Alternative approaches to modelling metabolism Bas Kooijmanvu nl
Alternative approaches to modelling metabolism Bas. Kooijman@vu. nl Tromsø, 2017/05/21 -30 deb. akvaplan. com/debschool. html
Contents 1. What is metabolism and its origins 2. Biochemical approaches 3. Pool approaches 4. Module approaches 5. Outlook
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
Metabolism during evolution Red algae Eukaryotes Anoxygenic photosynthesis Flesh Great Oxidation Event Life Vascular plants Cyanobacteria From: Judson, Nature Ecol & Evol 1, 0138 (2017)
Early ATP generation Fe. S + S 0 Fe. S 2 ADP + Pi ATP • ATPase • hydrogenase • S-reductase Fe. S 2 Fe. S H 2 S 0 H 2 S 2 e. S 0 H 2 S 2 H 2 O 2 OH- 2 H+ ADP Pi ATP 2 H+ Madigan et al 1997
Central Metabolism source polymers monomers waste/source
Evolution of central metabolism in prokaryotes (= bacteria) 3. 8 Ga 2. 7 Ga i = inverse ACS = acetyl-Co. A Synthase pathway RC = Respiratory Chain PP = Pentose Phosphate cycle Gly = Glycolysis TCA = Tri. Carboxylic Acid cycle Kooijman, Hengeveld 2005
Prokaryotic metabolic evolution Heterotrophy: • pentose phosph cycle • glycolysis • respiration chain Phototrophy: • el. transport chain • PS I & PS II • Calvin cycle Chemolithotrophy • acetyl-Co. A pathway • inverse TCA cycle • inverse glycolysis
Symbiogenesis 2. 7 Ga phagocytosis 2. 1 Ga 1. 27 Ga
Classic energetics heterotroph autotroph 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
ATP generation & use 5 106 ATP molecules in bacterial cell enough for 2 s of biosynthetic work mean life time of ATP molecule: 0. 3 s Only used if energy generating & energy demanding transformations are at different site/time If ADP/ATP ratio varies, then rates of generation & use varies, but not necessarily the rates of transformations they drive Processes that are not much faster than cell cycle, should be linked to large slow pools of metabolites, not to small fast pools
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
Self-ionization of water in cells modified Bessel function p. H confidence intervals of p. H 95, 90, 80, 60 % A cell of volume 0. 25 mm 3 and p. H 7 at 25°C has m = 14 protons N = 8 109 water molecules 7 cell volume, m 3
Diffusion cannot occur in cells
Uncatalyzed reaction Enzyme-catalyzed reaction Enzyme kinetics
Surface area/volume interactions 1. 2. 3 b Membrane-mediated transformation rates in isomorphs decrease with length because of transportation distance inactive 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
Crowding affects transport cytoskeletal polymers ribosomes nucleic acids proteins
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
Respiration
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
Static Energy Budgets (SEBs) Numbers: k. J 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
Static Energy Budgets (SEBs) SEBs are net production models gross ingested Losses are first subtracted from incoming resources, rest is allocated to various endpoints faeces apparent assimilated SEBs are single-pool models No metabolic memory or condition index urine gross metabolised No embryos spec dynamic action Problems in application maintenance = respiration production overheads? respiration & urine linked to current food intake somatic no Kleiber net metabolised maintenance thermo regulation production work activity growth products reproduction
Empirical patterns 1 From Sousa et al 2008 Phil. Trans. R. Soc. Lond. B 363: 2453 -2464
Empirical patterns 2 From Sousa et al 2008 Phil. Trans. R. Soc. Lond. B 363: 2453 -2464
J-first S+J-first E-first kappa-first Topological alternatives for 2 -pool models E reserve X food S som maint J mat maint G growth R reprod/mat From Lika & Kooijman 2011 J. Sea Res 66: 381 -391
Test of properties From Lika & Kooijman 2011 J. Sea Res, 66: 381 -391
Static vs Dynamic Budgets Net production models • time-dependent static models • no demping by reserve Assimilation models • dynamics by nature • reserve damps food fluctuations
Evolution of DEB systems 1 strong homeostasis for structure 2 delay of use of internal substrates 3 internalisation of maintenance as demand process increase of maintenance costs 4 5 7 Kooijman & Troost 2007 Biol Rev, 82, 1 -30 reproduction juvenile embryo + adult animals 8 strong homeostasis for reserve installation of maturation program prokaryotes variable structure composition 6 plants 9 specialization of structure
Symbiosis on the basis of syntrophy substrate product
Symbiosis on the basis of syntrophy substrate
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
Survey of organisms (brown algae) Phaeophyceae Basidiomycota Xanthophyceae Raphidophyceae Ascomycota Chrysophyceae Synurophyceae Actinopoda Zygomycota Eustigmatophyceae Microsporidia Labyrinthulomycota Dictyochophyceae Bicosoecia Pedinellophyceae Chytridiomycota Pelagophyceae Plasmodiophoromycota Pseudofungi Bacillariophyceae Chlorarachnida (diatoms) Opalinata Cercomonada Choanozoa Bolidophyceae Granuloreticulata Xenophyophora animals Apusozoa mitochondria primary chloroplast secondary chloroplast tertiary chloroplast photo symbionts Bacteria Myxomycota Protostelida Archaeprotista Rhizopoda Metamonada Parabasalia Percolozoa Euglenozoa Kinetoplastida Diplonemida Loukozoa Prymnesiophyceae Cryptophyceae Sporozoa Dinozoa Ciliophora (plants) Cormophyta (green algae) Chlorophyceae (red algae) Rhodophyceae Glaucophyceae
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