The number of catalytic cycles in an enzyme’s lifetime and why it matters to metabolic engineering

Hanson, Andrew D.; McCarty, Donald R.; Henry, Christopher S.; Xian, Xiaochen; Joshi, Jaya; Patterson, Jenelle A.; García-García, Jorge D.; Fleischmann, Scott D.; Tivendale, Nathan D.; Millar, A. Harvey

doi:10.1073/pnas.2023348118

The number of catalytic cycles in an enzyme’s lifetime and why it matters to metabolic engineering

Journal Article · Mon Mar 22 00:00:00 EDT 2021 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.2023348118· OSTI ID:1815850

^[1]; ^[2]; Henry, Christopher S. ^[3]; Xian, Xiaochen ^[4]; ^[2]; ^[2]; ^[2]; Fleischmann, Scott D. ^[2]; Tivendale, Nathan D. ^[5]; ^[5]

Univ. of Florida, Gainesville, FL (United States). Horticultural Sciences Dept.; OSTI
Univ. of Florida, Gainesville, FL (United States). Horticultural Sciences Dept.
Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; Univ. of Chicago, IL (United States). Computation Inst.
Univ. of Florida, Gainesville, FL (United States). Industrial and Systems Engineering Dept.
Univ. of Western Australia, Crawley, WA (Australia). School of Molecular Sciences. Australian Research Council Centre of Excellence in Plant Energy Biology

Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ~100–200 enzymes each from Lactococcus lactis, yeast, and Arabidopsis. CCRs in these organisms had similar ranges (<10³ to >10⁷) but different median values (3–4 × 10⁴ in L. lactis and yeast versus 4 × 10⁵ in Arabidopsis). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1815850

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 13 Vol. 118; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

References (67)

Activity-Based Protein Profiling: New Developments and Directions in Functional Proteomics Uttamchandani, Mahesh; Li, Junqi; Sun, Hongyan ChemBioChem, Vol. 9, Issue 5 https://doi.org/10.1002/cbic.200700755	journal	March 2008
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines Wang, Mingcong; Herrmann, Christina J.; Simonovic, Milan PROTEOMICS, Vol. 15, Issue 18 https://doi.org/10.1002/pmic.201400441	journal	March 2015
The McCree–de Wit–Penning de Vries–Thornley Respiration Paradigms: 30 Years Later Amthor, J. Annals of Botany, Vol. 86, Issue 1 https://doi.org/10.1006/anbo.2000.1175	journal	July 2000
YfiD of Escherichia coli and Y06I of Bacteriophage T4 as Autonomous Glycyl Radical Cofactors Reconstituting the Catalytic Center of Oxygen-Fragmented Pyruvate Formate-Lyase Wagner, A. F. Volker; Schultz, Sabine; Bomke, Jörg Biochemical and Biophysical Research Communications, Vol. 285, Issue 2 https://doi.org/10.1006/bbrc.2001.5186	journal	July 2001
Self-inactivation of an erythrocyte NAD glycohydrolase Pekala, Phillip H.; Yost, David A.; Anderson, Bruce M. Molecular and Cellular Biochemistry, Vol. 31, Issue 1 https://doi.org/10.1007/BF00817890	journal	January 1980
Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation Flahaut, Nicolas A. L.; Wiersma, Anne; van de Bunt, Bert Applied Microbiology and Biotechnology, Vol. 97, Issue 19 https://doi.org/10.1007/s00253-013-5140-2	journal	August 2013
Substrate-dependent inactivation of transaldolase activity with tetranitromethane Kobashi, Kyoichi; Brand, Karl Archives of Biochemistry and Biophysics, Vol. 148, Issue 1 https://doi.org/10.1016/0003-9861(72)90128-2	journal	January 1972
Products, requirements and efficiency of biosynthesis a quantitative approach De Vries, F. W. T. Penning; Brunsting, A. H. M.; Van Laar, H. H. Journal of Theoretical Biology, Vol. 45, Issue 2 https://doi.org/10.1016/0022-5193(74)90119-2	journal	June 1974
The energetics of microbes at slow growth rates: Maintenance energies and dormant organisms Pirt, S. John Journal of Fermentation Technology, Vol. 65, Issue 2 https://doi.org/10.1016/0385-6380(87)90161-0	journal	January 1987
Substrate inactivation of enzymes in vitro and in vivo Gray, Murray R. Biotechnology Advances, Vol. 7, Issue 4 https://doi.org/10.1016/0734-9750(89)90722-2	journal	January 1989
Non-enzymatic covalent modifications of proteins: mechanisms, physiological consequences and clinical applications Cloos, Paul A. C.; Christgau, Stephan Matrix Biology, Vol. 21, Issue 1 https://doi.org/10.1016/S0945-053X(01)00188-3	journal	January 2002
Aging as war between chemical and biochemical processes: Protein methylation and the recognition of age-damaged proteins for repair Clarke, Steven Ageing Research Reviews, Vol. 2, Issue 3 https://doi.org/10.1016/S1568-1637(03)00011-4	journal	July 2003
Stability of proteins: Temperature, pressure and the role of the solvent Scharnagl, Christina; Reif, Maria; Friedrich, Josef Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1749, Issue 2 https://doi.org/10.1016/j.bbapap.2005.03.002	journal	June 2005
Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency? Tawfik, Dan S. Current Opinion in Chemical Biology, Vol. 21 https://doi.org/10.1016/j.cbpa.2014.05.008	journal	August 2014
Synthetic metabolism: metabolic engineering meets enzyme design Erb, Tobias J.; Jones, Patrik R.; Bar-Even, Arren Current Opinion in Chemical Biology, Vol. 37 https://doi.org/10.1016/j.cbpa.2016.12.023	journal	April 2017
‘Negative’ and ‘positive catalysis’: complementary principles that shape the catalytic landscape of enzymes Vögeli, Bastian; Erb, Tobias J. Current Opinion in Chemical Biology, Vol. 47 https://doi.org/10.1016/j.cbpa.2018.09.013	journal	December 2018
Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go Way, Jeffrey C.; Collins, James J.; Keasling, Jay D. Cell, Vol. 157, Issue 1 https://doi.org/10.1016/j.cell.2014.02.039	journal	March 2014
Determinants and Regulation of Protein Turnover in Yeast Martin-Perez, Miguel; Villén, Judit Cell Systems, Vol. 5, Issue 3 https://doi.org/10.1016/j.cels.2017.08.008	journal	September 2017
Utilizing simple biochemical measurements to predict lifetime output of biocatalysts in continuous isothermal processes Rogers, Thomas A.; Bommarius, Andreas S. Chemical Engineering Science, Vol. 65, Issue 6 https://doi.org/10.1016/j.ces.2009.12.005	journal	March 2010
Lessons on enzyme kinetics from quantitative proteomics Davidi, Dan; Milo, Ron Current Opinion in Biotechnology, Vol. 46 https://doi.org/10.1016/j.copbio.2017.02.007	journal	August 2017
Probing the acetaldehyde-sensitivity of 2-deoxy-ribose-5-phosphate aldolase (DERA) leads to resistant variants Bramski, Julia; Dick, Markus; Pietruszka, Jörg Journal of Biotechnology, Vol. 258 https://doi.org/10.1016/j.jbiotec.2017.03.024	journal	September 2017
Replacement of oxidizable residues predicted by QM-MM simulation of a fungal laccase generates variants with higher operational stability Avelar, Mayra; Pastor, Nina; Ramirez-Ramirez, Joaquin Journal of Inorganic Biochemistry, Vol. 178 https://doi.org/10.1016/j.jinorgbio.2017.10.007	journal	January 2018
Opportunities for wheat proteomics to discover the biomarkers for respiration-dependent biomass production, stress tolerance and cytoplasmic male sterility Jacoby, Richard P.; Millar, A. Harvey; Taylor, Nicolas L. Journal of Proteomics, Vol. 143 https://doi.org/10.1016/j.jprot.2016.02.014	journal	June 2016
Redesigning thiamin synthesis: Prospects and potential payoffs Hanson, Andrew D.; Amthor, Jeffrey S.; Sun, Jiayi Plant Science, Vol. 273 https://doi.org/10.1016/j.plantsci.2018.01.019	journal	August 2018
Enzymes as Parts in Need of Replacement – and How to Extend Their Working Life Tivendale, Nathan D.; Hanson, Andrew D.; Henry, Christopher S. Trends in Plant Science, Vol. 25, Issue 7 https://doi.org/10.1016/j.tplants.2020.02.006	journal	July 2020
The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness Bar-Even, Arren; Milo, Ron; Noor, Elad Biochemistry, Vol. 54, Issue 32 https://doi.org/10.1021/acs.biochem.5b00621	journal	August 2015
The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters Bar-Even, Arren; Noor, Elad; Savir, Yonatan Biochemistry, Vol. 50, Issue 21 https://doi.org/10.1021/bi2002289	journal	May 2011
Mass Spectrometry of Membrane Proteins: A Focus on Aquaporins Schey, Kevin L.; Grey, Angus C.; Nicklay, Joshua J. Biochemistry, Vol. 52, Issue 22 https://doi.org/10.1021/bi301604j	journal	March 2013
“Turning Over” Definitions in Catalytic Cycles Kozuch, Sebastian; Martin, Jan M. L. ACS Catalysis, Vol. 2, Issue 12 https://doi.org/10.1021/cs3005264	journal	November 2012
Engineering explored Silver, Pamela A.; Way, Jeffrey C.; Arnold, Frances H. Nature, Vol. 509, Issue 7499 https://doi.org/10.1038/509166a	journal	May 2014
Protein degradation and protection against misfolded or damaged proteins Goldberg, Alfred L. Nature, Vol. 426, Issue 6968 https://doi.org/10.1038/nature02263	journal	December 2003
Saccharomyces cerevisiae THI4p is a suicide thiamine thiazole synthase Chatterjee, Abhishek; Abeydeera, N. Dinuka; Bale, Shridhar Nature, Vol. 478, Issue 7370 https://doi.org/10.1038/nature10503	journal	October 2011
High-throughput generation, optimization and analysis of genome-scale metabolic models Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A. Nature Biotechnology, Vol. 28, Issue 9 https://doi.org/10.1038/nbt.1672	journal	August 2010
Realizing the potential of synthetic biology Church, George M.; Elowitz, Michael B.; Smolke, Christina D. Nature Reviews Molecular Cell Biology, Vol. 15, Issue 4 https://doi.org/10.1038/nrm3767	journal	March 2014
The importance of catalytic promiscuity for enzyme design and evolution Leveson-Gower, Reuben B.; Mayer, Clemens; Roelfes, Gerard Nature Reviews Chemistry, Vol. 3, Issue 12 https://doi.org/10.1038/s41570-019-0143-x	journal	November 2019
Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies Dick, Markus; Hartmann, Rudolf; Weiergräber, Oliver H. Chemical Science, Vol. 7, Issue 7 https://doi.org/10.1039/C5SC04574F	journal	January 2016
Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins Valgepea, Kaspar; Adamberg, Kaarel; Seiman, Andrus Molecular BioSystems, Vol. 9, Issue 9 https://doi.org/10.1039/c3mb70119k	journal	January 2013
Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s Joshi, Jaya; Beaudoin, Guillaume A. W.; Patterson, Jenelle A. Biochemical Journal, Vol. 477, Issue 11 https://doi.org/10.1042/BCJ20200297	journal	June 2020
‘Nothing of chemistry disappears in biology’: the Top 30 damage-prone endogenous metabolites Lerma-Ortiz, Claudia; Jeffryes, James G.; Cooper, Arthur J. L. Biochemical Society Transactions, Vol. 44, Issue 3 https://doi.org/10.1042/BST20160073	journal	June 2016
Inhibition of rabbit muscle aldolase by phosphorylated aromatic compounds Blonski, Casimir; Moissac, Danielle DE; PÉRiÉ, Jacques Biochemical Journal, Vol. 323, Issue 1 https://doi.org/10.1042/bj3230071	journal	April 1997
Isotopically nonstationary ¹³ C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation Ma, Fangfang; Jazmin, Lara J.; Young, Jamey D. Proceedings of the National Academy of Sciences, Vol. 111, Issue 47 https://doi.org/10.1073/pnas.1319485111	journal	November 2014
Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage Gray, Harry B.; Winkler, Jay R. Proceedings of the National Academy of Sciences, Vol. 112, Issue 35 https://doi.org/10.1073/pnas.1512704112	journal	July 2015
Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro k _cat measurements Davidi, Dan; Noor, Elad; Liebermeister, Wolfram Proceedings of the National Academy of Sciences, Vol. 113, Issue 12 https://doi.org/10.1073/pnas.1514240113	journal	March 2016
Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion Katava, Marina; Stirnemann, Guillaume; Zanatta, Marco Proceedings of the National Academy of Sciences, Vol. 114, Issue 35 https://doi.org/10.1073/pnas.1707357114	journal	August 2017
Paracatalytic modification of aldolase: A side reaction of the catalytic cycle resulting in irreversible blocking of two active-site lysyl residues Lubini, D. G. E.; Christen, P. Proceedings of the National Academy of Sciences, Vol. 76, Issue 6 https://doi.org/10.1073/pnas.76.6.2527	journal	June 1979
Non-enzymatic molecular damage as a prototypic driver of aging Golubev, Alexey; Hanson, Andrew D.; Gladyshev, Vadim N. Journal of Biological Chemistry, Vol. 292, Issue 15 https://doi.org/10.1074/jbc.R116.751164	journal	March 2017
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
BRENDA in 2017: new perspectives and new tools in BRENDA Placzek, Sandra; Schomburg, Ida; Chang, Antje Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw952	journal	October 2016
Tuning the dials of Synthetic Biology Arpino, James A. J.; Hancock, Edward J.; Anderson, James Microbiology, Vol. 159, Issue Pt_7 https://doi.org/10.1099/mic.0.067975-0	journal	July 2013
Protein turnover forms one of the highest maintenance costs in Lactococcus lactis Lahtvee, Petri-Jaan; Seiman, Andrus; Arike, Liisa Microbiology, Vol. 160, Issue 7 https://doi.org/10.1099/mic.0.078089-0	journal	July 2014
Parts-Prospecting for a High-Efficiency Thiamin Thiazole Biosynthesis Pathway Sun, Jiayi; Sigler, Cindy L.; Beaudoin, Guillaume A. W. Plant Physiology, Vol. 179, Issue 3 https://doi.org/10.1104/pp.18.01085	journal	October 2018
Protein Degradation Rate in Arabidopsis thaliana Leaf Growth and Development Li, Lei; Nelson, Clark J.; Trösch, Josua The Plant Cell, Vol. 29, Issue 2 https://doi.org/10.1105/tpc.16.00768	journal	January 2017
Engineering Strategies to Boost Crop Productivity by Cutting Respiratory Carbon Loss Amthor, Jeffrey S.; Bar-Even, Arren; Hanson, Andrew D. The Plant Cell, Vol. 31, Issue 2 https://doi.org/10.1105/tpc.18.00743	journal	January 2019
The cost of enzyme synthesis in the genetics of energy balance and physiological performance Koehn, Richard K. Biological Journal of the Linnean Society, Vol. 44, Issue 3 https://doi.org/10.1111/j.1095-8312.1991.tb00618.x	journal	November 1991
Role of Nascent alpha-Ketoaldehyde in Substrate-Dependent Oxidative Inactivation of Aldolase Patthy, Laszlo European Journal of Biochemistry, Vol. 88, Issue 1 https://doi.org/10.1111/j.1432-1033.1978.tb12437.x	journal	July 1978
Effect of evolution on the kinetic properties of enzymes Pettersson, Gosta European Journal of Biochemistry, Vol. 184, Issue 3 https://doi.org/10.1111/j.1432-1033.1989.tb15050.x	journal	October 1989
Paracatalytic self-inactivation of fructose-1,6-bisphosphate aldolase. Structure of the crosslink formed at the active site Gupta, Sharad; Hollenstein, Roger; Kochhar, Sunil European Journal of Biochemistry, Vol. 214, Issue 2 https://doi.org/10.1111/j.1432-1033.1993.tb17949.x	journal	June 1993
Dynamic ¹³ C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains Hong, Kuk-Ki; Hou, Jin; Shoaie, Saeed FEMS Yeast Research, Vol. 12, Issue 7 https://doi.org/10.1111/j.1567-1364.2012.00823.x	journal	July 2012
Growth rate correlates negatively with protein turnover in Arabidopsis accessions Ishihara, Hirofumi; Moraes, Thiago Alexandre; Pyl, Eva-Theresa The Plant Journal, Vol. 91, Issue 3 https://doi.org/10.1111/tpj.13576	journal	June 2017
Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana Küken, Anika; Gennermann, Kristin; Nikoloski, Zoran The Plant Journal, Vol. 103, Issue 6 https://doi.org/10.1111/tpj.14890	journal	July 2020
Olefin Cyclopropanation via Carbene Transfer Catalyzed by Engineered Cytochrome P450 Enzymes Coelho, P. S.; Brustad, E. M.; Kannan, A. Science, Vol. 339, Issue 6117 https://doi.org/10.1126/science.1231434	journal	December 2012
Diversifying Carotenoid Biosynthetic Pathways by Directed Evolution Umeno, D.; Tobias, A. V.; Arnold, F. H. Microbiology and Molecular Biology Reviews, Vol. 69, Issue 1 https://doi.org/10.1128/MMBR.69.1.51-78.2005	journal	March 2005
The Scope, Functions, and Dynamics of Posttranslational Protein Modifications Millar, A. Harvey; Heazlewood, Joshua L.; Giglione, Carmela Annual Review of Plant Biology, Vol. 70, Issue 1 https://doi.org/10.1146/annurev-arplant-050718-100211	journal	April 2019
Regulated Proteolysis in Bacteria Mahmoud, Samar A.; Chien, Peter Annual Review of Biochemistry, Vol. 87, Issue 1 https://doi.org/10.1146/annurev-biochem-062917-012848	journal	June 2018
Quality Control and Infiltration of Translation by Amino Acids Outside of the Genetic Code Bullwinkle, Tammy; Lazazzera, Beth; Ibba, Michael Annual Review of Genetics, Vol. 48, Issue 1 https://doi.org/10.1146/annurev-genet-120213-092101	journal	November 2014
Connecting extracellular metabolomic measurements to intracellular flux states in yeast Mo, Monica L.; Palsson, Bernhard Ø; Herrgård, Markus J. BMC Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1186/1752-0509-3-37	journal	January 2009
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data Zomorrodi, Ali R.; Maranas, Costas D. BMC Systems Biology, Vol. 4, Issue 1 https://doi.org/10.1186/1752-0509-4-178	journal	December 2010

Similar Records

Structural and kinetic analysis of the unnatural fusion protein 4-coumaroyl-CoA ligase::stilbene synthase

Journal Article · Wed Oct 24 00:00:00 EDT 2012 · J. Am. Chem. Soc. · OSTI ID:1046239

Enzymes as parts in need of replacement - and how to extend their working life

Journal Article · Wed Jul 01 00:00:00 EDT 2020 · Trends in Plant Science · OSTI ID:1811305

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
catalytic cycles
energetic costs
enzyme longevity
protein turnover
synthetic biology

The number of catalytic cycles in an enzyme’s lifetime and why it matters to metabolic engineering

Citation Formats

References (67)

Similar Records

Related Subjects