ArticleJournal of chemical information and modeling2013
Modular architecture of metabolic pathways revealed by conserved sequences of reactions.
Article in Journal of chemical information and modeling, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
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- Metabolomics of early blight (Alternaria solani) susceptible tomato (Solanum lycopersicum) unfolds key biomarker metabolites and involved metabolic pathways.Scientific reports · 2023Article
- Insights into Common Octopus (Marine drugs · 2023Article
- A relationship between phages and organic carbon in wastewater treatment plant effluents.Water research X · 2022Article
- METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.Microbiome · 2022Article
- Transcriptome analysis of the effect of a novel human serine protease inhibitor SPINK13 on gene expression in MHCC97-H cells.Translational cancer research · 2021Article
- Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem.Microbiology spectrum · 2021Article
- Article
- Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior.Frontiers in genetics · 2021Review
- Improving the organization and interactivity of metabolic pathfinding with precomputed pathways.BMC bioinformatics · 2020Article
- The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae.Molecular systems biology · 2019Article
- Toward understanding the origin and evolution of cellular organisms.Protein science : a publication of the Protein Society · 2019Review
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6 authors.
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Abstract
The metabolic network is both a network of chemical reactions and a network of enzymes that catalyze reactions. Toward better understanding of this duality in the evolution of the metabolic network, we developed a method to extract conserved sequences of reactions called reaction modules from the analysis of chemical compound structure transformation patterns in all known metabolic pathways stored in the KEGG PATHWAY database. The extracted reaction modules are repeatedly used as if they are building blocks of the metabolic network and contain chemical logic of organic reactions. Furthermore, the reaction modules often correspond to traditional pathway modules defined as sets of enzymes in the KEGG MODULE database and sometimes to operon-like gene clusters in prokaryotic genomes. We identified well-conserved, possibly ancient, reaction modules involving 2-oxocarboxylic acids. The chain extension module that appears as the tricarboxylic acid (TCA) reaction sequence in the TCA cycle is now shown to be used in other pathways together with different types of modification modules. We also identified reaction modules and their connection patterns for aromatic ring cleavages in microbial biodegradation pathways, which are most characteristic in terms of both distinct reaction sequences and distinct gene clusters. The modular architecture of biodegradation modules will have a potential for predicting degradation pathways of xenobiotic compounds. The collection of these and many other reaction modules is made available as part of the KEGG database.
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