Enzymes as Parts in Need of Replacement – and How to Extend Their Working Life

Tivendale, Nathan D.; Hanson, Andrew D.; Henry, Christopher S.; Hegeman, Adrian D.; Millar, A. Harvey

doi:10.1016/j.tplants.2020.02.006

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

DOI:https://doi.org/10.1016/j.tplants.2020.02.006· OSTI ID:1632974

Tivendale, Nathan D.; Hanson, Andrew D.; Henry, Christopher S.; Hegeman, Adrian D.; Millar, A. Harvey

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Sponsoring Organization:: USDOE

OSTI ID:: 1632974

Journal Information:: Trends in Plant Science, Journal Name: Trends in Plant Science Journal Issue: 7 Vol. 25; ISSN 1360-1385

Publisher:: ElsevierCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (67)

Metabolic flux analysis inEscherichia coli by integrating isotopic dynamic and isotopic stationary13C labeling data Schaub, Jochen; Mauch, Klaus; Reuss, Matthias Biotechnology and Bioengineering, Vol. 99, Issue 5 https://doi.org/10.1002/bit.21675	journal	January 2008
Collisional fragmentation of central carbon metabolites in LC-MS/MS increases precision of 13C metabolic flux analysis Rühl, Martin; Rupp, Beat; Nöh, Katharina Biotechnology and Bioengineering, Vol. 109, Issue 3 https://doi.org/10.1002/bit.24344	journal	October 2011
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
Response of antioxidant enzymes to high NaCl concentration in different salt-tolerant plants Mallik, S.; Nayak, M.; Sahu, B. B. Biologia plantarum, Vol. 55, Issue 1 https://doi.org/10.1007/s10535-011-0029-3	journal	March 2011
Insights into the spatial and temporal organisation of plant metabolism from network flux analysis Moreira, Thiago Batista; Lima, Janderson Moraes; Coca, Guilherme Carvalho Theoretical and Experimental Plant Physiology, Vol. 31, Issue 1 https://doi.org/10.1007/s40626-018-0132-3	journal	December 2018
A systematic approach to describing and analysing metabolic control systems Crabtree, B.; Newsholme, E. A. Trends in Biochemical Sciences, Vol. 12 https://doi.org/10.1016/0968-0004(87)90004-1	journal	January 1987
Improved biocatalysts by directed evolution and rational protein design Bornscheuer, Uwe T.; Pohl, Martina Current Opinion in Chemical Biology, Vol. 5, Issue 2 https://doi.org/10.1016/S1367-5931(00)00182-4	journal	April 2001
High-throughput metabolic flux analysis based on gas chromatography–mass spectrometry derived 13C constraints Fischer, Eliane; Zamboni, Nicola; Sauer, Uwe Analytical Biochemistry, Vol. 325, Issue 2 https://doi.org/10.1016/j.ab.2003.10.036	journal	February 2004
Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds Ravikumar, Arjun; Arzumanyan, Garri A.; Obadi, Muaeen K. A. Cell, Vol. 175, Issue 7 https://doi.org/10.1016/j.cell.2018.10.021	journal	December 2018
Flux analysis in plant metabolic networks: increasing throughput and coverage Junker, Björn H. Current Opinion in Biotechnology, Vol. 26 https://doi.org/10.1016/j.copbio.2014.01.016	journal	April 2014
Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice Cheah, Yi Ern; Young, Jamey D. Current Opinion in Biotechnology, Vol. 54 https://doi.org/10.1016/j.copbio.2018.02.013	journal	December 2018
The Pivotal Role of Ethylene in Plant Growth Dubois, Marieke; Van den Broeck, Lisa; Inzé, Dirk Trends in Plant Science, Vol. 23, Issue 4 https://doi.org/10.1016/j.tplants.2018.01.003	journal	April 2018
Tandem mass spectrometry: A novel approach for metabolic flux analysis Choi, Jungik; Antoniewicz, Maciek R. Metabolic Engineering, Vol. 13, Issue 2 https://doi.org/10.1016/j.ymben.2010.11.006	journal	March 2011
Synthesis/Degradation Ratio Mass Spectrometry for Measuring Relative Dynamic Protein Turnover Cargile, Benjamin J.; Bundy, Jonathan L.; Grunden, Amy M. Analytical Chemistry, Vol. 76, Issue 1 https://doi.org/10.1021/ac034841a	journal	January 2004
geoRge: A Computational Tool To Detect the Presence of Stable Isotope Labeling in LC/MS-Based Untargeted Metabolomics Capellades, Jordi; Navarro, Miriam; Samino, Sara Analytical Chemistry, Vol. 88, Issue 1 https://doi.org/10.1021/acs.analchem.5b03628	journal	December 2015
MID Max: LC–MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications McCloskey, Douglas; Young, Jamey D.; Xu, Sibei Analytical Chemistry, Vol. 88, Issue 2 https://doi.org/10.1021/acs.analchem.5b03887	journal	December 2015
Integrating MS1 and MS2 Scans in High-Resolution Parallel Reaction Monitoring Assays for Targeted Metabolite Quantification and Dynamic ¹³ C-Labeling Metabolism Analysis Li, Zhucui; Li, Yujing; Chen, Wujiu Analytical Chemistry, Vol. 89, Issue 1 https://doi.org/10.1021/acs.analchem.6b03947	journal	December 2016
Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants Fan, Kai-Ting; Rendahl, Aaron K.; Chen, Wen-Ping Journal of Proteome Research, Vol. 15, Issue 3 https://doi.org/10.1021/acs.jproteome.5b00772	journal	January 2016
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
Quantification of mRNA and protein and integration with protein turnover in a bacterium Maier, Tobias; Schmidt, Alexander; Güell, Marc Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.38	journal	January 2011
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome‐scale metabolic modeling Wodke, Judith A. H.; Puchałka, Jacek; Lluch‐Senar, Maria Molecular Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1038/msb.2013.6	journal	January 2013
Protein turnover in plant biology Nelson, Clark J.; Millar, A. Harvey Nature Plants, Vol. 1, Issue 3 https://doi.org/10.1038/nplants.2015.17	journal	March 2015
Flux profiling of photosynthetic carbon metabolism in intact plants Heise, Robert; Arrivault, Stéphanie; Szecowka, Marek Nature Protocols, Vol. 9, Issue 8 https://doi.org/10.1038/nprot.2014.115	journal	July 2014
CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window Halperin, Shakked O.; Tou, Connor J.; Wong, Eric B. Nature, Vol. 560, Issue 7717 https://doi.org/10.1038/s41586-018-0384-8	journal	August 2018
Understanding carbon utilization routes between high and low starch-producing cultivars of cassava through Flux Balance Analysis Chiewchankaset, Porntip; Siriwat, Wanatsanan; Suksangpanomrung, Malinee Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-39920-w	journal	February 2019
Fluxes through plant metabolic networks: measurements, predictions, insights and challenges Kruger, Nicholas J.; Ratcliffe, R. George Biochemical Journal, Vol. 465, Issue 1 https://doi.org/10.1042/BJ20140984	journal	December 2014
Advances in metabolic flux analysis toward genome-scale profiling of higher organisms Basler, Georg; Fernie, Alisdair R.; Nikoloski, Zoran Bioscience Reports, Vol. 38, Issue 6 https://doi.org/10.1042/BSR20170224	journal	November 2018
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations Samoilov, M.; Plyasunov, S.; Arkin, A. P. Proceedings of the National Academy of Sciences, Vol. 102, Issue 7 https://doi.org/10.1073/pnas.0406841102	journal	February 2005
Methionine catabolism in Arabidopsis cells is initiated by a γ-cleavage process and leads to S-methylcysteine and isoleucine syntheses Rebeille, F.; Jabrin, S.; Bligny, R. Proceedings of the National Academy of Sciences, Vol. 103, Issue 42, p. 15687-15692 https://doi.org/10.1073/pnas.0606195103	journal	October 2006
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
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource Seaver, Samuel M. D.; Gerdes, Svetlana; Frelin, Océane Proceedings of the National Academy of Sciences, Vol. 111, Issue 26 https://doi.org/10.1073/pnas.1401329111	journal	June 2014
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
Dissecting the Subcellular Compartmentation of Proteins and Metabolites in Arabidopsis Leaves Using Non-aqueous Fractionation Arrivault, Stéphanie; Guenther, Manuela; Florian, Alexandra Molecular & Cellular Proteomics, Vol. 13, Issue 9 https://doi.org/10.1074/mcp.M114.038190	journal	May 2014
Drought and Recovery: Independently Regulated Processes Highlighting the Importance of Protein Turnover Dynamics and Translational Regulation in Medicago truncatula Lyon, David; Castillejo, Maria Angeles; Mehmeti-Tershani, Vlora Molecular & Cellular Proteomics, Vol. 15, Issue 6 https://doi.org/10.1074/mcp.M115.049205	journal	June 2016
13CFLUX2—high-performance software suite for 13C-metabolic flux analysis Weitzel, Michael; Nöh, Katharina; Dalman, Tolga Bioinformatics, Vol. 29, Issue 1 https://doi.org/10.1093/bioinformatics/bts646	journal	October 2012
NTFD--a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data Hiller, K.; Wegner, A.; Weindl, D. Bioinformatics, Vol. 29, Issue 9 https://doi.org/10.1093/bioinformatics/btt119	journal	March 2013
INCA: a computational platform for isotopically non-stationary metabolic flux analysis Young, J. D. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu015	journal	January 2014
MIA: non-targeted mass isotopolome analysis Weindl, Daniel; Wegner, Andre; Hiller, Karsten Bioinformatics, Vol. 32, Issue 18 https://doi.org/10.1093/bioinformatics/btw317	journal	June 2016
IsotopicLabelling: an R package for the analysis of MS isotopic patterns of labelled analytes Ferrazza, Ruggero; Griffin, Julian L.; Guella, Graziano Bioinformatics, Vol. 33, Issue 2 https://doi.org/10.1093/bioinformatics/btw588	journal	September 2016
DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS Dagley, Michael J.; McConville, Malcolm J. Bioinformatics, Vol. 34, Issue 11 https://doi.org/10.1093/bioinformatics/bty025	journal	January 2018
Whole-Body Protein Turnover in Chicks at Early Stages of Growth Muramatsu, Tatsuo; Okumura, Jun-Ichi The Journal of Nutrition, Vol. 115, Issue 4 https://doi.org/10.1093/jn/115.4.483	journal	April 1985
Quantifying ATP turnover in anoxic coleoptiles of rice (Oryza sativa) demonstrates preferential allocation of energy to protein synthesis Edwards, Joshua M.; Roberts, Thomas H.; Atwell, Brian J. Journal of Experimental Botany, Vol. 63, Issue 12 https://doi.org/10.1093/jxb/ers114	journal	May 2012
Fluxomics links cellular functional analyses to whole-plant phenotyping Salon, Christophe; Avice, Jean-Christophe; Colombié, Sophie Journal of Experimental Botany, Vol. 68, Issue 9 https://doi.org/10.1093/jxb/erx126	journal	April 2017
Subcellular metabolomics: the choice of method depends on the aim of the study Dietz, Karl-Josef Journal of Experimental Botany, Vol. 68, Issue 21-22 https://doi.org/10.1093/jxb/erx406	journal	November 2017
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
Proteins with High Turnover Rate in Barley Leaves Estimated by Proteome Analysis Combined with in Planta Isotope Labeling Nelson, Clark J.; Alexova, Ralitza; Jacoby, Richard P. Plant Physiology, Vol. 166, Issue 1 https://doi.org/10.1104/pp.114.243014	journal	July 2014
Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) Enables Time-Resolved Analysis of Protein Synthesis in Native Plant Tissue Glenn, Weslee S.; Stone, Shannon E.; Ho, Samuel H. Plant Physiology, Vol. 173, Issue 3 https://doi.org/10.1104/pp.16.01762	journal	January 2017
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
Tandem Fluorescent Protein Timers for Noninvasive Relative Protein Lifetime Measurement in Plants Zhang, Hongtao; Linster, Eric; Gannon, Lucy Plant Physiology, Vol. 180, Issue 2 https://doi.org/10.1104/pp.19.00051	journal	March 2019
Modeling Protein Destiny in Developing Fruit Belouah, Isma; Nazaret, Christine; Pétriacq, Pierre Plant Physiology, Vol. 180, Issue 3 https://doi.org/10.1104/pp.19.00086	journal	April 2019
A Genome-Scale Metabolic Model of Soybean ( Glycine max ) Highlights Metabolic Fluxes in Seedlings Moreira, Thiago Batista; Shaw, Rahul; Luo, Xinyu Plant Physiology, Vol. 180, Issue 4 https://doi.org/10.1104/pp.19.00122	journal	June 2019
Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light Shameer, Sanu; Ratcliffe, R. George; Sweetlove, Lee J. Plant Physiology, Vol. 180, Issue 4 https://doi.org/10.1104/pp.19.00624	journal	June 2019
A Combined Metabolomics and Fluxomics Analysis Identifies Steps Limiting Oil Synthesis in Maize Embryos Cocuron, Jean-Christophe; Koubaa, Mohamed; Kimmelfield, Rebecca Plant Physiology, Vol. 181, Issue 3 https://doi.org/10.1104/pp.19.00920	journal	September 2019
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
The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation Masakapalli, Shyam K.; Bryant, Fiona M.; Kruger, Nicholas J. The Plant Journal, Vol. 78, Issue 6 https://doi.org/10.1111/tpj.12522	journal	May 2014
Concurrent isotope-assisted metabolic flux analysis and transcriptome profiling reveal responses of poplar cells to altered nitrogen and carbon supply Zhang, Xiaofeng; Misra, Ashish; Nargund, Shilpa The Plant Journal, Vol. 93, Issue 3 https://doi.org/10.1111/tpj.13792	journal	January 2018
Resolving subcellular plant metabolism Fürtauer, Lisa; Küstner, Lisa; Weckwerth, Wolfram The Plant Journal, Vol. 100, Issue 3 https://doi.org/10.1111/tpj.14472	journal	September 2019
OpenMebius: An Open Source Software for Isotopically Nonstationary ¹³ C-Based Metabolic Flux Analysis Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio BioMed Research International, Vol. 2014 https://doi.org/10.1155/2014/627014	journal	January 2014
iMS2Flux – a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis Poskar, C. Hart; Huege, Jan; Krach, Christian BMC Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2105-13-295	journal	January 2012
Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling Ahmed, Zeeshan; Zeeshan, Saman; Huber, Claudia BMC Bioinformatics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2105-14-218	journal	January 2013
OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis Quek, Lake-Ee; Wittmann, Christoph; Nielsen, Lars K. Microbial Cell Factories, Vol. 8, Issue 1 https://doi.org/10.1186/1475-2859-8-25	journal	January 2009
An automated growth enclosure for metabolic labeling of Arabidopsis thaliana with 13C-carbon dioxide - an in vivo labeling system for proteomics and metabolomics research Chen, Wen-Ping; Yang, Xiao-Yuan; Harms, Geoffrey L. Proteome Science, Vol. 9, Issue 1 https://doi.org/10.1186/1477-5956-9-9	journal	January 2011
A 13C isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems Wang, Peng; Guo, Longyun; Jaini, Rohit Plant Methods, Vol. 14, Issue 1 https://doi.org/10.1186/s13007-018-0318-3	journal	June 2018
Shoot tip culture: a step towards 13C metabolite flux analysis of sink leaf metabolism Koley, Somnath; Raorane, Manish L.; Junker, Björn H. Plant Methods, Vol. 15, Issue 1 https://doi.org/10.1186/s13007-019-0434-8	journal	May 2019
SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis Kogadeeva, Maria; Zamboni, Nicola PLOS Computational Biology, Vol. 12, Issue 9 https://doi.org/10.1371/journal.pcbi.1005109	journal	September 2016
Metabolic Patterns in Spirodela polyrhiza Revealed by 15N Stable Isotope Labeling of Amino Acids in Photoautotrophic, Heterotrophic, and Mixotrophic Growth Conditions Evans, Erin M.; Freund, Dana M.; Sondervan, Veronica M. Frontiers in Chemistry, Vol. 6 https://doi.org/10.3389/fchem.2018.00191	journal	May 2018
Flux-P: Automating Metabolic Flux Analysis Ebert, Birgitta E.; Lamprecht, Anna-Lena; Steffen, Bernhard Metabolites, Vol. 2, Issue 4 https://doi.org/10.3390/metabo2040872	journal	November 2012

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