Alternative approaches to modelling metabolism

1. Alternative approaches to modelling metabolism Bas.Kooijman@vu.nl Tromsø, 2017/05/21-30 deb.akvaplan.com/debschool.html

2. Contents 1. What is metabolism and its origins 2. Biochemical approaches 3. Pool approaches 4. Module approaches 5. Outlook

3. Metabolism Transformation of chemical compounds in cells to maintain and propagate life conversion of food/fuel to energy to run cellular processes, conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates elimination of nitrogenous wastes. The concept energy was first proposed by Thomas T. Young in 1807 Life originated as prokaryotes metabolism of prokaryotes is basic to metabolism From Wikipedia

4. Metabolism during evolution Red algae Eukaryotes Anoxygenic photosynthesis Flesh Great Oxidation Event Life Vascular plants Cyanobacteria From: Judson, Nature Ecol & Evol 1, 0138 (2017)

5. Early ATP generation FeS + S0  FeS2 ADP + Pi ATP • ATPase • hydrogenase • S-reductase FeS2 FeS 2H+ H2 S0 H2S ADP ATP 2e- Pi S0 H2S 2H2O 2H+ 2OH- Madigan et al 1997

6. Central Metabolism source polymers monomers waste/source

7. Evolution of central metabolism in prokaryotes (= bacteria) 3.8 Ga 2.7 Ga i = inverse ACS = acetyl-CoA Synthase pathway PP = Pentose Phosphate cycle TCA = TriCarboxylic Acid cycle RC = Respiratory Chain Gly = Glycolysis Kooijman, Hengeveld 2005

8. Prokaryotic metabolic evolution Heterotrophy: • pentose phosph cycle • glycolysis • respiration chain Phototrophy: • el. transport chain • PS I & PS II • Calvin cycle Chemolithotrophy • acetyl-CoA pathway • inverse TCA cycle • inverse glycolysis

9. Symbiogenesis 2.7 Ga 2.1 Ga 1.27 Ga phagocytosis

11. Classic energetics autotroph heterotroph The classic concept on metabolic regulation focusses on ATP generation and use. The application of this concept in DEB theory is problematic. From: Duve, C. de 1984 A guided tour of the living cell, Sci. Am. Lib., New York

12. ATP generation & use 5 106ATP molecules in bacterial cell enough for 2 s of biosynthetic work mean life time of ATP molecule: 0.3 s If ADP/ATP ratio varies, then rates of generation & use varies, but not necessarily the rates of transformations they drive Only used if energy generating & energy demanding transformations are at different site/time Processes that are not much faster than cell cycle, should be linked to large slow pools of metabolites, not to small fast pools

13. Weird world at small scale Almost all transformations in cells are enzyme mediated Classic enzyme kinetics: based on chemical kinetics (industrial enzymes) • diffusion/convection • law of mass action: transformation rate  product of conc. of substrates • larger number of molecules • constant reactor volume Problematic application in cellular metabolism: • definition of concentration (compartments, moving organelles) • transport mechanisms (proteins with address labels, targetting, allocation) • crowding (presence of many macro-molecules that do not partake in transformation) • intrinsic stochasticity due to small numbers of molecules • liquid crystalline properties • surface area - volume relationships: membrane-cytoplasm; polymer-liquid • connectivity (many metabolites are energy substrate & building block; dilution by growth) Alternative approach: reconstruction of transformation kinetics on the basis of cellular input/output kinetics

14. Self-ionization of water in cells modified Bessel function pH confidence intervals of pH 95, 90, 80, 60 % A cell of volume 0.25 mm3 and pH 7 at 25°C has m = 14 protons N = 8 109water molecules 7 cell volume, m3

15. Diffusion cannot occur in cells

16. Enzyme kinetics Uncatalyzed reaction Enzyme-catalyzed reaction

17. Surface area/volume interactions 1.2.3b Membrane-mediated transformation rates in isomorphs decrease with length because of transportation distance inactive enzyme active enzyme in binding phase active enzyme in production phase substrate product Cells can “know” their size from the rate at which concentrations of substrate & product change if transformation is by membrane-bound enzymes

18. Crowding affects transport cytoskeletal polymers ribosomes nucleic acids proteins

19. Biochemical approaches Weak: Too many players of the game: selection is required implication: energy & mass conservation cannot be exploited Huge range in time and space scales involved for growth Limited generality due to diversity implication: no comparison on the basis of parameter values Complex dynamics, complex link between flux and function spatial structure, small numbers, liquid crystals Strong: Clear identification of players of the game implication: close connection with molecular biology Rather direct link with genes

20. Respiration

21. Pool approaches Weak: Complex identification of players of the game if > 1 implication: difficult connection with molecular biology Complex link with genes Weak homeostasis is a simplification of a complex reality Strong: Few players of the game: implication: energy & mass conservation can be exploited Limited range in time and space scales involved Large generality implication: comparison on the basis of parameter values Direct link between flux and function

22. Static Energy Budgets (SEBs) Numbers: kJ in 28 d C energy from food A assimilation energy P production (growth) F energy in faeces U energy in urine R respiration (heat) From: Brafield, A. E. and Llewellyn, M. J. 1982 Animal energetics, Blackie, Glasgow

23. Static Energy Budgets (SEBs) SEBs are net production models Losses are first subtracted from incoming resources, rest is allocated to various endpoints gross ingested faeces apparent assimilated SEBs are single-pool models No metabolic memory or condition index No embryos urine gross metabolised spec dynamic action Problems in application maintenance = respiration production overheads? respiration & urine linked to current food intake no Kleiber net metabolised maintenance work production somatic maintenance activity growth products thermo regulation reproduction

24. Empirical patterns 1 From Sousa et al 2008 Phil. Trans. R. Soc. Lond. B 363:2453 -2464

25. Empirical patterns 2 From Sousa et al 2008 Phil. Trans. R. Soc. Lond. B 363:2453 -2464

26. Topological alternatives for 2-pool models kappa-first E reserve X food S som maint J mat maint G growth R reprod/mat E-first S+J-first From Lika & Kooijman 2011 J. Sea Res 66: 381-391 S-first J-first

27. Test of properties From Lika & Kooijman 2011 J. Sea Res, 66: 381-391

28. Static vs Dynamic Budgets Assimilation models • dynamics by nature • reserve damps food fluctuations Net production models • time-dependent static models • no demping by reserve

29. Evolution of DEB systems internalisation of maintenance as demand process variable structure composition strong homeostasis for structure increase of maintenance costs delay of use of internal substrates installation of maturation program prokaryotes 3 4 5 2 1 6 7 plants 9 animals 8 strong homeostasis for reserve Kooijman & Troost 2007 Biol Rev, 82, 1-30 reproduction juvenile  embryo + adult specialization of structure

30. Symbiosis on the basis of syntrophy substrate product

31. Symbiosis on the basis of syntrophy substrate substrate

32. Promising future development Delineate > 1 reserve & > types of food to model niches and changes in diet e.g. protein & carbohydrate and pay maintenance and overheads preferably from carbs Delineate organisation between cell & molecules: modules Model central metabolism as 5 biochemical modules that exchange metabolites on the basis of syntrophy using the rules for Synthesizing Units Model cell compartments (mitochondria, chloroplasts) as modules

33. Survey of organisms (brown algae) Phaeophyceae Granuloreticulata Xenophyophora Basidiomycota Ascomycota Xanthophyceae Raphidophyceae Chrysophyceae Synurophyceae Actinopoda Zygomycota Microsporidia Chytridiomycota Eustigmatophyceae Dictyochophyceae Pedinellophyceae Labyrinthulomycota Bicosoecia Pelagophyceae Plasmodiophoromycota Chlorarachnida Cercomonada Pseudofungi Bacillariophyceae (diatoms) Bolidophyceae Opalinata Choanozoa animals Prymnesiophyceae Cryptophyceae Metamonada Apusozoa Parabasalia mitochondria primary chloroplast secondary chloroplast tertiary chloroplast photo symbionts Sporozoa (plants) Cormophyta (green algae) Chlorophyceae (red algae) Rhodophyceae Glaucophyceae Percolozoa Myxomycota Protostelida Dinozoa Ciliophora Euglenozoa Kinetoplastida Diplonemida Archaeprotista Rhizopod a Loukozoa Bacteria