Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology
description
Transcript of Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology
![Page 1: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/1.jpg)
1
Prebiotic Evolution of Molecular Assemblies:From Molecules to Ecology
Omer Markovitch and Doron Lancet
Department of Molecular Genetics, Weizmann Institute of Science, Israel
![Page 2: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/2.jpg)
Metabolism
Eco-system
![Page 3: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/3.jpg)
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
3
![Page 4: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/4.jpg)
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 NiNn
nkNkdtdn G
...11 1
b
Rate enhancement
Molecular repertoire
Synthetic chemistry Kinetic model Catalytic network (b) of
rate-enhancement values
![Page 5: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/5.jpg)
b ; Catalytic Network (environmental chemistry)
More mutualistic More selfish
bNG = 100
bij
“Metabolic” network
![Page 6: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/6.jpg)
GARD model (Graded Autocatalysis Replication Domain)Following a single lineage.
6
Composome (compositional genome) = a faithfully replicating composition/assembly.
Compotype (composome type) = a collection of similar composomes quasispecies.
Generation
Gene
ratio
n
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
1C
ompo
sitio
nal S
imila
rity
Similarity ‘carpet’
![Page 7: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/7.jpg)
Present-day organism – Complex
From organisms to food webs – Complex
Prebiotic Ecology: From molecules to Ecosystem.
( from species inner structure to food web )
![Page 8: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/8.jpg)
Population Dynamics in GARD
8
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
embl
y
seed=45
1000 2000 3000 4000 5000
102030405060708090
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]
Com
poty
pe p
opul
atio
n fra
ctio
n
C1C2C3
Mem
ber o
f pop
ulat
ion
![Page 9: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/9.jpg)
Population Dynamics in GARD
9
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]
Com
poty
pe p
opul
atio
n fra
ctio
n
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]
Com
poty
pe p
opul
atio
n fra
ctio
n
27
C1
One example Another example
Each simulation with a different chemistry (b network).
Simulations exhibiting a single compotype species:
![Page 10: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/10.jpg)
Population Dynamics in GARD
10
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]
Com
poty
pe p
opul
atio
n fra
ctio
n
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]
Com
poty
pe p
opul
atio
n fra
ctio
n
170
C1C2
![Page 11: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/11.jpg)
11
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
![Page 12: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/12.jpg)
Population Dynamics in GARD
<<Data removed from published version>>
![Page 13: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/13.jpg)
Why plateau is lower than 1.0 ?
<<Data removed from published version>>
![Page 14: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/14.jpg)
GARD’s Ecology
14
Compotype sub-network part of b
<<Data removed from published version>>
![Page 15: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/15.jpg)
Based on experimental data of 111 bacteria.
Freilich et al, Genome Biology (2009)
GARD’s Ecology
15
0 100 200 300 400 500 600 7000
5
10
15
20
25
30
35
Metabolic network size
Dou
blin
g tim
e [h
our]
Freilich 2009; SOM;
0 100 200 300 400 500 600 7000
1
2
3
4
5
6
Metabolic network size
Doub
ling r
ate [1
/hour
]
Freilich 2009; SOM;
Correlation = -0.38P-value = 0.000031
![Page 16: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/16.jpg)
Population Dynamics in GARD
“Takeover” of a fast-rising compotype by a slower one.
<<Data removed from published version>>
![Page 17: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/17.jpg)
Population Dynamics in GARD
17
![Page 18: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/18.jpg)
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
![Page 19: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/19.jpg)
Simple
Complicated
![Page 20: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/20.jpg)
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”.
20
![Page 21: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/21.jpg)
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
Prob
abilit
y
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.
21
GARD portrays selection.
![Page 22: Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology](https://reader035.fdocuments.net/reader035/viewer/2022062521/568166b5550346895ddababf/html5/thumbnails/22.jpg)
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
Freq
uenc
y
Vasas, Szathmary & Santos, PNAS 107, 1470-1475 (2010): Imposing Darwinian selection in GARD has, at most, negligible effect…
–– Regular–– Beneficial–– Detrimental
22