1 prebiotic evolution of molecular assemblies: from molecules to ecology omer markovitch and doron...
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Prebiotic Evolution of Molecular Assemblies:From Molecules to Ecology
Omer Markovitch and Doron Lancet
Department of Molecular Genetics, Weizmann Institute of Science, Israel
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Metabolism
Eco-system
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RNAMicelles
&Vesicles
DNA / RNA / Polymers Sequencecovalent bonds
Assemblies / Clusters / Vesicles / Membranes Compositionnon-covalent bonds
Segre and Lancet, EMBO Reports 1 (2000)
RNA world Lipid world
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GARD model (Graded Autocatalysis Replication Domain)
Fission / Split
Homeostatic growth
b
Segre, Ben-Eli and Lancet, Proc. Natl. Acad. Sci. 97 (2000)
GjN
jijibif
i NiN
nnkNk
dt
dn G
...11 1
Rate enhancement
Molecular repertoire
Synthetic chemistry Kinetic model Catalytic network (b) of
rate-enhancement values
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b ; Catalytic Network (environmental chemistry)
More mutualistic More selfish
bNG = 100
bij
“Metabolic” network
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GARD model (Graded Autocatalysis Replication Domain)
Following a single lineage.
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Composome (compositional genome) = a faithfully replicating composition/assembly.
Compotype (composome type) = a collection of similar composomes quasispecies.
Generation
Gen
erat
ion
ng=30; split=1.5; seed=361
200 400 600 800 1000
200
400
600
800
1000
0
0.2
0.4
0.6
0.8
1
Com
posi
tion
al S
imil
arit
y
Similarity ‘carpet’
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Present-day organism – Complex
From organisms to food webs – Complex
Prebiotic Ecology: From molecules to Ecosystem.
( from species inner structure to food web )
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Population Dynamics in GARD
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Following the dynamics of a constant-size population of assemblies.
Buffered environment (=unlimited food).
At each time point, each assembly is colored by its compotype.
Time [split]
Ass
emb
ly
seed=45
1000 2000 3000 4000 5000
10
20
30
40
50
60
70
80
90
100
0 1 2 3 4 50
0.1
0.2
0.3
0.4
0.5seed=45; omer new; no selection
Time [104 splits]
Co
mp
otyp
e p
opul
atio
n fr
act
ion
C1C2C3
Mem
ber
of p
opul
atio
n
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Population Dynamics in GARD
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0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 50
0.2
0.4
0.6
0.8
1
Time [104 splits]
Co
mp
otyp
e p
opul
atio
n fr
act
ion
1
C1
0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 50
0.2
0.4
0.6
0.8
1
Time [104 splits]
Co
mp
otyp
e p
opul
atio
n fr
act
ion
27
C1
One example Another example
Each simulation with a different chemistry (b network).
Simulations exhibiting a single compotype species:
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Population Dynamics in GARD
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One example Another example
Each simulation with a different chemistry (b network).
Simulations exhibiting multiple compotypes:
0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 50
0.1
0.2
0.3
0.4
0.5
0.6
Time [104 splits]
Co
mp
otyp
e p
opul
atio
n fr
act
ion
45
C1C2C3
0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 50
0.1
0.2
0.3
0.4
0.5
0.6
0.7
Time [104 splits]
Co
mp
otyp
e p
opul
atio
n fr
act
ion
170
C1C2
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Logistic Growth
C = compotype frequency in the populationr = compotype intrinsic growth rateK = compotype carrying capacitya = competition parameters between two species
[Gause (1934)]
Independently cultivated
0 5 10 15 20
Lotka-Volterra
10-6 m
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Population Dynamics in GARD
<<Data removed from published version>>
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Why plateau is lower than 1.0 ?
<<Data removed from published version>>
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GARD’s Ecology
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Compotype sub-network part of b
<<Data removed from published version>>
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Based on experimental data of 111 bacteria.
Freilich et al, Genome Biology (2009)
GARD’s Ecology
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0 100 200 300 400 500 600 7000
5
10
15
20
25
30
35
Metabolic network size
Do
ublin
g tim
e [
hour
]
Freilich 2009; SOM;
0 100 200 300 400 500 600 7000
1
2
3
4
5
6
Metabolic network size
Dou
blin
g ra
te [1
/hou
r]
Freilich 2009; SOM;
Correlation = -0.38P-value = 0.000031
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Population Dynamics in GARD
“Takeover” of a fast-rising compotype by a slower one.
<<Data removed from published version>>
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Population Dynamics in GARD
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Lipid-world & GARD model: compositional assemblies
Compotypes (clusters of faithfully replicating compositions)
Populations dynamics
Logistic behavior
Species competition, takeover
Molecular parameters Population ecology
Carrying capacity (K)
Molecular repertoire effects r & K
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Simple
Complicated
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Omer Markovitch
Acknowledgements:Doron Lancet.Avi Mayo (Weizmann).Raphael Zidovetzki (U. California Riverside, USA).Natalio Krasnogor (U. Nottingham, UK).Lancet group.
Funding:* Minerva Center for Life Under Extreme Planetary Conditions, at Weizmann Institute.
* E.U. FP7 “MATCHIT”.
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0 0.5 1 1.5 2 2.5 30
0.1
0.2
0.3
0.4
0.5
0.6seeds=1-1000; ng=split=100;
Selection excess
Pro
babi
lity
Markovitch and Lancet, Artificial Life 18:3 (2012)
PositiveNegative
beforefrequency Target
afterfrequency Target ExcessSelection
Selection in GARD
Selection of GARD assemblies towards a target compotype.
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GARD portrays selection.
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Lack of selectivity in GARD? NO.
Their weak points:(1) Target is not a composome.(2) Only a single simulation performed.(3) Small repertoire (NG=10) and assembly size (Nmax=6).
(4) Arbitrary fitness threshold.
Index of assembly composition
Fre
quen
cy
Vasas, Szathmary & Santos, PNAS 107, 1470-1475 (2010): Imposing Darwinian selection in GARD has, at most, negligible effect…
–– Regular–– Beneficial–– Detrimental
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