ArticlePloS one2014
Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Lipoic acid attachment to proteins: stimulating new developments.Microbiology and molecular biology reviews : MMBR · 2024Review
- Oxygen and the Spark of Human Brain Evolution: Complex Interactions of Metabolism and Cortical Expansion across Development and Evolution.The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry · 2024Article
- Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes.PLoS biology · 2023Article
- Carbon Fixation in the Chemolithoautotrophic BacteriumLife (Basel, Switzerland) · 2023Article
- Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins.ACS omega · 2023Review
- EP-Pred: A Machine Learning Tool for Bioprospecting Promiscuous Ester Hydrolases.Biomolecules · 2022Article
- Advances in the Structural Biology, Mechanism, and Physiology of Cyclopropane Fatty Acid Modifications of Bacterial Membranes.Microbiology and molecular biology reviews : MMBR · 2022Review
- Cell-Free Expression to Probe Co-Translational Insertion of an Alpha Helical Membrane Protein.Frontiers in molecular biosciences · 2022Article
- Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea.Communications chemistry · 2021Article
- Introduction-First Billion Years: Habitability.Astrobiology · 2021Review
- The Semi-Enzymatic Origin of Metabolic Pathways: Inferring a Very Early Stage of the Evolution of Life.Journal of molecular evolution · 2021Article
- Progress in the Enzymology of the Mitochondrial Diseases of Lipoic Acid Requiring Enzymes.Frontiers in genetics · 2020Review
- Decoding the ocean's microbiological secrets for marine enzyme biodiscovery.FEMS microbiology letters · 2019Review
- QnAs with John E. Cronan.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Assessing the Zoantharian Diversity of the Tropical Eastern Pacific through an Integrative Approach.Scientific reports · 2018Article
- Development and retention of a primordial moonlighting pathway of protein modification in the absence of selection presents a puzzle.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Metabolic evolution and the self-organization of ecosystems.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Assembly of Lipoic Acid on Its Cognate Enzymes: an Extraordinary and Essential Biosynthetic Pathway.Microbiology and molecular biology reviews : MMBR · 2016Review
- The universal tree of life: an update.Frontiers in microbiology · 2015Review
- The stereochemical basis of the genetic code and the (mostly) autotrophic origin of life.Life (Basel, Switzerland) · 2014Review
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.
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