1. Global coordination of metabolic pathways in Escherichia coli by active and passive regulation
- Author
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Karl Kochanowski, Hiroyuki Okano, James R. Williamson, Terence Hwa, Vadim Patsalo, and Uwe Sauer
- Subjects
Medicine (General) ,Transcription, Genetic ,Anabolism ,Bioinformatics ,QH301-705.5 ,13C flux analysis ,Crp ,metabolomics ,proteomics ,regulation analysis ,Metabolite ,Computational biology ,Biology ,Proteomics ,Article ,General Biochemistry, Genetics and Molecular Biology ,chemistry.chemical_compound ,Metabolomics ,R5-920 ,Escherichia coli ,Biology (General) ,Transcription factor ,General Immunology and Microbiology ,Catabolism ,Escherichia coli Proteins ,Applied Mathematics ,Gene Expression Regulation, Bacterial ,Articles ,Metabolism ,Metabolic Flux Analysis ,Microbiology, Virology & Host Pathogen Interaction ,Metabolic pathway ,Computational Theory and Mathematics ,chemistry ,Trans-Activators ,Biochemistry and Cell Biology ,Other Biological Sciences ,General Agricultural and Biological Sciences ,Metabolic Networks and Pathways ,Transcription Factors ,Information Systems ,C-13 flux analysis - Abstract
Microorganisms adjust metabolic activity to cope with diverse environments. While many studies have provided insights into how individual pathways are regulated, the mechanisms that give rise to coordinated metabolic responses are poorly understood. Here, we identify the regulatory mechanisms that coordinate catabolism and anabolism in Escherichia coli. Integrating protein, metabolite, and flux changes in genetically implemented catabolic or anabolic limitations, we show that combined global and local mechanisms coordinate the response to metabolic limitations. To allocate proteomic resources between catabolism and anabolism, E. coli uses a simple global gene regulatory program. Surprisingly, this program is largely implemented by a single transcription factor, Crp, which directly activates the expression of catabolic enzymes and indirectly reduces the expression of anabolic enzymes by passively sequestering cellular resources needed for their synthesis. However, metabolic fluxes are not controlled by this regulatory program alone; instead, fluxes are adjusted mostly through passive changes in the local metabolite concentrations. These mechanisms constitute a simple but effective global regulatory program that coarsely partitions resources between different parts of metabolism while ensuring robust coordination of individual metabolic reactions., Molecular Systems Biology, 17 (4), ISSN:1744-4292
- Published
- 2021