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Pyrimidine homeostasis is accomplished by directed overflow metabolism

Nature volume 500, pages 237–241 (2013)Cite this article

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Abstract

Cellular metabolism converts available nutrients into usable energy and biomass precursors. The process is regulated to facilitate efficient nutrient use and metabolic homeostasis. Feedback inhibition of the first committed step of a pathway by its final product is a classical means of controlling biosynthesis1,2,3,4. In a canonical example, the first committed enzyme in the pyrimidine pathway in Escherichia coli is allosterically inhibited by cytidine triphosphate1,4,5. The physiological consequences of disrupting this regulation, however, have not been previously explored. Here we identify an alternative regulatory strategy that enables precise control of pyrimidine pathway end-product levels, even in the presence of dysregulated biosynthetic flux. The mechanism involves cooperative feedback regulation of the near-terminal pathway enzyme uridine monophosphate kinase6. Such feedback leads to build-up of the pathway intermediate uridine monophosphate, which is in turn degraded by a conserved phosphatase, here termed UmpH, with previously unknown physiological function7,8. Such directed overflow metabolism allows homeostasis of uridine triphosphate and cytidine triphosphate levels at the expense of uracil excretion and slower growth during energy limitation. Disruption of the directed overflow regulatory mechanism impairs growth in pyrimidine-rich environments. Thus, pyrimidine homeostasis involves dual regulatory strategies, with classical feedback inhibition enhancing metabolic efficiency and directed overflow metabolism ensuring end-product homeostasis.

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Figure 1: Increased pyrimidine flux triggers overflow to uracil.
Figure 2: Pyrimidine overflow pathway is initiated by catabolism of UMP by UmpH.
Figure 3: Cooperative inhibition of UMP kinase by UTP maintains end-product homeostasis.
Figure 4: Directed overflow metabolism in biosynthesis is analogous to central carbon overflow metabolism.

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Acknowledgements

M.L.R. was supported by an National Science foundation (NSF) Graduate Research Fellowship. J.D.R. was supported by NSF CDI Award CBET-0941143 and CAREER Award MCB-0643859, and DOE-AFOSR Award DE-SC0002077/FA9550-09-1-0580, and an American Heart Association Scientist Development Grant.

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Authors and Affiliations

  1. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, 08544, New Jersey, USA

    Marshall Louis Reaves, Brian D. Young, Aaron M. Hosios, Yi-Fan Xu & Joshua D. Rabinowitz

  2. Department of Molecular Biology, Princeton University, Princeton, 08544, New Jersey, USA

    Marshall Louis Reaves, Brian D. Young, Aaron M. Hosios & Joshua D. Rabinowitz

  3. Department of Chemistry, Princeton University, Princeton, 08544, New Jersey, USA

    Yi-Fan Xu & Joshua D. Rabinowitz

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  1. Marshall Louis Reaves
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Contributions

M.L.R., A.M.H., B.D.Y., Y.-F.X. and J.D.R. designed experiments and analyses. B.D.Y. generated feedback-dysregulated strains and performed experiments on regulation of the de novo pathway. A.M.H. performed competitions, microarrays and metabolite quantification. M.L.R. generated overflow and cooperativity mutants and measured their metabolites and growth. M.L.R. and J.D.R. wrote the paper with input from all authors.

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Correspondence to Joshua D. Rabinowitz.

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Reaves, M., Young, B., Hosios, A. et al. Pyrimidine homeostasis is accomplished by directed overflow metabolism. Nature 500, 237–241 (2013). https://doi.org/10.1038/nature12445

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