Skip to main content

Respiratory Metabolism in Heterotrophic Plant Cells as Revealed by Isotopic Labeling and Metabolic Flux Analysis

  • Chapter
  • First Online:
  • 1300 Accesses

Part of the book series: Advances in Photosynthesis and Respiration ((AIPH,volume 43))

Summary

Mitochondrial respiration requires redox power that is mainly provided by the tricarboxylic acid (TCA) cycle in heterotrophic tissues. Glycolysis is commonly assumed to be the major pathway for carbon replenishment of the TCA cycle in most plant cells. However, the TCA cycle also provides precursors for amino acids and organic acids synthesis, a process that requires 4- or 5-C molecules supplied by anaplerotic pathways. The TCA cycle is thus involved in both anabolism and catabolism. Despite the good knowledge of enzymes and pathways involved in these processes, the regulation of carbon partitioning between catabolism and anabolism remains poorly understood. Metabolic flux analysis (MFA) aims at quantifying fluxes in metabolic networks and provides new insights for the study of the TCA cycle and associated pathways. This chapter presents briefly the principles of MFA, and describes how 14C-tracing evolved to 13C-MFA, and more recently to 13C-INST-MFA. Such analyses have provided insights about the origin of carbon atoms entering the TCA cycle and the partitioning between respiration and biosyntheses.

This is a preview of subscription content, log in via an institution.

References

  • Alonso AP, Vigeolas H, Raymond P, Rolin D, Dieuaide-Noubhani M (2005) A New Substrate Cycle in Plants: Evidence for a High Glucose-Phosphate - Glucose Turnover from in Vivo Steady State and Pulse Labeling Experiments with [13C]- and [14C]Glucose. Plant Physiol 138:2220–2232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alonso AP, Goffman FD, Ohlrogge JB, Shachar-Hill Y (2007a) Carbon conversion efficiency and central metabolic fluxes in developing sunflower (Helianthus annuus L.) embryos. Plant J 52:296–308

    Article  CAS  PubMed  Google Scholar 

  • Alonso AP, Raymond P, Hernould M, Rondeau-Mouro C, de Graaf A, Chourey P, Dieuaide-Noubhani M (2007b) A metabolic flux analysis to study the role of sucrose synthase in the regulation of the carbon partitioning in central metabolism in maize root tips. Metab Eng 9:419–432

    Article  CAS  PubMed  Google Scholar 

  • Alonso AP, Dale VL, Shachar-Hill Y (2010) Understanding fatty acid synthesis in developing maize embryos using metabolic flux analysis. Metab Eng 12:488–497

    Article  PubMed  Google Scholar 

  • Antoniewicz MR, Kelleher JK, Stephanopoulos G (2007) Elementray metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng 9:68–86

    Article  CAS  PubMed  Google Scholar 

  • Baghalian K, Hajirezaei MR, Schreiber F (2014) Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. Plant Cell 26:3847–3866

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bathellier C, Tcherkez G, Bligny R, Gout E, Cornic G, Ghashghaie J (2009) Metabolic origin of the δ13C of respired CO2 in roots of Phaseolus vulgari. New Phytol 181:387–399

    Article  CAS  PubMed  Google Scholar 

  • Beauvoit BP, Colombié S, Monier A, Andrieu MH, Biais B, Bénard C, …, Gibon Y (2014) Model-Assisted Analysis of Sugar Metabolism throughout Tomato Fruit Development Reveals Enzyme and Carrier Properties in Relation to Vacuole expansion. Plant Cell 26: 3224--3242.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brouquisse R, James F, Raymond P et al (1991) Study of glucose starvation in excised maize root tips. Plant Physiol 96:619–626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Canvin DT, Beevers H (1961) Sucrose synthesis from acetate in the germinating castor bean: kinetics and pathway. J Biol Chem 236:988–995

    CAS  PubMed  Google Scholar 

  • Chen X, Alonso AP, Shachar-Hill Y (2013) Dynamic metabolic flux analysis of plant cell wall synthesis. Metab Eng 18:78–85

    Article  CAS  PubMed  Google Scholar 

  • Colombié S, Nazaret C, Bénard C, Biais B, Mengin V, Solé M, …, Gibon Y. (2015) Modeling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit. Plant J. 81: 24--39.

    Article  PubMed  Google Scholar 

  • Colón AM, Sengupta N, Rhodes D, Dudareva N, Morgan J (2010) A kinetic model describes metabolic response to perturbations and distribution of flux control in the benzenoid network of Petunia hybrid. Plant J 62:64–76

    Article  PubMed  Google Scholar 

  • Cornah JE, Germain V, Ward JL, Beale MH, Smith SM (2004) Lipid utilization, gluconeogenesis, and seedling growth in arabidopsis mutants lacking the glyoxylate cycle enzyme malate synthase. J Biol Chem 279:42916–42923

    Article  CAS  PubMed  Google Scholar 

  • Crown SB, Antoniewicz MR (2013) Publishing 13C metabolic flux analysis studies: A review and future perspectives. Metab Eng 20:42–48

    Article  CAS  PubMed  Google Scholar 

  • Curien G, Ravanel S, Dumas R (2003) A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana. Eur J Biochem 270:4615–4627

    Article  CAS  PubMed  Google Scholar 

  • Curien G, Bastien O, Robert-Genthon M, Cornish-Bowden A, Cárdenas ML, Dumas R (2009) Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. Mol Sys Biol 5:271–281

    Google Scholar 

  • de Oliveira Dal’Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol 152:579–589

    Article  PubMed  PubMed Central  Google Scholar 

  • de Oliveira Dal’Molin CG, Quek LE, Saa PA, Nielsen LK (2015) A multi-tissue genome-scale metabolic modeling framework for the analysis of whole plant systems. Front Plant Sci 6:4

    Google Scholar 

  • Dersch LM, Beckers V, Wittmann C (2016) Green pathways: Metabolic network analysis of plant systems. Metab Eng 34:1–24

    Article  CAS  PubMed  Google Scholar 

  • Devaux C, Baldet P, Joubès J, Dieuaide-Noubhani M, Just D, Chevalier C, Raymond P (2003) Physiological, biochemical and molecular analysis of sugar-starvation responses in tomato roots. J Exp Bot 54:1143–1151

    Article  CAS  PubMed  Google Scholar 

  • Dieuaide M, Bouquisse R, Pradet A, Raymond P (1992) Increased fatty acid beta-oxidation after glucose starvation in maize root tips. Plant Physiol 99:595–600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dieuaide-Noubhani M, Alonso AP (2014) Plant metabolic flux analysis: methods and protocols. In: Dieuaide-Noubhani M, Alonso AP (eds) Methods in molecular biology, vol 1090. Humana Press-Springer, Berlin, pp 1–17

    Google Scholar 

  • Dieuaide-Noubhani M, Raffard G, Canioni P, Pradet A, Raymond P (1995) Quantification of compartmented metabolic fluxes in maize root tips using isotope distribution from 13C- or 14C-labeled glucose. J Biol Chem 270:13147–13159

    Article  CAS  PubMed  Google Scholar 

  • Dieuaide-Noubhani M, Canioni P, Raymond P et al (1997) Sugar-starvation-induced changes of carbon metabolism in excised maize root tips. Plant Physiol 115:1505–1513

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Droste P, Miebach S, Niedenfuhr S, Wiechert W, Noh K (2011) Visualizing multi-omics data in metabolic networks with the software Omix-A case study. Biosystems 105:154–161

    Article  CAS  PubMed  Google Scholar 

  • Eastmond PJ, Germain V, Lange PR, Bryce JH, Smith SM, Graham IA (2000) Postgerminative growth and lipid catabolism in oilseeds lacking the glyoxylate cycle. Proc Natl Acad Sci USA 97:5669–5674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geigenberger P, Reimholz R, Geiger M, Merlo L, Canale V, Stitt M (1997) Regulation of sucrose and starch metabolism in potato tubers in response to short-term water deficit. Planta 201:502–518

    Article  CAS  Google Scholar 

  • Germain V, Rylott EL, Larson TR, Sherson SM, Bechtold N, Carde JP et al (2001) Requirement for 3--ketoacyl-CoA thiolase-2 in peroxisome development, fatty acid β-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings. Plant J 28:1–12

    Article  CAS  PubMed  Google Scholar 

  • Grafahrend-Belau E, Schreiber F, Koschützki D, Junker BH (2009) Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol 149:585–598

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grafahrend-Belau E, Junker A, Eschenroder A, Muller J, Schreiber F, Junker BH (2013) Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale. Plant Physiol 163:637–647

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hatzfeld WD, Stitt M (1990) A study of the rate of recycling of triose phosphates in heterotrophic Chenopodium rubrum cells, potato tubers, and maize endosperm. Planta 180:198–204

    CAS  PubMed  Google Scholar 

  • Hayashi M, Toriyama K, Kondo M, Nishimura M (1998) 2,4--dichlorophenoxybutyric acid-resistant mutants of arabidopsis have defects in glyoxysomal fatty acid beta-oxidation. Plant Cell 10:183–195

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hill SA, ap Rees T (1994) Fluxes of carbohydrate metabolism in ripening bananas. Planta 192:52–60

    Article  CAS  Google Scholar 

  • Hill SA, ap Rees T (1995) The effect of hypoxia on the control of carbohydrate metabolism in ripening bananas. Planta 197:313–323

    Article  CAS  Google Scholar 

  • James F, Brouquisse R, Pradet A, Raymond P (1993) Changes in proteolytic activities in glucose-starved maize root tips – regulation by sugars. Plant Physiol Biochem 31:845–856

    CAS  Google Scholar 

  • Journet EP, Bligny R, Douce R (1986) Biochemical changes during sucrose deprivation in higher plant cells. J Biol Chem 261:3193–3199

    CAS  PubMed  Google Scholar 

  • Junker BH, Lonien J, Heady LE, Rogers A, Schwender J (2007) Parallel determination of enzyme activities and in vivo fluxes in Brassica napus embryos grown on organic or inorganic nitrogen source. Phytochemistry 68:2232–2242

    Article  CAS  PubMed  Google Scholar 

  • Kim TY, Sohn SB, Kim YB, Kim WJ, Lee SY (2012) Recent advances in reconstruction and applications of genome-scale metabolic models. Curr Op. Biotech 23:617–623

    CAS  Google Scholar 

  • Kunz H-H, Scharnewski M, Feussner K, Feussner I, Flügge U-I, Fulda M, Giertha M (2009) The ABC transporter PXA1 and peroxisomal β-oxidation are vital for metabolism in mature leaves of Arabidopsis during extended darkness. Plant Cell 21:2733–2749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lonien J, schwender J (2009) Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis. Plant Physiol 151:1617–1634

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Massou S, Nicolas C, Letisse F, Portais JC (2007) NMR-based fluxomics: Quantitative 2D NMR methods for isotopomers analysis. Phytochemistry 68:2330–2340

    Article  CAS  PubMed  Google Scholar 

  • Pracharoenwattana I, Cornah JE, Smith SM (2005) Arabidopsis peroxisomal citrate synthase is required for fatty acid respiration and seed germination. Plant Cell 17:2037–2048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raymond P, Spiteri A, Dieuaide M, Gerhardt B, Pradet A (1992) Peroxisomal β-oxidation of fatty acids and citrate formation by a particulate fraction from early germinating sunflower seeds. Plant Physiol Biochem 30:153–161

    CAS  Google Scholar 

  • Rohwer JM, Botha FC (2001) Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem J 358:437–445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rontein D, Dieuaide-Noubhani M, Dufourc EJ, Raymond P, Rolin D (2002) The metabolic architecture of plant cells. Stability of central carbon metabolism and flexibility of anabolic pathways during the growth cycle of tomato cells. J Biol Chem 46(43):948–43960

    Google Scholar 

  • Saglio PH, Pradet A (1980) Soluble sugars, respiration and energy charge during aging of excised maize root tips. Plant Physiol 66:516–519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saha R, Suthers PF, Maranas CD (2011) Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLOS ONE 6:e21784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Salon C, Raymond P, Pradet A (1988) Quantification of carbon fluxes through the tricarboxylic acid cycle in early germinating lettuce embryos. J Biol Chem 263:12278–12287

    CAS  PubMed  Google Scholar 

  • Schuster S, Dandekar T, Fell DA (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 17:53–60

    Article  CAS  PubMed  Google Scholar 

  • Schwender J, Shachar-Hill Y, Ohlrogge JB (2006) Mitochondrial metabolism in developing embryos of Brassica napus. J Biol Chem 281:34040–34047

    Article  CAS  PubMed  Google Scholar 

  • Shastri AA, Morgan JA (2007) A transient isotopic labeling methodology for 13C metabolic flux analysis of photoautotrophic microorganisms. Phytochemistry 68:2302–2312

    Article  CAS  PubMed  Google Scholar 

  • Sriram G, Fulton DB, Iyer VV, Peterson JM, Zhou R, Westgate ME, Spalding MH, Shanks JV (2004) Quantification of compartmented metabolic fluxes in developing soybean embryos by employing biosynthetically directed fractional 13C labeling, two-dimensional [13C, 1H] nuclear magnetic resonance, and comprehensive isotopomer balancing. Plant Physiol 136:3043–3057

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sriram G, Fulton DB, Shanks JV (2007) Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing. Phytochemistry 68:2243–2257

    Article  CAS  PubMed  Google Scholar 

  • Szecowka M, Heise R, Tohge T, Nunes-Nesi A, Vosloh D, Huege J, …, Arrivault S (2013) Metabolic fluxes in an illuminated Arabidopsis rosette. Plant Cell 25: 694--714.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tcherkez G, Nogués S, Bleton J, Cornic G, Badeck F, Ghashghaie J (2003) Metabolic origin of carbon isotope composition of leaf dark-respired CO2 in French bean. Plant Physiol 131:237–244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van der Graaff E, Schwacke R, Schneider A, Desimone M, Flügge U-I, Kunze R (2006) Transcription analysis of Arabidopsis membrane transporters and hormone pathways during developmental and induced leaf senescence. Plant Physiol 141:776–792

    Article  PubMed  PubMed Central  Google Scholar 

  • Wiechert W, Noh K (2005) From stationary to instationary metabolic flux analysis. Adv Biochem Eng Biotechnol 92:145–172

    CAS  PubMed  Google Scholar 

  • Williams TCR, Miguet L, Masakapalli SK, Kruger NJ, Sweetlove JJ, Ratcliffe RG (2008) Metabolic network fluxes in heterotrophic Arabidopsis cells: stability of the flux distribution under different oxygenation conditions. Plant Physiol 148:704–718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Young JD (2014) INCA: a computational platform for isotopically non-stationary metabolic flux analysis. Bioinformatics 30:1333–1335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Young JD, Walther JL, Antoniewicz MR, Yoo H, Stephanopoulos G (2008) An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis. Biotechnol Bioeng 99:686–699

    Article  CAS  PubMed  Google Scholar 

  • Young JD, Shastri AA, Stephanopoulos G, Morgan JA (2011) Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis. Metab Eng 13:656–665

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Martine Dieuaide-Noubhani .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Dieuaide-Noubhani, M., Rolin, D. (2017). Respiratory Metabolism in Heterotrophic Plant Cells as Revealed by Isotopic Labeling and Metabolic Flux Analysis. In: Tcherkez, G., Ghashghaie, J. (eds) Plant Respiration: Metabolic Fluxes and Carbon Balance. Advances in Photosynthesis and Respiration, vol 43. Springer, Cham. https://doi.org/10.1007/978-3-319-68703-2_12

Download citation

Publish with us

Policies and ethics