Coordination of bacterial proteome with metabolism by cyclic AMP signalling

Abstract

The cyclic AMP (cAMP)-dependent catabolite repression effect in Escherichia coli is among the most intensely studied regulatory processes in biology. However, the physiological function(s) of cAMP signalling and its molecular triggers remain elusive. Here we use a quantitative physiological approach to show that cAMP signalling tightly coordinates the expression of catabolic proteins with biosynthetic and ribosomal proteins, in accordance with the cellular metabolic needs during exponential growth. The expression of carbon catabolic genes increased linearly with decreasing growth rates upon limitation of carbon influx, but decreased linearly with decreasing growth rate upon limitation of nitrogen or sulphur influx. In contrast, the expression of biosynthetic genes showed the opposite linear growth-rate dependence as the catabolic genes. A coarse-grained mathematical model provides a quantitative framework for understanding and predicting gene expression responses to catabolic and anabolic limitations. A scheme of integral feedback control featuring the inhibition of cAMP signalling by metabolic precursors is proposed and validated. These results reveal a key physiological role of cAMP-dependent catabolite repression: to ensure that proteomic resources are spent on distinct metabolic sectors as needed in different nutrient environments. Our findings underscore the power of quantitative physiology in unravelling the underlying functions of complex molecular signalling networks.

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Figure 1: Catabolic and biosynthetic gene expression under nutrient limitations.
Figure 2: Proteome fractions and the partition model.
Figure 3: Transient repression by metabolic precursors.
Figure 4: Mechanism of cAMP-dependent signalling.

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Acknowledgements

We are grateful to R. Bender, A. Danchin, P. Geiduschek, J. Ingraham, S. Kustu, W. F. Loomis, A. Narang, J. Rabinowitz, M. H. Saier and members of the Hwa laboratory for valuable comments. This work was supported by the Human Frontiers in Science Program (RGP0022), and by the NSF to T.H. (PHY1058793) and through the Center for Theoretical Biological Physics (PHY0822283).

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C.Y., D.Y. and T.H. designed the study. C.Y., H.O., S.H., Z.Z. M.K., C.W.G. and D.Y. performed experiments. C.Y., S.H., Y.P.W. and T.H. analysed the data. P.L. and T.H. developed the model. All authors contributed to writing the paper and the supplement.

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Correspondence to Terence Hwa.

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The authors declare no competing financial interests.

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You, C., Okano, H., Hui, S. et al. Coordination of bacterial proteome with metabolism by cyclic AMP signalling. Nature 500, 301–306 (2013). https://doi.org/10.1038/nature12446

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