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Genetically encoded tools for measuring and manipulating metabolism

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Abstract

Over the past few years, we have seen an explosion of novel genetically encoded tools for measuring and manipulating metabolism in live cells and animals. Here, we will review the genetically encoded tools that are available, describe how these tools can be used and outline areas where future development is needed in this fast-paced field. We will focus on tools for direct measurement and manipulation of metabolites. Metabolites are master regulators of metabolism and physiology through their action on metabolic enzymes, signaling enzymes, ion channels and transcription factors, among others. We hope that this Perspective will encourage more people to use these novel reagents or even join this exciting new field to develop novel tools for measuring and manipulating metabolism.

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Fig. 1: Metabolism regulation.
Fig. 2: Schematic structures of select fluorescent sensors for measuring metabolism.
Fig. 3: Structures and reactions catalyzed by several available GEMMs.
Fig. 4: Schematic of the use of GEMMs and fluorescent sensors.

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References

  1. Mair, W. & Dillin, A. Aging and survival: the genetics of life span extension by dietary restriction. Annu. Rev. Biochem. 77, 727–754 (2008).

    Article  CAS  PubMed  Google Scholar 

  2. Warburg, O., Wind, F. & Negelein, E. The metabolism of tumors in the body. J. Gen. Physiol. 8, 519–530 (1927).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. DeBerardinis, R. J. & Chandel, N. S. We need to talk about the Warburg effect. Nat. Metab. 2, 127–129 (2020).

    Article  PubMed  Google Scholar 

  4. Fontana, L., Meyer, T. E., Klein, S. & Holloszy, J. O. Long-term calorie restriction is highly effective in reducing the risk for atherosclerosis in humans. Proc. Natl Acad. Sci. USA 101, 6659–6663 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lean, M. E. et al. Primary care-led weight management for remission of type 2 diabetes (DiRECT): an open-label, cluster-randomised trial. Lancet 391, 541–551 (2018).

    Article  PubMed  Google Scholar 

  6. Wen, C. P. et al. Minimum amount of physical activity for reduced mortality and extended life expectancy: a prospective cohort study. Lancet 378, 1244–1253 (2011).

    Article  PubMed  Google Scholar 

  7. Aune, D. et al. Fruit and vegetable intake and the risk of cardiovascular disease, total cancer and all-cause mortality—a systematic review and dose–response meta-analysis of prospective studies. Int. J. Epidemiol. 46, 1029–1056 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Blangy, D., Buc, H. & Monod, J. Kinetics of the allosteric interactions of phosphofructokinase from Escherichia coli. J. Mol. Biol. 31, 13–35 (1968).

    Article  CAS  PubMed  Google Scholar 

  9. Pettit, F. H., Pelley, J. W. & Reed, L. J. Regulation of pyruvate dehydrogenase kinase and phosphatase by acetyl-CoA/CoA and NADH/NAD ratios. Biochem. Biophys. Res. Commun. 65, 575–582 (1975).

    Article  CAS  PubMed  Google Scholar 

  10. Carling, D., Clarke, P. R., Zammit, V. A. & Hardie, D. G. Purification and characterization of the AMP-activated protein kinase. Copurification of acetyl-CoA carboxylase kinase and 3-hydroxy-3-methylglutaryl-CoA reductase kinase activities. Eur. J. Biochem. 186, 129–136 (1989).

    Article  CAS  PubMed  Google Scholar 

  11. Zhang, Q., Piston, D. W. & Goodman, R. H. Regulation of corepressor function by nuclear NADH. Science 295, 1895–1897 (2002).

    Article  CAS  PubMed  Google Scholar 

  12. Dunne, M. J. & Petersen, O. H. Intracellular ADP activates K+ channels that are inhibited by ATP in an insulin-secreting cell line. FEBS Lett. 208, 59–62 (1986).

    Article  CAS  PubMed  Google Scholar 

  13. Gibson, D. & Harris, R. A. Metabolic Regulation in Mammals (CRC Press, 2001).

  14. Lin, V. S., Dickinson, B. C. & Chang, C. J. Boronate-based fluorescent probes: imaging hydrogen peroxide in living systems. Methods Enzymol. 526, 19–43 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Su, Y. & Hammond, M. C. RNA-based fluorescent biosensors for live cell imaging of small molecules and RNAs. Curr. Opin. Biotechnol. 63, 157–166 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Mannan, A. A., Liu, D., Zhang, F. & Oyarzún, D. A. Fundamental design principles for transcription-factor-based metabolite biosensors. ACS Synth. Biol. 6, 1851–1859 (2017).

    Article  CAS  PubMed  Google Scholar 

  17. Greenwald, E. C., Mehta, S. & Zhang, J. Genetically encoded fluorescent biosensors illuminate the spatiotemporal regulation of signaling networks. Chem. Rev. 118, 11707–11794 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Gutscher, M. et al. Real-time imaging of the intracellular glutathione redox potential. Nat. Methods 5, 553–559 (2008). This article introduces GPX1–roGFP1 as a fluorescent sensor for measuring the GSSG/GSH ratio.

    Article  CAS  PubMed  Google Scholar 

  19. Gutscher, M. et al. Proximity-based protein thiol oxidation by H2O2-scavenging peroxidases. J. Biol. Chem. 284, 31532–31540 (2009). This article introduces Orp1–roGFP1 as a fluorescent sensor for measuring H2O2 levels.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Morgan, B. et al. Real-time monitoring of basal H2O2 levels with peroxiredoxin-based probes. Nat. Chem. Biol. 12, 437–443 (2016).

    Article  CAS  PubMed  Google Scholar 

  21. Tao, R. et al. Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism. Nat. Methods 14, 720–728 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhao, Y. et al. SoNar, a highly responsive NAD+/NADH sensor, allows high-throughput metabolic screening of anti-tumor agents. Cell Metab. 21, 777–789 (2015). This article introduces SoNar as a fluorescent sensor for measuring the NADH/NAD+ ratio.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Sanderson, M. J., Smith, I., Parker, I. & Bootman, M. D. Fluorescence microscopy. Cold Spring Harb. Protoc. 2014, pdb.top071795 (2014).

  24. Pomorski, A., Kochańczyk, T., Miłoch, A. & Krężel, A. Method for accurate determination of dissociation constants of optical ratiometric systems: chemical probes, genetically encoded sensors, and interacting molecules. Anal. Chem. 85, 11479–11486 (2013).

    Article  CAS  PubMed  Google Scholar 

  25. Bhakdi, S. et al. Staphylococcal α-toxin, streptolysin-O, and Escherichia coli hemolysin: prototypes of pore-forming bacterial cytolysins. Arch. Microbiol. 165, 73–79 (1996).

    Article  CAS  PubMed  Google Scholar 

  26. Shepard, L. A. et al. Identification of a membrane-spanning domain of the thiol-activated pore-forming toxin Clostridium perfringens perfringolysin O: an α-helical to β-sheet transition identified by fluorescence spectroscopy. Biochemistry 37, 14563–14574 (1998).

    Article  CAS  PubMed  Google Scholar 

  27. Titov, D. V. et al. Complementation of mitochondrial electron transport chain by manipulation of the NAD+/NADH ratio. Science 352, 231–235 (2016). This article reports the use of LbNOX as a tool for manipulation of NADH/NAD+ ratio. The authors use LbNOX to demonstrate that NA+ recycling, not ATP synthesis, is an essential function of the mitochondrial ETC required for cell proliferation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Cracan, V., Titov, D. V., Shen, H., Grabarek, Z. & Mootha, V. K. A genetically encoded tool for manipulation of NADP+/NADPH in living cells. Nat. Chem. Biol. 13, 1088–1095 (2017). This article introduces TPNOX as a tool for manipulation of the NADPH/NADP+ ratio.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Patgiri, A. et al. An engineered enzyme that targets circulating lactate to alleviate intracellular NADH:NAD+ imbalance. Nat. Biotechnol. 38, 309–313 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Guarás, A. et al. The CoQH2/CoQ ratio serves as a sensor of respiratory chain efficiency. Cell Rep. 15, 197–209 (2016).

    Article  PubMed  CAS  Google Scholar 

  31. Tkatch, T. et al. Optogenetic control of mitochondrial metabolism and Ca2+ signaling by mitochondria-targeted opsins. Proc. Natl Acad. Sci. USA 114, E5167–E5176 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Graf, S. A., Haigh, S. E., Corson, E. D. & Shirihai, O. S. Targeting, import, and dimerization of a mammalian mitochondrial ATP binding cassette (ABC) transporter, ABCB10 (ABC-me). J. Biol. Chem. 279, 42954–42963 (2004).

    Article  CAS  PubMed  Google Scholar 

  33. Berry, B. J. et al. Optogenetic control of mitochondrial protonmotive force to impact cellular stress resistance. EMBO Rep. 21, e49113 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Imai, Y. et al. Light-driven activation of mitochondrial proton-motive force improves motor behaviors in a Drosophila model of Parkinson’s disease. Commun. Biol. 2, 424 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Bulina, M. E. et al. A genetically encoded photosensitizer. Nat. Biotechnol. 24, 95–99 (2006). This article introduces KillerRed as a photosensitizer and superoxide producer.

    Article  CAS  PubMed  Google Scholar 

  36. Pletnev, S. et al. Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed*. J. Biol. Chem. 284, 32028–32039 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Shu, X. et al. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol. 9, e1001041 (2011). This article describes the development of miniSOG.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Haskew-Layton, R. E. et al. Controlled enzymatic production of astrocytic hydrogen peroxide protects neurons from oxidative stress via an Nrf2-independent pathway. Proc. Natl Acad. Sci. USA 107, 17385–17390 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Seo, B. B., Wang, J., Flotte, T. R., Yagi, T. & Matsuno-Yagi, A. Use of the NADH-quinone oxidoreductase (NDI1) gene of Saccharomyces cerevisiae as a possible cure for complex I defects in human cells. J. Biol. Chem. 275, 37774–37778 (2000).

    Article  CAS  PubMed  Google Scholar 

  40. Kido, Y. et al. Purification and kinetic characterization of recombinant alternative oxidase from Trypanosoma brucei brucei. Biochim. Biophys. Acta 1797, 443–450 (2010).

    Article  CAS  PubMed  Google Scholar 

  41. Goodman, R. P. et al. Hepatic NADH reductive stress underlies common variation in metabolic traits. Nature 583, 122–126 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. McElroy, G. S. et al. NAD+ regeneration rescues lifespan, but not ataxia, in a mouse model of brain mitochondrial complex I dysfunction. Cell Metab. 32, 301–308 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Martínez-Reyes, I. et al. Mitochondrial ubiquinol oxidation is necessary for tumour growth. Nature 585, 288–292 (2020).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Weinberg, S. E. et al. Mitochondrial complex III is essential for suppressive function of regulatory T cells. Nature 565, 495–499 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Diebold, L. P. et al. Mitochondrial complex III is necessary for endothelial cell proliferation during angiogenesis. Nat. Metab. 1, 158–171 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Das, A. T., Tenenbaum, L. & Berkhout, B. Tet-on systems for doxycycline-inducible gene expression. Curr. Gene Ther. 16, 156–167 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Moullan, N. et al. Tetracyclines disturb mitochondrial function across eukaryotic models: a call for caution in biomedical research. Cell Rep. 10, 1681–1691 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Lin, M. Z. & Schnitzer, M. J. Genetically encoded indicators of neuronal activity. Nat. Neurosci. 19, 1142–1153 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Shen, Y., Nasu, Y., Shkolnikov, I., Kim, A. & Campbell, R. E. Engineering genetically encoded fluorescent indicators for imaging of neuronal activity: progress and prospects. Neurosci. Res. 152, 3–14 (2020).

    Article  PubMed  Google Scholar 

  50. Zhao, Y. et al. An expanded palette of genetically encoded Ca2+ indicators. Science 333, 1888–1891 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Tantama, M., Martínez-François, J. R., Mongeon, R. & Yellen, G. Imaging energy status in live cells with a fluorescent biosensor of the intracellular ATP-to-ADP ratio. Nat. Commun. 4, 2550 (2013). This article introduces PercevalHR as a fluorescent sensor for measuring the ATP/ADP ratio.

    Article  PubMed  CAS  Google Scholar 

  52. Bilan, D. S. et al. HyPer-3: a genetically encoded H2O2 probe with improved performance for ratiometric and fluorescence lifetime imaging. ACS Chem. Biol. 8, 535–542 (2013).

    Article  CAS  PubMed  Google Scholar 

  53. Zhao, Y., Shen, Y., Wen, Y. & Campbell, R. E. High-performance intensiometric direct- and inverse-response genetically encoded biosensors for citrate. ACS Cent. Sci. 6, 1441–1450 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Park, J. O. et al. Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nat. Chem. Biol. 12, 482–489 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Chen, W. W., Freinkman, E., Wang, T., Birsoy, K. & Sabatini, D. M. Absolute quantification of matrix metabolites reveals the dynamics of mitochondrial metabolism. Cell 166, 1324–1337 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Hung, Y. P., Albeck, J. G., Tantama, M. & Yellen, G. Imaging cytosolic NADH-NAD+ redox state with a genetically encoded fluorescent biosensor. Cell Metab. 14, 545–554 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Krebs, H. A. The redox state of nicotinamide adenine dinucleotide in the cytoplasm and mitochondria of rat liver. Adv. Enzym. Regul. 5, 409–434 (1967).

    Article  CAS  Google Scholar 

  58. Zhao, Y. et al. Genetically encoded fluorescent sensors for intracellular NADH detection. Cell Metab. 14, 555–566 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Cambronne, X. A. et al. Biosensor reveals multiple sources for mitochondrial NAD+. Science 352, 1474–1477 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Lu, W., Wang, L., Chen, L., Hui, S. & Rabinowitz, J. D. Extraction and quantitation of nicotinamide adenine dinucleotide redox cofactors. Antioxid. Redox Signal. 28, 167–179 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Zhu, X.-H., Lu, M., Lee, B.-Y., Ugurbil, K. & Chen, W. In vivo NAD assay reveals the intracellular NAD contents and redox state in healthy human brain and their age dependences. Proc. Natl Acad. Sci. USA 112, 2876–2881 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Yu, Q. & Heikal, A. A. Two-photon autofluorescence dynamics imaging reveals sensitivity of intracellular NADH concentration and conformation to cell physiology at the single-cell level. J. Photochem. Photobiol. B 95, 46–57 (2009).

    Article  CAS  PubMed  Google Scholar 

  63. Zou, Y. et al. Illuminating NAD+ metabolism in live cells and in vivo using a genetically encoded fluorescent sensor. Dev. Cell 53, 240–252 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Sallin, O. et al. Semisynthetic biosensors for mapping cellular concentrations of nicotinamide adenine dinucleotides. eLife 7, e32638 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  65. Gribble, F. M. et al. A novel method for measurement of submembrane ATP concentration. J. Biol. Chem. 275, 30046–30049 (2000).

    Article  CAS  PubMed  Google Scholar 

  66. Dragon, S., Hille, R., Götz, R. & Baumann, R. Adenosine 3′:5′-cyclic monophosphate (cAMP)-inducible pyrimidine 5′-nucleotidase and pyrimidine nucleotide metabolism of chick embryonic erythrocytes. Blood 91, 3052–3058 (1998).

    Article  CAS  PubMed  Google Scholar 

  67. Imamura, H. et al. Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators. Proc. Natl Acad. Sci. USA 106, 15651–15656 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Yaginuma, H. et al. Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging. Sci. Rep. 4, 6522 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Lobas, M. A. et al. A genetically encoded single-wavelength sensor for imaging cytosolic and cell surface ATP. Nat. Commun. 10, 711 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Gu, H. et al. A novel analytical method for in vivo phosphate tracking. FEBS Lett. 580, 5885–5893 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. van Eunen, K. et al. Measuring enzyme activities under standardized in vivo-like conditions for systems biology: standardized enzyme assays for systems biology. FEBS J. 277, 749–760 (2010).

    Article  PubMed  CAS  Google Scholar 

  72. Veech, R. L., Eggleston, L. V. & Krebs, H. A. The redox state of free nicotinamide–adenine dinucleotide phosphate in the cytoplasm of rat liver. Biochem. J. 115, 609–619 (1969).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Shaik, I. H. & Mehvar, R. Rapid determination of reduced and oxidized glutathione levels using a new thiol-masking reagent and the enzymatic recycling method: application to the rat liver and bile samples. Anal. Bioanal. Chem. 385, 105–113 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Montero, D., Tachibana, C., Rahr Winther, J. & Appenzeller-Herzog, C. Intracellular glutathione pools are heterogeneously concentrated. Redox Biol. 1, 508–513 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Sies, H. Hydrogen peroxide as a central redox signaling molecule in physiological oxidative stress: oxidative eustress. Redox Biol. 11, 613–619 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Stone, J. R. & Yang, S. Hydrogen peroxide: a signaling messenger. Antioxid. Redox Signal. 8, 243–270 (2006).

    Article  CAS  PubMed  Google Scholar 

  77. Pak, V. V. et al. Ultrasensitive genetically encoded indicator for hydrogen peroxide identifies roles for the oxidant in cell migration and mitochondrial function. Cell Metab. 31, 642–653 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Takanaga, H., Chaudhuri, B. & Frommer, W. B. GLUT1 and GLUT9 as major contributors to glucose influx in HepG2 cells identified by a high sensitivity intramolecular FRET glucose sensor. Biochim. Biophys. Acta 1778, 1091–1099 (2008).

    Article  CAS  PubMed  Google Scholar 

  79. Hu, H. et al. Glucose monitoring in living cells with single fluorescent protein-based sensors. RSC Adv. 8, 2485–2489 (2018).

    Article  CAS  Google Scholar 

  80. Arce-Molina, R. et al. A highly responsive pyruvate sensor reveals pathway-regulatory role of the mitochondrial pyruvate carrier MPC. eLife 9, e53917 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  81. Bulusu, V. et al. Spatiotemporal analysis of a glycolytic activity gradient linked to mouse embryo mesoderm development. Dev. Cell 40, 331–341 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. San Martín, A. et al. A genetically encoded FRET lactate sensor and its use to detect the Warburg effect in single cancer cells. PLoS ONE 8, e57712 (2013).

  83. Leippe, D., Sobol, M., Vidugiris, G., Cali, J. J. & Vidugiriene, J. Bioluminescent assays for glucose and glutamine metabolism: high-throughput screening for changes in extracellular and intracellular. SLAS Discov. 22, 366–377 (2017).

    Article  CAS  PubMed  Google Scholar 

  84. Lønbro, S. et al. Reliability of blood lactate as a measure of exercise intensity in different strains of mice during forced treadmill running. PLoS ONE 14, e0215584 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  85. Zhang, C., Wei, Z.-H. & Ye, B.-C. Quantitative monitoring of 2-oxoglutarate in Escherichia coli cells by a fluorescence resonance energy transfer-based biosensor. Appl. Microbiol. Biotechnol. 97, 8307–8316 (2013).

    Article  CAS  PubMed  Google Scholar 

  86. Wang, W. et al. A ratiometric fluorescent biosensor reveals dynamic regulation of long-chain fatty acyl-CoA esters metabolism. Angew. Chem. Int. Ed. Engl. 60, 13996–14004 (2021).

    Article  CAS  PubMed  Google Scholar 

  87. Faergeman, N. J. & Knudsen, J. Role of long-chain fatty acyl-CoA esters in the regulation of metabolism and in cell signalling. Biochem. J. 323, 1–12 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Gruenwald, K. et al. Visualization of glutamine transporter activities in living cells using genetically encoded glutamine sensors. PLoS ONE 7, e38591 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Marvin, J. S. et al. An optimized fluorescent probe for visualizing glutamate neurotransmission. Nat. Methods 10, 162–170 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Hires, S. A., Zhu, Y. & Tsien, R. Y. Optical measurement of synaptic glutamate spillover and reuptake by linker optimized glutamate-sensitive fluorescent reporters. Proc. Natl Acad. Sci. USA 105, 4411–4416 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Hu, H. et al. A genetically encoded toolkit for tracking live-cell histidine dynamics in space and time. Sci. Rep. 7, 43479 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  92. Okada, S., Ota, K. & Ito, T. Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor. Protein Sci. 18, 2518–2527 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Yoshida, T., Nakajima, H., Takahashi, S., Kakizuka, A. & Imamura, H. OLIVe: a genetically encoded fluorescent biosensor for quantitative imaging of branched-chain amino acid levels inside single living cells. ACS Sens. 4, 3333–3342 (2019).

    Article  CAS  PubMed  Google Scholar 

  94. Liu, X. et al. PPM1K regulates hematopoiesis and leukemogenesis through CDC20-mediated ubiquitination of MEIS1 and p21. Cell Rep. 23, 1461–1475 (2018).

    Article  CAS  PubMed  Google Scholar 

  95. Zhang, W. H. et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nat. Chem. Biol. 14, 861–869 (2018).

    Article  CAS  PubMed  Google Scholar 

  96. Kaper, T. et al. Nanosensor detection of an immunoregulatory tryptophan influx/kynurenine efflux cycle. PLoS Biol. 5, e257 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  97. Zhu, A., Romero, R. & Petty, H. R. A sensitive fluorimetric assay for pyruvate. Anal. Biochem. 396, 146–151 (2010).

    Article  CAS  PubMed  Google Scholar 

  98. Liu, X. et al. Acetate production from glucose and coupling to mitochondrial metabolism in mammals. Cell 175, 502–513 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Rosini, E., Caldinelli, L. & Piubelli, L. Assays of d-amino acid oxidase activity. Front. Mol. Biosci. 4, 102 (2017).

    Article  PubMed  CAS  Google Scholar 

  100. Velázquez, I. & Pardo, J. P. Kinetic characterization of the rotenone-insensitive internal NADH: ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae. Arch. Biochem. Biophys. 389, 7–14 (2001).

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

D.V.T. is supported by the NIH Director’s New Innovator Award (DP2-GM132933).

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Authors and Affiliations

  1. Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA

    Mangyu Choe & Denis V. Titov

  2. Center for Computational Biology, University of California, Berkeley, CA, USA

    Mangyu Choe & Denis V. Titov

  3. Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA

    Mangyu Choe & Denis V. Titov

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Correspondence to Denis V. Titov.

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D.V.T. is listed as an inventor on a patent application (US patent application 15/749,218) describing the use of LbNOX and TPNOX that are discussed in this perspective.

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Nature Chemical Biology thanks Yi Yang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Choe, M., Titov, D.V. Genetically encoded tools for measuring and manipulating metabolism. Nat Chem Biol 18, 451–460 (2022). https://doi.org/10.1038/s41589-022-01012-8

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