Underground isoleucine biosynthesis pathways in E. coli
- Max Planck Institute of Molecular Plant Physiology, Germany
- Max Planck Institute of Terrestrial Microbiology, Germany
- Max Planck Insitute of Molecular Plant Physiology, Germany
Abstract
The promiscuous activities of enzymes provide fertile ground for the evolution of new metabolic pathways. Here, we systematically explore the ability of E. coli to harness underground metabolism to compensate for the deletion of an essential biosynthetic pathway. By deleting all threonine deaminases, we generated a strain in which isoleucine biosynthesis was interrupted at the level of 2-ketobutyrate. Incubation of this strain under aerobic conditions resulted in the emergence of a novel 2-ketobutyrate biosynthesis pathway based upon the promiscuous cleavage of O-succinyl-L-homoserine by cystathionine γ-synthase (MetB). Under anaerobic conditions, pyruvate formate-lyase enabled 2-ketobutyrate biosynthesis from propionyl-CoA and formate. Surprisingly, we found this anaerobic route to provide a substantial fraction of isoleucine in a WT strain, when propionate is available in the medium. This study demonstrates the selective advantage underground metabolism offers, providing metabolic redundancy and flexibility which allow for the best use of environmental carbon sources.
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 2 and 7 as well as for the metabolomic analysis.
Article and author information
Author details
Iria Bernhardsgrütter
Funding
Max Planck Society
- Arren Bar-Even
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Pimchai Chaiyen, Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand
Version history
- Received: December 5, 2019
- Accepted: August 22, 2020
- Accepted Manuscript published: August 24, 2020 (version 1)
- Version of Record published: September 7, 2020 (version 2)
Copyright
© 2020, Cotton et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Underground isoleucine biosynthesis pathways in E. coli
eLife 9:e54207.
https://doi.org/10.7554/eLife.54207
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