ArticleProceedings of the National Academy of Sciences of the United States of America2007
The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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83 citing papers in PubMed, 166 citations in OpenAlex.
- The history of enzyme evolution embedded in metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Tracing the Origin and Evolution of the Secondary Structure of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Phylogeny Building for Structural Phylogenomic Research.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Coenzyme-protein interactions since early life.eLife · 2025Article
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Ancient nitrogenases are ATP dependent.mBio · 2024Article
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- Article
- A Short Tale of the Origin of Proteins and Ribosome Evolution.Microorganisms · 2022Review
- Multienzyme interactions of the de novo purine biosynthetic protein PAICS facilitate purinosome formation and metabolic channeling.The Journal of biological chemistry · 2022Article
- Engineering Climate-Change-Resilient Crops: New Tools and Approaches.International journal of molecular sciences · 2021Review
- Evolution of networks of protein domain organization.Scientific reports · 2021Article
- Bridging Themes: Short Protein Segments Found in Different Architectures.Molecular biology and evolution · 2021Article
- The Compressed Vocabulary of Microbial Life.Frontiers in microbiology · 2021Article
- Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design.Journal of molecular biology · 2020Article
- First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments.Die Naturwissenschaften · 2020Article
- RNA Aptamers for a tRNA-Binding Protein fromLife (Basel, Switzerland) · 2020Article
- The evolution of metabolism: How to test evolutionary hypotheses at the genomic level.Computational and structural biotechnology journal · 2020Review
- Reconstructing the Remote Origins of a Fold Singleton from a Flavodoxin-Like Ancestor.Biochemistry · 2019Article
23 more citing papers are in PubMed but not listed here.
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Metabolism represents a complex collection of enzymatic reactions and transport processes that convert metabolites into molecules capable of supporting cellular life. Here we explore the origins and evolution of modern metabolism. Using phylogenomic information linked to the structure of metabolic enzymes, we sort out recruitment processes and discover that most enzymatic activities were associated with the nine most ancient and widely distributed protein fold architectures. An analysis of newly discovered functions showed enzymatic diversification occurred early, during the onset of the modern protein world. Most importantly, phylogenetic reconstruction exercises and other evidence suggest strongly that metabolism originated in enzymes with the P-loop hydrolase fold in nucleotide metabolism, probably in pathways linked to the purine metabolic subnetwork. Consequently, the first enzymatic takeover of an ancient biochemistry or prebiotic chemistry was related to the synthesis of nucleotides for the RNA world.
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