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

DEB-ontogeny-IBM

DEB-ontogeny-IBM

Tom Hallamvisits Delft1985/08/12

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

1 Reserve – 1 Structure

2 Reserves – 1 Structure

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/

Organism

product

substrate

An organism converts substrates into products and a bit more of itself

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 fungi: lichenes

From: Nash, T. H. 1996 Lichen biology, Cambridge UP

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

Thank you for your attention

Free internet course on DEB theoryFebruary-April 2003 (part time)

http://www.bio.vu.nl/thb/deb/course/

Tom: congratulations !