title: 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.
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton, New Jersey, United States of America. adg@princeton.edu
authors.forename: Aaron David
authors.initials: AD
authors.lastname: Goldman
authors.forename: John A
authors.initials: JA
authors.lastname: Baross
authors.forename: Ram
authors.initials: R
authors.lastname: Samudrala
mesh_terms: D019295:Computational Biology; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D008670:Metals / Q000378:metabolism; D009711:Nucleotides / Q000378:metabolism; D017433:Protein Structure, Secondary
chemical_list: D004798:Enzymes; D008670:Metals; D009711:Nucleotides