ArticleBMC systems biology2013
Inferring ancient metabolism using ancestral core metabolic models of enterobacteria.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 18 citations in OpenAlex.
- Virulence Regulation and Lifestyle Transitions: The Role of c-di-GMP and Two-Component Systems in Erwinia amylovora and Their Evolutionary Context Within Enterobacterales.Molecular plant pathology · 2026Review
- Molecular Phylogeny of "Chemosensory Proteins" in Bacteria and Arthropods: CSP as an Extremely Ancient Gene.Journal of molecular evolution · 2026Article
- Origin and adaptive evolutionary trajectory of the 3' UTR-derived sRNA UhpU in Enterobacteriaceae.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Harnessing the chromium reduction potential ofHeliyon · 2024Article
- Article
- Positive Selection during Niche Adaptation Results in Large-Scale and Irreversible Rearrangement of Chromosomal Gene Order in Bacteria.Molecular biology and evolution · 2022Article
- Article
- A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments.PloS one · 2016Article
- Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis.Genome biology and evolution · 2015Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundEnterobacteriaceae diversified from an ancestral lineage ~300-500 million years ago (mya) into a wide variety of free-living and host-associated lifestyles. Nutrient availability varies across niches, and evolution of metabolic networks likely played a key role in adaptation.
resultsHere we use a paleo systems biology approach to reconstruct and model metabolic networks of ancestral nodes of the enterobacteria phylogeny to investigate metabolism of ancient microorganisms and evolution of the networks. Specifically, we identified orthologous genes across genomes of 72 free-living enterobacteria (16 genera), and constructed core metabolic networks capturing conserved components for ancestral lineages leading to E. coli/Shigella (~10 mya), E. coli/Shigella/Salmonella (~100 mya), and all enterobacteria (~300-500 mya). Using these models we analyzed the capacity for carbon, nitrogen, phosphorous, sulfur, and iron utilization in aerobic and anaerobic conditions, identified conserved and differentiating catabolic phenotypes, and validated predictions by comparison to experimental data from extant organisms.
conclusionsThis is a novel approach using quantitative ancestral models to study metabolic network evolution and may be useful for identification of new targets to control infectious diseases caused by enterobacteria.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.