ArticlePloS one2013
Structural phylogenomics reveals gradual evolutionary replacement of abiotic chemistries by protein enzymes in purine metabolism.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes.Scientific reports · 2025Article
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- Mechanisms of protein evolution.Protein science : a publication of the Protein Society · 2022Review
- Evolution of networks of protein domain organization.Scientific reports · 2021Article
- Phosphates as Energy Sources to Expand Metabolic Networks.Life (Basel, Switzerland) · 2019Article
- Article
- Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.Evolutionary bioinformatics online · 2019Review
- Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification.Science progress · 2018Review
- On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes.Journal of molecular evolution · 2018Article
- Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks.Life (Basel, Switzerland) · 2016Article
- The early history and emergence of molecular functions and modular scale-free network behavior.Scientific reports · 2016Article
- Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology.Computational and structural biotechnology journal · 2015Review
- The place of RNA in the origin and early evolution of the genetic machinery.Life (Basel, Switzerland) · 2014Article
- Purine biosynthetic intermediate-containing ribose-phosphate polymers as evolutionary precursors to RNA.Journal of molecular evolution · 2014Article
- The natural history of biocatalytic mechanisms.PLoS computational biology · 2014Article
- The natural history of transfer RNA and its interactions with the ribosome.Frontiers in genetics · 2014Article
- A calibrated chronology of biochemistry reveals a stem line of descent responsible for planetary biodiversity.Frontiers in genetics · 2014Article
- Global patterns of protein domain gain and loss in superkingdoms.PLoS computational biology · 2014Article
- Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus.Archaea (Vancouver, B.C.) · 2013Article
- Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.PloS one · 2013Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The origin of metabolism has been linked to abiotic chemistries that existed in our planet at the beginning of life. While plausible chemical pathways have been proposed, including the synthesis of nucleobases, ribose and ribonucleotides, the cooption of these reactions by modern enzymes remains shrouded in mystery. Here we study the emergence of purine metabolism. The ages of protein domains derived from a census of fold family structure in hundreds of genomes were mapped onto enzymes in metabolic diagrams. We find that the origin of the nucleotide interconversion pathway benefited most parsimoniously from the prebiotic formation of adenine nucleosides. In turn, pathways of nucleotide biosynthesis, catabolism and salvage originated ∼300 million years later by concerted enzymatic recruitments and gradual replacement of abiotic chemistries. Remarkably, this process led to the emergence of the fully enzymatic biosynthetic pathway ∼3 billion years ago, concurrently with the appearance of a functional ribosome. The simultaneous appearance of purine biosynthesis and the ribosome probably fulfilled the expanding matter-energy and processing needs of genomic information.
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