Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis

In response to the stress of infection, Mycobacterium tuberculosis (Mtb) reprograms its metabolism to accommodate nutrient and energetic demands in a changing environment. Pyruvate kinase (PYK) is an essential glycolytic enzyme in the phosphoenolpyruvate-pyruvate-oxaloacetate node that is a central...

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Main Authors: Zhong, Wenhe, Guo, Jingjing, Cui, Liang, Chionh, Yok Hian, Li, Kuohan, El Sahili, Abbas, Cai, Qixu, Yuan, Meng, Michels, Paul A. M., Fothergill-Gilmore, Linda A., Walkinshaw, Malcolm D., Mu, Yuguang, Lescar, Julien, Dedon, Peter C.
Other Authors: School of Biological Sciences
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Language:English
Published: 2021
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Online Access:https://hdl.handle.net/10356/151959
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spelling sg-ntu-dr.10356-1519592021-07-10T20:11:33Z Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis Zhong, Wenhe Guo, Jingjing Cui, Liang Chionh, Yok Hian Li, Kuohan El Sahili, Abbas Cai, Qixu Yuan, Meng Michels, Paul A. M. Fothergill-Gilmore, Linda A. Walkinshaw, Malcolm D. Mu, Yuguang Lescar, Julien Dedon, Peter C. School of Biological Sciences Lee Kong Chian School of Medicine (LKCMedicine) Institute of Structural Biology Singapore Centre for Environmental Life Sciences and Engineering (SCELSE) Singapore-MIT Alliance for Research and Technology Science::Biological sciences Allosteric Regulation Structural Dynamics In response to the stress of infection, Mycobacterium tuberculosis (Mtb) reprograms its metabolism to accommodate nutrient and energetic demands in a changing environment. Pyruvate kinase (PYK) is an essential glycolytic enzyme in the phosphoenolpyruvate-pyruvate-oxaloacetate node that is a central switch point for carbon flux distribution. Here we show that the competitive binding of pentose monophosphate inhibitors or the activator glucose 6-phosphate (G6P) to MtbPYK tightly regulates the metabolic flux. Intriguingly, pentose monophosphates were found to share the same binding site with G6P. The determination of a crystal structure of MtbPYK with bound ribose 5-phosphate (R5P), combined with biochemical analyses and molecular dynamic simulations, revealed that the allosteric inhibitor pentose monophosphate increases PYK structural dynamics, weakens the structural network communication, and impairs substrate binding. G6P, on the other hand, primes and activates the tetramer by decreasing protein flexibility and strengthening allosteric coupling. Therefore, we propose that MtbPYK uses these differences in conformational dynamics to up- and down-regulate enzymic activity. Importantly, metabolome profiling in mycobacteria reveals a significant increase in the levels of pentose monophosphate during hypoxia, which provides insights into how PYK uses dynamics of the tetramer as a competitive allosteric mechanism to retard glycolysis and facilitate metabolic reprogramming toward the pentose-phosphate pathway for achieving redox balance and an anticipatory metabolic response in Mtb. Ministry of Education (MOE) National Medical Research Council (NMRC) National Research Foundation (NRF) Accepted version This research was supported by the National Research Foundation of Singapore through the Singapore–MIT Alliance for Research and Technology Antimicrobial Resistance research program, and a Singapore–MIT Alliance for Research and Technology Postdoctoral Fellowship (W.Z.). During the course of this study, the J.L. laboratory was supported by grant NMRC/CBRG/ 0073/2014. The Y. M. laboratory was supported by the grant of MOE Tier 1 RG146/17 from Ministry of Education Singapore. 2021-07-08T02:06:48Z 2021-07-08T02:06:48Z 2019 Journal Article Zhong, W., Guo, J., Cui, L., Chionh, Y. H., Li, K., El Sahili, A., Cai, Q., Yuan, M., Michels, P. A. M., Fothergill-Gilmore, L. A., Walkinshaw, M. D., Mu, Y., Lescar, J. & Dedon, P. C. (2019). Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis. Journal of Molecular Biology, 431(19), 3690-3705. https://dx.doi.org/10.1016/j.jmb.2019.07.033 0022-2836 https://hdl.handle.net/10356/151959 10.1016/j.jmb.2019.07.033 31381898 2-s2.0-85070557671 19 431 3690 3705 en NMRC/CBRG/ 0073/2014 RG146/17 Journal of Molecular Biology © 2019 Elsevier Ltd. All rights reserved. This paper was published in Journal of Molecular Biology and is made available with permission of Elsevier Ltd. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Science::Biological sciences
Allosteric Regulation
Structural Dynamics
spellingShingle Science::Biological sciences
Allosteric Regulation
Structural Dynamics
Zhong, Wenhe
Guo, Jingjing
Cui, Liang
Chionh, Yok Hian
Li, Kuohan
El Sahili, Abbas
Cai, Qixu
Yuan, Meng
Michels, Paul A. M.
Fothergill-Gilmore, Linda A.
Walkinshaw, Malcolm D.
Mu, Yuguang
Lescar, Julien
Dedon, Peter C.
Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis
description In response to the stress of infection, Mycobacterium tuberculosis (Mtb) reprograms its metabolism to accommodate nutrient and energetic demands in a changing environment. Pyruvate kinase (PYK) is an essential glycolytic enzyme in the phosphoenolpyruvate-pyruvate-oxaloacetate node that is a central switch point for carbon flux distribution. Here we show that the competitive binding of pentose monophosphate inhibitors or the activator glucose 6-phosphate (G6P) to MtbPYK tightly regulates the metabolic flux. Intriguingly, pentose monophosphates were found to share the same binding site with G6P. The determination of a crystal structure of MtbPYK with bound ribose 5-phosphate (R5P), combined with biochemical analyses and molecular dynamic simulations, revealed that the allosteric inhibitor pentose monophosphate increases PYK structural dynamics, weakens the structural network communication, and impairs substrate binding. G6P, on the other hand, primes and activates the tetramer by decreasing protein flexibility and strengthening allosteric coupling. Therefore, we propose that MtbPYK uses these differences in conformational dynamics to up- and down-regulate enzymic activity. Importantly, metabolome profiling in mycobacteria reveals a significant increase in the levels of pentose monophosphate during hypoxia, which provides insights into how PYK uses dynamics of the tetramer as a competitive allosteric mechanism to retard glycolysis and facilitate metabolic reprogramming toward the pentose-phosphate pathway for achieving redox balance and an anticipatory metabolic response in Mtb.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Zhong, Wenhe
Guo, Jingjing
Cui, Liang
Chionh, Yok Hian
Li, Kuohan
El Sahili, Abbas
Cai, Qixu
Yuan, Meng
Michels, Paul A. M.
Fothergill-Gilmore, Linda A.
Walkinshaw, Malcolm D.
Mu, Yuguang
Lescar, Julien
Dedon, Peter C.
format Article
author Zhong, Wenhe
Guo, Jingjing
Cui, Liang
Chionh, Yok Hian
Li, Kuohan
El Sahili, Abbas
Cai, Qixu
Yuan, Meng
Michels, Paul A. M.
Fothergill-Gilmore, Linda A.
Walkinshaw, Malcolm D.
Mu, Yuguang
Lescar, Julien
Dedon, Peter C.
author_sort Zhong, Wenhe
title Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis
title_short Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis
title_full Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis
title_fullStr Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis
title_full_unstemmed Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis
title_sort pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in mycobacterium tuberculosis
publishDate 2021
url https://hdl.handle.net/10356/151959
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