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

Metabolism

Eco-system

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

b ; Catalytic Network (environmental chemistry)

More mutualistic More selfish

bNG = 100

bij

“Metabolic” network

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’

Present-day organism – Complex

From organisms to food webs – Complex

Prebiotic Ecology: From molecules to Ecosystem.

( from species inner structure to food web )

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

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

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C1

One example Another example

Each simulation with a different chemistry (b network).

Simulations exhibiting a single compotype species:

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

Population Dynamics in GARD

<<Data removed from published version>>

Why plateau is lower than 1.0 ?

<<Data removed from published version>>

GARD’s Ecology

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Compotype sub-network part of b

<<Data removed from published version>>

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

Population Dynamics in GARD

“Takeover” of a fast-rising compotype by a slower one.

<<Data removed from published version>>

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

Simple

Complicated

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.

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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