Principles of transcriptional regulation and evolution of the metabolic system in E. coli
- 1 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom;
- 2 Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
- 3 MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
- 4 EMBL-Heidelberg Gene Expression Unit, Heidelberg D-69117, Germany
Abstract
Organisms must adapt to make optimal use of the metabolic system in response to environmental changes. In the long-term, this involves evolution of the genomic repertoire of enzymes; in the short-term, transcriptional control ensures that appropriate enzymes are expressed in response to transitory extracellular conditions. Unicellular organisms are particularly susceptible to environmental changes; however, genome-scale impact of these modulatory effects has not been explored so far in bacteria. Here, we integrate genome-scale data to investigate the evolutionary trends and transcriptional control of metabolism in Escherichia coli K12. Globally, the regulatory system is organized in a clear hierarchy of general and specific transcription factors (TFs) that control differing ranges of metabolic functions. Further, catabolic, anabolic, and central metabolic pathways are targeted by distinct combinations of these TFs. Locally, enzymes catalyzing sequential reactions in a metabolic pathway are co-regulated by the same TFs. Regulation is more complex at junctions: General TFs control the overall activity of all connecting reactions, whereas specific TFs control individual enzymes. Divergent junctions play a special role in delineating metabolic pathways and decouple the regulation of incoming and outgoing reactions. We find little evidence for differential usage of isozymes, which are generally co-expressed in similar conditions, and thus are likely to reinforce the metabolic system through redundancy. Finally, we show that enzymes controlled by the same TFs have a strong tendency to co-evolve, suggesting a significant constraint to maintain similar regulatory regimes during evolution. Catabolic, anabolic, and central energy pathways evolve differently, emphasizing the role of the environment in shaping the metabolic system. Many of the observations also occur in yeast, and our findings may apply across large evolutionary distances.
Footnotes
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↵5 Corresponding authors.
↵E-mail aswin{at}ebi.ac.uk; fax 44 (0) 1223 492829.
↵E-mail luscombe{at}ebi.ac.uk; fax 44 (0) 1223 492572.
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[Supplemental material is available online at www.genome.org.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.079715.108.
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- Received April 13, 2008.
- Accepted September 29, 2008.
- Copyright © 2009, Cold Spring Harbor Laboratory Press