quantitative symbiogenesis van gogh nwo-exchange programme f-nl on aggregation methods & time...
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Quantitative symbiogenesis
Van Gogh NWO-exchange programme F-NL on aggregation methods & time scale separation
Kooijman, Bas, VU-AmsterdamKooi, Bob, VU-AmsterdamAuger, Pierre, Claude-Bernard Univ.-LyonPoggiale, Jean-Christophe, Centre d’Oceanol. -Marseilles
Dept of Theoretical Biology Vrije Universiteit, Amsterdam
http://www.bio.vu.nl/thb/
Contents of lecture
• symbiosis in context of DEB research• elements of simplest DEB model• symbiosis in context of evolution• application of DEB theory to symbiogenesis• results
Internat Conf on Mathematics and Biology of the SMB Knoxville, 2002/07/13-16
Dynamic Energy Budget theoryfor metabolic organisation of all life on earth• first principles• quantitativeBiological equivalent of Theoretical Physics
Primary target: the individual with consequences for• sub-organismal organization• supra-organismal organizationRelationships between levels of organisation
Applications in• ecotoxicology• biotechnologyDirect link with empiry
Reserve dynamics
Increase: assimilation surface areaDecrease: catabolism reserve/structure
First order process on the basis of densities follows from• weak homeostatis of biomass = structure + reserve• partitionability of reserve dynamics
Mechanism: structural homeostasis key feature: avoiding dilution by growth
Product Formation
throughput rate, 1/h
glyc
erol
, eth
anol
, g/l
pyr
uva
te,m
g/l
glycerol
ethanol
pyru
vate
Glucose-limited growth of Saccharomyces
According to Dynamic Energy Budget theory:
Product formation rate = wA . Assimilation rate + wM . Maintenance rate + wG . Growth rate
For pyruvate: wG<0
Simultaneous Substrate Processing
Chemical reaction: 1A + 1B 1CPoisson arrival events for molecules A and B
Standard enzyme kinetics:Substrate Conc. product flux (MM-kinetics)
Synthesizing Unit-concept: irreversible SU-substrate bindingSubstrate conc substrate flux (transport module)Substrate flux product flux + rejected substrate flux
11111 BABACmC JJJJJJFlux of C:
Simultaneous Nutrient Limitation
Specific growth rate of Pavlova lutheri as function of intracellular phosphorus and vitamin B12 at 20 ºC
Data from Droop 1974Note the absence of high contents for both compounds
due to damming up of reserves, andlow contents in structure (at zero growth)
P content, fmol/cell
B12 content,
10 -21 mol/cell
Reserve Capacity & Growth
low turnover rate: large reserve capacity
high turnover rate: small reserve capacity
DEBtool is freely downloadable fromhttp://www.bio.vu.nl/thb/deb/
Symbiosis
substrate substrate
Major basis:exchange of products between partners: syntrophy with transitions to competition & parasitism & predation
Mutualism: not essential “beneficial” involves an optimization criterion
Green animals
From: Streble, H. & Krauter, D. 1973 Das Leben im Wassertropfen. Komos, Stuttgart
Encentrumsaundersiae
Dicranophoruscaudatus
Ituraaurita
Typhloplanaviridata
Dalyelliaviridis
Chlorohydraviridissima
Rotifera
Platyhelminthes Cnidaria
corals
Green ciliates
From: Streble, H. & Krauter, D. 1973 Das Leben im Wassertropfen. Komos, Stuttgart
Urostyla viridis
Strongylidiumcrassum
Stentorpolymorphus
Strombidiumviride
Ophrydiumversatile
Parameciumbursaria
Spathidiumopimum
Didiniumfaurei
Prorodonviridis
Teuthophrystrisulcata
Acanthocystismimetica
From: Streble, H. & Krauter, D. 1973 Das Leben im Wassertropfen. Komos, StuttgartWolf-Gladrow, D. A., Bijma, J. & Zeebe, R. E.1999 Mar. Chem 64: 181-198
Raphidiophrysviridis
Green protists
Globigerinoidessacculifer
Heterophrysmyriepoda
Heliozoa
Foraminifera
Choroplast evolution
Delwiche, C. F. 1999. Tracing the thread of plastid diversity through the tapestry of life.
Am. Nat. 154, S164-S177
Survey of Organisms
diatomsBacillariophyceae
brown algaePhaeophyceae
Prymnesiophyceae
Raphidophyceae
Xanthophyceae
Eustigmatophyceae
Dictyochophyceae
Pelagophyceae
Chrysophyceae
Synurophyceae
Cryptophyceae
plantsCormophyta
green algaeChlorophyceae
red algaeRhodophyceae
Glaucophyceae
animals
EuglenozoaDinozoa
Rhizopoda
Bicosoecia
Actinopoda
Pseudofungi
Labyrinthulomycota
Myxomycota
Protostelida
Ciliophora
Sporozoa
Bacteria
Zygomycota
BasidiomycotaAscomycota
Archaeprotista
Chlorarachnida
Kinetoplastida
PlasmodiophoromycotaMicrosporidia
Chytridiomycota
Percolozoa
Trichozoa
Opalinata
Metamonada
Cercomonada
Neomonada
Diplonemida
GranuloreticulataXenophyophora
http://www.bio.vu.nl/thb/ “education”,”cycles”many life cycle pictures
Internalization
Structures merge Reserves merge
Free-living, clusteringFree-living, homogeneous
Steps in symbiogenesis
Steps in symbiogenesis
• 2 populations, substrates, products• from substitutable to complementary products• spatial clustering• internalization• weak homeostasis for structure• from concentrations to fluxes of internal prod.• strong homeostasis for structure• coupling of assimilation fluxes• coupling of reserve dynamics• weak homeostasis for reserves• strong homeostasis for reserves
in the context of the DEB theory
throughput rate
Chemostat Steady Statesbi
omas
s de
nsit
y
hostsymbiont
Free livingProducts substitutable
Free livingProducts complementary
EndosymbiosisExchange on conc-basis
Exchange on flux-basis Structures merged Reserves mergedHost uses 2 substrates
ResultsIt is possible to merge partners smoothly through incremental changes of parameter values
Homeostasis can be achieved gradually range of ratio of structures reduces
Partitionability argument for reserve kinetics can be reformulated in a mergebility argument
If partners follow DEB rules, symbiogenesis can be such that symbiosis again follows DEB rules
We made some progress in understanding the modular organization of cell’s metabolism in an evolutionary context