Metabolic processes are regulated by the relative need for the end product, but this control mechanism may fail if demand is very low. A safety mechanism that copes with low demand has been discovered in bacteria. See Letter p.237
In bacterial cells, the overproduction of metabolites is normally avoided by mechanisms that are similar in principle to control systems in engineering. In this issue, Reaves et al.1 (page 237) report what happens in mutant bacteria that lack a supposedly essential control mechanism to prevent excessive production of pyrimidine nucleotides — metabolites that act as building blocks for the synthesis of genes, but which are potentially toxic if allowed to accumulate. Instead of observing the expected accumulation, the authors discovered a mechanism in which excess nucleotides are eliminated. In so doing, they identified a plausible role for an enzyme whose physiological function had hitherto been unknownFootnote 1.
We all know that a kitchen sink is liable to overflow if the tap is left on with the plughole blocked. In most domestic sinks this danger is averted, at least partially, by having an overflow outlet near the top. But in more elaborate engineered systems, such as the domestic toilet, an overflow is avoided by means of negative feedback: as soon as the water in the tank reaches a certain level, the inflow is switched off. Bacterial metabolism is in many ways similar, in that feedback mechanisms prevent the potentially harmful build-up of metabolites. The great explosion of interest in biological regulatory mechanisms in the 1960s followed the realization that negative feedback in metabolism operates in the same way2,3 as in engineered systems, by allowing the output of an end product to match demand4 (Fig. 1a).
From an evolutionary perspective, what matters in metabolism is not so much the 'overflow' that occurs in the absence of biological feedback controls, but the build-up of compounds that arises when the requirement for a metabolite is too low to be handled adequately by feedback inhibition (Fig. 1b). This is difficult to test experimentally, but one can mimic the situation by studying mutant bacteria in which the feedback mechanism is suppressed. For example, mutants of Escherichia coli bacteria that are insensitive to feedback inhibition of the production of the amino acid lysine have been studied5, and behaved as expected: the cells grew poorly, probably as a result of lysine accumulation. By contrast, Reaves et al. observed that the expected overflow does not occur in mutant E. coli lacking feedback inhibition of the first enzyme in the biosynthetic pathway leading to pyrimidine nucleotides. Furthermore, the authors saw little effect of this lack of inhibition on the levels of the pathway's end product, cytidine triphosphate (CTP), and they found that the growth rates of the bacteria were normal, except under energy-limiting conditions.
CTP is essential for the synthesis of genes. Although it is produced from aspartate, an amino acid, it is about as different in structure from aspartate as a metabolite can be. Enzymes are normally inhibited by molecules that resemble their substrates, and the discovery that the first step of CTP biosynthesis — the one that uses aspartate as a substrate — is inhibited by CTP was one of the factors that led to the recognition of feedback regulation in metabolism2.
Surprisingly, Reaves and co-workers observed that neither CTP nor the biosynthetic intermediates leading to it accumulated in the mutant bacteria that lacked feedback regulation. So why not, and what happened to the excess CTP produced? The authors found that it was degraded and excreted in the form of uracil (an RNA base). They describe this mode of regulation as “directed overflow metabolism”; others have called it “catabolic demand”4. The degradation involved a phosphatase enzyme that is evolutionarily conserved, but whose function was previously unknown.
Metabolic regulation is most easily analysed in economic terms of supply and demand4,6, especially given that the primary function of feedback inhibition is to regulate metabolite concentrations, rather than fluxes. Biological responses to the demand for metabolic end products are common in many systems, thus explaining the occurrence of cooperative feedback inhibition, such as that by CTP in pyrimidine biosynthesis. But the degradation of CTP to uracil observed by Reaves et al. is not a response to demand for uracil, because there is no particular demand for it. Instead, this degradation is a response to the excessive supply of nucleotides, and allows the concentrations of CTP and its biosynthetic precursors to be kept essentially constant when demand for CTP is low (Fig. 1c). Regulation according to supply occurs in biological detoxication pathways, and also in central metabolism. In particular, the mammalian liver does not phosphorylate glucose to form glycogen — the polymer used for energy storage in mammals — to satisfy its own demand for energy, but to maintain glucose homeostasis in other organs by maintaining a constant concentration of glucose in the blood7.
The CTP-production pathway is therefore an example of a system in which regulation by demand for end product occurs side-by-side with regulation by degradation and excretion of excess end products. Evolution cannot have generated and conserved the excretion mechanism purely to compensate for the artificial deletion of feedback in experiments, so this pathway must represent a back-up strategy for physiological states in which demand falls below the finite range within which feedback is effective. If so, then we should expect to find examples of the same sort of behaviour in other pathways.
One other point will have occurred to alert readers. If excess production of pyrimidine nucleotides is overcome by converting the excess into uracil and excreting it, this implies that nutrients are not being used efficiently by the bacteria. That is why the mutant bacteria grew as well as normal ones when energy supplies were abundant, but somewhat more slowly when energy was limited.
*This article and the paper under discussion1 were published online on 31 July 2013.
Reaves, M. L., Young, B. D., Hosios, A. M., Xu, Y.-F. & Rabinowitz, J. D. Nature 500, 237–241 (2013).
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Yates, R. A. & Pardee, A. B. J. Biol. Chem. 221, 757–770 (1956).
Hofmeyr, J.-H. S. Essays Biochem. 45, 57–66 (2008).
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Hofmeyr, J.-H. S. & Cornish-Bowden, A. FEBS Lett. 476, 47–51 (2000).
Cárdenas, M. L. “Glucokinase”: Its Regulation and Role in Liver Metabolism (Landes Bioscience, 1995).
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