The enzymatic and metabolic capabilities of early life

Abstract

We introduce the concept of metaconsensus and employ it to make high confidence predictions of early enzyme functions and the metabolic properties that they may have produced. Several independent studies have used comparative bioinformatics methods to identify taxonomically broad features of genomic sequence data, protein structure data, and metabolic pathway data in order to predict physiological features that were present in early, ancestral life forms. But all such methods carry with them some level of technical bias. Here, we cross-reference the results of these previous studies to determine enzyme functions predicted to be ancient by multiple methods. We survey modern metabolic pathways to identify those that maintain the highest frequency of metaconsensus enzymes. Using the full set of modern reactions catalyzed by these metaconsensus enzyme functions, we reconstruct a representative metabolic network that may reflect the core metabolism of early life forms. Our results show that ten enzyme functions, four hydrolases, three transferases, one oxidoreductase, one lyase, and one ligase, are determined by metaconsensus to be present at least as late as the last universal common ancestor. Subnetworks within central metabolic processes related to sugar and starch metabolism, amino acid biosynthesis, phospholipid metabolism, and CoA biosynthesis, have high frequencies of these enzyme functions. We demonstrate that a large metabolic network can be generated from this small number of enzyme functions.

Figure 1. Metaconsensus analysis of conserved enzyme functions identified by three independent comparative bioinformatics methods.

These methods include comparisons of clusters of orthologous protein sequences , protein fold architectures , and metabolic reactions . Members in each of these datasets are converted to enzyme functions represented by a three-term EC code and the resulting datasets are made nonredundant. Six metaconsensus enzyme functions are found in all three datasets and thus are very likely to have been present in LUCA. Because the universal reactions data were acquired by comparing only autotrophic organisms, this analysis may be overly dependent on whether or not LUCA was also autotrophic. Thus, the four EC groups common between the universal sequence and universal structure datasets, but not present in the universal reaction dataset, are also likely to have been present in LUCA.

Figure 2. Ancestral folds associated with metaconsensus enzyme functions.

Folds are given in the horizontal axis by their SCOP code . Orange boxes indicate associations with metaconsensus enzyme reactions in the vertical axis. These folds (with ancestry values between 0% and 19%) were previously predicted to have originated before the establishment of the DNA genome . All of the metaconsensus enzyme functions are associated with a number of ancient folds. The three transferases (EC codes 2.4.1.-, 2.7.1.-, and 2.7.7.-) are associated with the highest number of these ancient folds.

Figure 3. Modern metabolic pathways with the highest frequencies of metaconsensus enzyme functions.

Pathways were identified as ancient through a survey of all pathways stored in the KEGG database . For each pathway, the frequency of metaconsensus enzyme functions is presented as both a percentage of the list of pathway enzymes and a percentage of the list of metaconsensus enzyme functions. A negative control is represented by yellow bars, which indicate the average value of pathway enzymes randomly assigned from all enzyme functions in the KEGG database. This analysis identifies amino acid, phospholipid, CoA, and carbohydrate metabolisms as ancient. Diagrams of these pathways with highlighted metaconsensus enzyme functions are available as Figure S1.

Figure 4. A reconstructed metabolism composed of reactions imparted by metaconsensus enzyme functions.

Nodes represent reactants and products while the edges connecting them represent metaconsensus enzyme functions. The network is composed of 119 nodes and 135 edges. Reactions were assembled from the KEGG reactions database and small molecules and cofactors were removed. Yellow edges represent metaconsensus enzyme functions predicted by the universal sequence, universal structure, and universal reaction datasets. Green edges represent metaconsensus enzyme functions predicted by the universal sequence and universal structure datasets, but not the universal reaction dataset. Subnetworks circled in red roughly reflect subsets of metabolism related to amino acids and peptides, nucleotides and RNA, sugars and starches, and phospholipids. This reconstructed metabolism demonstrates that significant metabolic complexity is possible with only these ten metaconsensus enzyme functions.