent domain segments.¹

Now a new study² attempts to elucidate the phylogeny of modern metabolic networks from their architectural details and determine which metabolic subnetworks were foundational to life. The authors examined 185 fully sequenced genomes representing all three superkingdoms. They searched for 776 folds defined by the Structural Classification of Proteins (SCOP). Only 16 of these were present in all organisms, and nine of these appeared at the base of the tree.

These nine ancient folds represent architectures of fundamental importance (SI Table 1) undisputedly encoded in a genetic core that can be traced back to the universal ancestor of the three superkingdoms of life (20). These architectures are widespread in metabolism and are present even in parasitic organisms with highly reduced genomes and proteome complements. Phylogenomic reconstruction of evolutionary relationships between these ancestral folds showed that the P-loop-containing nucleoside triphosphate hydrolase fold (c.37) was the most ancient architecture, followed by the DNA/RNA-binding three-helical bundle fold (a.4), and then by the two most multifunctional and widely shared folds in metabolism, the TIM βα-barrel (c.1) and the NAD(P)-binding Rossmann (c.2) folds (Fig. 1). The P-loop hydrolase fold represents a single superfamily that was also basal in trees of superfamilies (15). Phylogenetic relationships in the tree of nine ancient folds were congruent with those in the global tree of architectures (Fig. 1). All of these omnipresent architectures were also widely distributed throughout metabolism.

Thus, the last universal common ancestor already had a complex toolkit of enzymes, meaning these must have originated in precellular chemical evolution. A few more folds were added prior to divergence of the prokaryotes, and later the various superfamilies added unique folds to these 16 universal ones. The authors observed repeatedly that the origin of a new fold was followed by a burst of enzymatic innovation.

Having sorted out the fold phylogeny, the authors’ next step was to examine metabolic subnetworks and determine when these likely originated. There are 133 metabolic subnetworks, 28 were found not to contain the ancestral folds and were likely highly derived. Among these were subnetworks for oxygenic mitochondrial ATP synthesis and oxygenic photosynthesis, which is consistent with the geologic record showing little oxygen at the first appearance of life and with anaerobic pathways indicating adaptation to oxygen following prokaryotic divergence. However, subnetworks for amino acid metabolism, carbohydrate metabolism, lipid metabolism, and nucleotide metabolism were ancestral.

Their final task was to determine which subnetwork was the most ancient. The starting point was the most ancient fold, the P-loop hydrolase fold. The subnetworks that contained this fold were examined using a “subnetwork wheel” to examine interrelationships and determine whether the subnetworks were ancestral or more derived.

Because recruitment erases historical patterns of enzymes in networks, we used “subnetwork wheels” to reveal patterns of origin and evolution in metabolism. For each fold, these graphs represent subnetworks as vertices (nodes) and sharing of enzymatic activities (EC numbers at different levels of classification) as edges (lines connecting nodes). We assume that in network evolution, enzymes take over ancient or prebiotic reactions. In this process, a copy of a protein domain used in one metabolic context (donor site) begins functioning in a new context (host site), performing that function de novo or taking it over from the previous catalyst at the host site. This process overlaps with the invention of new architectures, beginning with the most ancient one, each new one contributing novel functions and new opportunities for recruitment. Although extant donor and host domains may differ, we assume successful recruitment results in evolutionary lockin at a structural level [structural canalization (25)] necessary to guarantee the maintenance of the fold architecture. Similarly, we consider that change is costly, and that takeovers are more plausible among sublevels within each EC classification level. Given these assumptions, four criteria were used to reveal evolutionary patterns of recruitment between subnetworks: (i) the abundance of the fold in each subnetwork, (ii) the ancestry of each subnetwork derived from trees of subnetworks, (iii) the sharing of enzymatic activities by subnetworks at different levels of EC classification, and (iv) phylogenomic superfamily relationships of the shared enzymes. These criteria provided weights to the vertices and edges of the subnetwork wheels that helped establish direction of enzyme recruitment.

They concluded that purine metabolism was the most ancient subnetwork. Probably the initial enzymes involved were phosphotransferases involved in “nucleotide interconversion, distribution (storage and recycling) of chemical energy in acid-anhydride bonds of nucleotides, and terminal production of nucleotides and cofactors”. These enyzmes would phosphorylate purines to produce nucleotides for construction of RNA (and later DNA) and for use in energy-requiring reactions.

Our results suggest strongly that modern metabolism originated in nucleotide metabolism, probably in pathways of purine metabolism. This is of great significance. The first enzymatic takeover of an ancient biochemistry or prebiotic chemistry involved processes related to the synthesis of nucleotides for a world in which RNA was the only genetically encoded catalyst (26). Although the RNA world has considerable explanatory power, explaining, for example, why RNA is at the core of translation (27), we know little of how this world transitioned into modern biochemistry (28). The origin of protein synthesis must have been the first step toward a ribonucleoprotein world, and the transition was probably driven by the superior catalytic ability of polypeptides and then proteins. Our findings suggest that modern metabolism developed early at the onset of protein discovery and had origins that benefited the formation of building blocks for the RNA world.

The results of this study are consistent with what we know of early life on earth and with an early RNA world. The interrelationships between the metabolic subnetworks demonstrate again how more complex systems are derived from simpler ones and evolutionary innovation spurs rapid radiation.

1. Lupas, A. N.; Ponting, C. P.; Russell, R. B. “On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?” Journal of Structural Biology 2001, 134, 191. doi:10.1006/jsbi.2001.4393

2. Caetano-Anolles, G.; Kim, H. S.; Mittenthal, J. E. “The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture.” Proceedings of the National Academy of Sciences, USA 2007, 104, 9358.