ArticleMolecular systems biology2014
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.
Article in Molecular systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- Pan-genome-scale metabolic modeling ofmSystems · 2024Article
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- CsrA Shows Selective Regulation of sRNA-mRNA Networks.bioRxiv : the preprint server for biology · 2023Article
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- Basics on network theory to analyze biological systems: a hands-on outlook.Functional & integrative genomics · 2022Article
- Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.Communications biology · 2021Article
- Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks.Nucleic acids research · 2020Article
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.Nature protocols · 2019Article
- Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.PLoS computational biology · 2018Article
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- Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data.BMC systems biology · 2017Article
- SeqTU: A Web Server for Identification of Bacterial Transcription Units.Scientific reports · 2017Article
- Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units inFrontiers in microbiology · 2017Article
- Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models.Bioinformatics (Oxford, England) · 2016Article
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8 authors.
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Abstract
Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we introduce an unbiased, pathway structure for genome-scale metabolic networks defined based on principles of parsimony that do not mimic canonical human-defined textbook pathways. Instead, these minimal pathways better describe multiple independent pathway-associated biomolecular interaction datasets suggesting a functional organization for metabolism based on parsimonious use of cellular components. We use the inherent predictive capability of these pathways to experimentally discover novel transcriptional regulatory interactions in Escherichia coli metabolism for three transcription factors, effectively doubling the known regulatory roles for Nac and MntR. This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated.
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