81

RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

  • Upload
    others

  • View
    89

  • Download
    0

Embed Size (px)

Citation preview

Page 1: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with
Page 2: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

RNA – Das Zaubermolekül

Peter SchusterInstitut für Theoretische Chemie und Molekulare

Strukturbiologie der Universität Wien

Dies Academicus

Leipzig, 02.12.2002

Page 3: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

++

Replication:DNA 2 DNA→Tr

ansc

riptio

n:

D

NA

RN

A→

Metabolism

Food

Waste

NucleotidesAmino Acids

Lipids Carbohydrates

Small Molecules

Translation: RNA Protein→

ProteinmRNA

Ribosom

A conventional simplified sketch of cellular metabolism

Page 4: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

OCH2

OHO

O

PO

O

O

N1

OCH2

OHO

PO

O

O

N2

OCH2

OHO

PO

O

O

N3

OCH2

OHO

PO

O

O

N4

N A U G Ck = , , ,

3' - end

5' - end

NaØ

NaØ

NaØ

NaØ

RNA

nd 3’-endGCGGAU AUUCGCUUA AGUUGGGA G CUGAAGA AGGUC UUCGAUC A ACCAGCUC GAGC CCAGA UCUGG CUGUG CACAG

3'-end

5’-end

70

60

50

4030

20

10

Definition of RNA structure

5'-e

Page 5: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Canonical or Watson-Crick base pairs:

cytosine – guanineGÍC

uracil – adenineA=U

W.Saenger, Principles of Nucleic Acid Structure, Springer, Berlin 1984

Page 6: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

The three-dimensional structure of a short double helical stack

Page 7: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

O

O

OO

O

H

H

HH

H

H

H

HH

H

H

N

NNN

N

N

N

N

N

N

NO

O

HN

N

H

O

NN

N

NN

N

N

G=U

G CÍ

U=G

Canonical Watson-Crick base-pair Wobble base-pairs

Wobble base pairs in RNA double-helical stacks

Page 8: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

RNA

RNA as scaffold for supramolecular complexes

ribosome

? ? ? ? ?

RNA as adapter molecule

GA

C...

CU

G ..

.

leu

genetic code

RNA as transmitter of genetic information

DNA

...AGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUC...

messenger-RNA

protein

transcription

translation

RNA as of genetic informationworking copy

RNA as carrier of genetic information

RNA

RNA

viruses and retroviruses

as information carrier inevolution and

evolutionary biotechnologyin vitro

RNA as catalyst

ribozyme

The RNA

DNA protein

world as a precursor of

the current + biology

RNA as regulator of gene expression

gene silencing by small interfering RNAs

RNA is modified by epigenetic control

RNA

RNA

editing

Alternative splicing of messenger

RNA is the catalytic subunit in supramolecular complexes

Functions of RNA molecules

Page 9: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Evolution of RNA molecules based on Qβ phage

D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc.Natl.Acad.Sci.USA 58 (1967), 217-224

S.Spiegelman, An approach to the experimental analysis of precellular evolution. Quart.Rev.Biophys. 4 (1971), 213-253

C.K.Biebricher, Darwinian selection of self-replicating RNA molecules. Evolutionary Biology 16 (1983), 1-52

G.Bauer, H.Otten, J.S.McCaskill, Travelling waves of in vitro evolving RNA.Proc.Natl.Acad.Sci.USA 86 (1989), 7937-7941

C.K.Biebricher, W.C.Gardiner, Molecular evolution of RNA in vitro. Biophysical Chemistry 66 (1997), 179-192

G.Strunk, T.Ederhof, Machines for automated evolution experiments in vitro based on the serial transfer concept. Biophysical Chemistry 66 (1997), 193-202

Page 10: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

RNA sample

Stock solution: Q RNA-replicase, ATP, CTP, GTP and UTP, bufferb

Time0 1 2 3 4 5 6 69 70

The serial transfer technique applied to RNA evolution in vitro

Page 11: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Reproduction of the original figure of theserial transfer experiment with Q RNAβ

D.R.Mills, R,L,Peterson, S.Spiegelman,

. Proc.Natl.Acad.Sci.USA (1967), 217-224

An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule58

Page 12: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Decrease in mean fitnessdue to quasispecies formation

The increase in RNA production rate during a serial transfer experiment

Page 13: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

No new principle will declare itself from below a heap of facts.

Sir Peter Medawar, 1985

Page 14: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

G

G

G

G

C

C

C G

C

C

G

C

C

G

C

C

G

C

C

G

C

C

C

C

G

G

G

G

G

C

G

C

Plus Strand

Plus Strand

Minus Strand

Plus Strand

Plus Strand

Minus Strand

3'

3'

3'

3'

3'

5'

5'

5'

3'

3'

5'

5'

5'+

Complex Dissociation

Synthesis

Synthesis

Complementary replication as thesimplest copying mechanism of RNAComplementarity is determined byWatson-Crick base pairs:

GÍC and A=U

Page 15: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

dx / dt = x - x

x

i i i

j j

; Σ = 1 ; i,j

f

f

i

j

Φ

Φ

fi Φ = (

= Σ

x - i )

j jx =1,2,...,n

[I ] = x 0 ; i i Æ i =1,2,...,n ; Ii

I1

I2

I1

I2

I1

I2

I i

I n

I i

I nI n

+

+

+

+

+

+

(A) +

(A) +

(A) +

(A) +

(A) +

(A) +

fn

fi

f1

f2

I mI m I m++(A) +(A) +fm

fm fj= max { ; j=1,2,...,n}

xm(t) 1 for t Á Á¸

[A] = a = constant

Reproduction of organisms or replication of molecules as the basis of selection

Page 16: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

s = ( f2-f1) / f1; f2 > f1 ; x1(0) = 1 - 1/N ; x2(0) = 1/N

200 400 600 800 1000

0.2

00

0.4

0.6

0.8

1

Time [Generations]

Frac

tion

of a

dvan

tage

ous v

aria

nt

s = 0.1

s = 0.01

s = 0.02

Selection of advantageous mutants in populations of N = 10 000 individuals

Page 17: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

G

G

G

C

C

C

G

C

C

G

C

C

C

G

C

C

C

G

C

G

G

G

G

C

Plus Strand

Plus Strand

Minus Strand

Plus Strand

3'

3'

3'

3'

5'

3'

5'

5'

5'

Point Mutation

Insertion

Deletion

GAA AA UCCCG

GAAUCC A CGA

GAA AAUCCCGUCCCG

GAAUCCA

Mutations in nucleic acids represent the mechanism of variation of genotypes.

Page 18: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Theory of molecular evolution

M.Eigen, Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58 (1971), 465-526

C.J.Thompson, J.L.McBride, On Eigen's theory of the self-organization of matter and the evolution of biological macromolecules. Math. Biosci. 21 (1974), 127-142

B.L.Jones, R.H.Enns, S.S.Rangnekar, On the theory of selection of coupled macromolecular systems.Bull.Math.Biol. 38 (1976), 15-28

M.Eigen, P.Schuster, The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. Naturwissenschaften 58 (1977), 465-526

M.Eigen, P.Schuster, The hypercycle. A principle of natural self-organization. Part B: The abstract hypercycle. Naturwissenschaften 65 (1978), 7-41

M.Eigen, P.Schuster, The hypercycle. A principle of natural self-organization. Part C: The realistic hypercycle. Naturwissenschaften 65 (1978), 341-369

J.Swetina, P.Schuster, Self-replication with errors - A model for polynucleotide replication.Biophys.Chem. 16 (1982), 329-345

J.S.McCaskill, A localization threshold for macromolecular quasispecies from continuously distributed replication rates. J.Chem.Phys. 80 (1984), 5194-5202

M.Eigen, J.McCaskill, P.Schuster, The molecular quasispecies. Adv.Chem.Phys. 75 (1989), 149-263

C. Reidys, C.Forst, P.Schuster, Replication and mutation on neutral networks. Bull.Math.Biol. 63(2001), 57-94

Page 19: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Ij

In

I2

Ii

I1 I j

I j

I j

I j

I j

I j +

+

+

+

+

(A) +

fj Qj1

fj Qj2

fj Qji

fj Qjj

fj Qjn

Q (1- ) ij-d(i,j) d(i,j) = lp p

p .......... Error rate per digit

d(i,j) .... Hamming distance between Ii and Ij

........... Chain length of the polynucleotidel

dx / dt = x - x

x

i j j i

j j

Σ

; Σ = 1 ;

f

f x

j

j j i

Φ

Φ = Σ

Qji

QijΣi = 1

[A] = a = constant

[Ii] = xi 0 ; Æ i =1,2,...,n ;

Chemical kinetics of replication and mutation as parallel reactions

Page 20: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Error rate p = 1-q0.00 0.05 0.10

Quasispecies Uniform distribution

Quasispecies as a function of the replication accuracy q

Page 21: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

spaceSequence

Con

cent

ratio

n

Master sequence

Mutant cloud

The molecular quasispecies in sequence space

Page 22: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

In the case of non-zero mutation rates (p>0 or q<1) the Darwinian principle of optimization of mean fitness can be understood only as an optimization heuristic. It is valid only on part of the concentration simplex. There are other well defined areas were the mean fitness decreases monotonously or were it may show non-monotonous behavior. The volume of the part of the simplex where mean fitness isnon-decreasing in the conventional sense decreases with inreasing mutation rate p.

In systems with recombination a similar restriction holds for Fisher‘s „universal selection equation“. Its global validity is restricted to the one-gene (single locus) model.

Page 23: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Theory of genotype – phenotype mapping

P. Schuster, W.Fontana, P.F.Stadler, I.L.Hofacker, From sequences to shapes and back: A case study in RNA secondary structures. Proc.Roy.Soc.London B 255 (1994), 279-284

W.Grüner, R.Giegerich, D.Strothmann, C.Reidys, I.L.Hofacker, P.Schuster, Analysis of RNA sequence structure maps by exhaustive enumeration. I. Neutral networks. Mh.Chem. 127 (1996), 355-374

W.Grüner, R.Giegerich, D.Strothmann, C.Reidys, I.L.Hofacker, P.Schuster, Analysis of RNA sequence structure maps by exhaustive enumeration. II. Structure of neutral networks and shape space covering. Mh.Chem. 127 (1996), 375-389

C.M.Reidys, P.F.Stadler, P.Schuster, Generic properties of combinatory maps. Bull.Math.Biol. 59 (1997), 339-397

I.L.Hofacker, P. Schuster, P.F.Stadler, Combinatorics of RNA secondary structures. Discr.Appl.Math. 89 (1998), 177-207

C.M.Reidys, P.F.Stadler, Combinatory landscapes. SIAM Review 44 (2002), 3-54

Page 24: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Genotype-phenotype relations are highly complex and only the mostsimple cases can be studied. One example is the folding of RNA sequences into RNA structures represented in course-grained form as secondary structures.

The RNA genotype-phenotype relation is understood as a mapping from the space of RNA sequences into a space of RNA structures.

Page 25: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

5'-End

5'-End

5'-End

3'-End

3'-End

3'-End

70

60

50

4030

20

10

GCGGAU AUUCGCUUA AGDDGGGA M CUGAAYA AGMUC TPCGAUC A ACCAGCUC GAGC CCAGA UCUGG CUGUG CACAGSequence

Secondary structure Tertiary structure

Symbolic notation

The RNA secondary structure is a listing of GC, AU, and GU base pairs. It is understood in contrast to the full 3D-or tertiary structure at the resolution of atomic coordinates. RNA secondary structures are biologically relevant. They are, for example, conserved in evolution.

Page 26: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

RNA Minimum Free Energy Structures

Efficient algorithms based on dynamical programming are available for computation of secondary structures for given sequences. Inverse folding algorithms compute sequences for given secondary structures.

M.Zuker and P.Stiegler. Nucleic Acids Res. 9:133-148 (1981)

Vienna RNA Package: http:www.tbi.univie.ac.at (includes inverse folding, suboptimal structures, kinetic folding, etc.)

I.L.Hofacker, W. Fontana, P.F.Stadler, L.S.Bonhoeffer, M.Tacker, and P. Schuster. Mh.Chem. 125:167-188 (1994)

Page 27: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

UUUAGCCAGCGCGAGUCGUGCGGACGGGGUUAUCUCUGUCGGGCUAGGGCGC

GUGAGCGCGGGGCACAGUUUCUCAAGGAUGUAAGUUUUUGCCGUUUAUCUGG

UUAGCGAGAGAGGAGGCUUCUAGACCCAGCUCUCUGGGUCGUUGCUGAUGCG

CAUUGGUGCUAAUGAUAUUAGGGCUGUAUUCCUGUAUAGCGAUCAGUGUCCG

GUAGGCCCUCUUGACAUAAGAUUUUUCCAAUGGUGGGAGAUGGCCAUUGCAG

Minimum free energycriterion

Inverse folding

1st2nd3rd trial4th5th

The inverse folding algorithm searches for sequences that form a given RNA secondary structure under the minimum free energy criterion.

Page 28: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

UUUAGCCAGCGCGAGUCGUGCGGACGGGGUUAUCUCUGUCGGGCUAGGGCGC

GUGAGCGCGGGGCACAGUUUCUCAAGGAUGUAAGUUUUUGCCGUUUAUCUGG

UUAGCGAGAGAGGAGGCUUCUAGACCCAGCUCUCUGGGUCGUUGCUGAUGCG

CAUUGGUGCUAAUGAUAUUAGGGCUGUAUUCCUGUAUAGCGAUCAGUGUCCG

GUAGGCCCUCUUGACAUAAGAUUUUUCCAAUGGUGGGAGAUGGCCAUUGCAG

Criterion ofMinimum Free Energy

Sequence Space Shape Space

Page 29: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

CGTCGTTACAATTTA GTTATGTGCGAATTC CAAATT AAAA ACAAGAG.....

CGTCGTTACAATTTA GTTATGTGCGAATTC CAAATT AAAA ACAAGAG.....

G A G T

A C A C

Hamming distance d (S ,S ) = H 1 2 4

d (S ,S ) = 0H 1 1

d (S ,S ) = d (S ,S )H H1 2 2 1

d (S ,S ) d (S ,S ) + d (S ,S )H H H1 3 1 2 2 3¶

(i)

(ii)

(iii)

The Hamming distance induces a metric in sequence space

Page 30: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

The RNA model considers RNA sequences as genotypes and simplified RNA structures, called secondary structures, as phenotypes.

The mapping from genotypes into phenotypes is many-to-one. Hence, it is redundant and not invertible.

Genotypes, i.e. RNA sequences, which are mapped onto the same phenotype, i.e. the same RNA secondary structure, form neutral networks. Neutral networks are represented by graphsin sequence space.

Page 31: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Sk I. = ( )ψfk f Sk = ( )

Sequence space Phenotype space Non-negativenumbers

Mapping from sequence space into phenotype space and into fitness values

Page 32: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Sk I. = ( )ψfk f Sk = ( )

Sequence space Phenotype space Non-negativenumbers

Page 33: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Sk I. = ( )ψfk f Sk = ( )

Sequence space Phenotype space Non-negativenumbers

The pre-image of the structure Sk in sequence space is the neutral network Gk

Page 34: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Neutral networks are sets of sequences forming the same structure. Gk is the pre-image of the structure Sk in sequence space:

Gk = y-1(Sk) π {yj | y(Ij) = Sk}

The set is converted into a graph by connecting all sequences of Hamming distance one.

Neutral networks of small RNA molecules can be computed by exhaustive folding of complete sequence spaces, i.e. all RNA sequences of a given chain length. This number, N=4n , becomes very large with increasing length, and is prohibitive for numerical computations.

Neutral networks can be modelled by random graphs in sequence space. In this approach, nodes are inserted randomly into sequence space until the size of the pre-image, i.e. the number of neutral sequences, matches the neutral network to be studied.

Page 35: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 00

Page 36: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 01

Page 37: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 02

Page 38: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 03

Page 39: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 04

Page 40: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 05

Page 41: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 10

Page 42: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 15

Page 43: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 25

Page 44: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 50

Page 45: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 75

Page 46: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Random graph approach to neutral networks

Sketch of sequence spaceStep 100

Page 47: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

λj = 27 ,/12 λk = ø l (k)j

| |Gk

λ κcr = 1 - -1 ( 1)/ κ-

λ λk cr . . . .>

λ λk cr . . . .<

network is connectedGk

network is connectednotGk

Connectivity threshold:

Alphabet size : = 4k ñ kAUGC

G S Sk k k= ( ) | ( ) = y y-1 U { }I Ij j

k lcr

2 0.5

3 0.4226

4 0.3700

Mean degree of neutrality and connectivity of neutral networks

Page 48: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Giant Component

A multi-component neutral network

Page 49: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

A connected neutral network

Page 50: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

CUGGGAAAAAUCCCCAGACCGGGGGUUUCCCCGG

CUGGGAAAAAUCCCCAGACCGGGGGUUUCCGCGG

G G

G G

G GG G

G G

G G

G G

C C

C G

C C

C C

U U

U UG G

G GG GG GG G

C CC C

C C

C C

C CC C

C C

U U

U U

A AA A

A A

A A

A A

U U

Com

patib

le

Inco

mpa

tible

5’-end 5’-end

3’-end 3’-end

Compatibility of sequences with structures

A sequence is compatible with its minimum free energy structure and all its suboptimal structures.

Page 51: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

G Ck à k Gk

Neutral network

Compatible set Ck

The compatible set Ck of a structure Sk consists of all sequences which form Sk as its minimum free energy structure (neutral network Gk) or one of itssuboptimal structures.

Page 52: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

CUGGGAAAAAUCCCCAGACCGGGGGUUUCCCCGG

G

G

G

G

GG

G

G

G

G

G

G

G

G

G

G

G

G

C

C

C

C

C

C

CC

UU

UU

U

U

G

G

G

G

G

C

C

C

C

C

C

C

CC

C

C

C

CU

UU

AA

A

AA

A

A

A

A

A

U

3’- end

Min

imum

free

ene

rgy

conf

orm

atio

n S 0

Subo

ptim

al c

onfo

rmat

ion

S 1

C

G

A sequence at the intersection of two neutral networks is compatible with both structures

Page 53: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

: á ì âC1 C2

: â ì áC1 C2

G1

G2

The intersection of two compatible sets is always non empty: C1 Ú C2 â Ù

Page 54: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Reference for the definition of the intersection and the proof of the intersection theorem

Page 55: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Optimization of RNA molecules in silico

W.Fontana, P.Schuster, A computer model of evolutionary optimization. Biophysical Chemistry 26 (1987), 123-147

W.Fontana, W.Schnabl, P.Schuster, Physical aspects of evolutionary optimization and adaptation. Phys.Rev.A 40 (1989), 3301-3321

M.A.Huynen, W.Fontana, P.F.Stadler, Smoothness within ruggedness. The role of neutralityin adaptation. Proc.Natl.Acad.Sci.USA 93 (1996), 397-401

W.Fontana, P.Schuster, Continuity in evolution. On the nature of transitions. Science 280(1998), 1451-1455

W.Fontana, P.Schuster, Shaping space. The possible and the attainable in RNA genotype-phenotype mapping. J.Theor.Biol. 194 (1998), 491-515

B.M.R.Stadler, P.F.Stadler, G.P.Wagner, W.Fontana, The topology of the possible: Formal spaces underlying patterns of evolutionary change. J.Theor.Biol. 213 (2001), 241-274

Page 56: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

5'-End

3'-End

70

60

50

4030

20

10

Randomly chosen initial structure

Phenylalanyl-tRNA as target structure

Page 57: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Stock Solution Reaction Mixture

Fitness function:

fk = g / [a + DdS(k)]

DdS(k) = ds(Ik,It)

The flowreactor as a device for studies of evolution in vitro and in silico

Page 58: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

spaceSequence

Con

cent

ratio

n

Master sequence

Mutant cloud

“Off-the-cloud” mutations

The molecular quasispeciesin sequence space

Page 59: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

S{ = y( )I{

f S{ {ƒ= ( )

S{

f{

I{M

utat

ion

Genotype-Phenotype Mapping

Evaluation of the

Phenotype

Q{jI1

I2

I3

I4 I5

In

Q

f1

f2

f3

f4 f5

fn

I1

I2

I3

I4

I5

I{

In+1

f1

f2

f3

f4

f5

f{

fn+1

Q

Evolutionary dynamics including molecular phenotypes

Page 60: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

In silico optimization in the flow reactor: Trajectory (biologists‘ view)

Time (arbitrary units)

Aver

age

dist

ance

from

initi

al s

truct

ure

50

-d

D

S

500 750 1000 12502500

50

40

30

20

10

0

Evolutionary trajectory

Page 61: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

In silico optimization in the flow reactor: Trajectory (physicists‘ view)

Time (arbitrary units)

Aver

age

stru

ctur

e di

stan

ce to

targ

et

d

DS

500 750 1000 12502500

50

40

30

20

10

0

Evolutionary trajectory

Page 62: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

In silico optimization in the flow reactor: Main transitions

Main transitionsRelay steps

Time (arbitrary units)

Aver

age

stru

ctur

e di

stan

ce to

targ

et

d

DS

500 750 1000 12502500

50

40

30

20

10

0

Evolutionary trajectory

Page 63: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Shift Roll-Over

Flip Double Flipa a b

aa

b

α α

αα

β

β

Closing of Constrained Stacks

Multi-loop

Main or discontinuous transitions: Structural innovations, occurrarely on single point mutations

Page 64: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

In silico optimization in the flow reactor

Time (arbitrary units)

Aver

age

stru

ctur

e di

stan

ce to

targ

et

d

DS

500 750 1000 12502500

50

40

30

20

10

0

Relay steps Main transitions

Uninterrupted presence

Evolutionary trajectory

Page 65: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Elongation of StacksShortening of Stacks

Opening of Constrained Stacks

Multi-loop

Minor or continuous transitions: Occur frequently on single point mutations

Page 66: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Statistics of evolutionary trajectories

Population size

N

Number of replications

< n >rep

Number of transitions

< n >tr

Number of main transitions

< n >dtr

The number of main transitions or evolutionary innovations is constant.

Page 67: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

„...Variations neither useful not injurious would not be affected by natural selection, and would be left either a fluctuating element, as perhaps we see in certain polymorphic species, or would ultimately become fixed, owing to the nature of the organism and the nature of the conditions. ...“

Charles Darwin, Origin of species (1859)

Page 68: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Genotype Space

Fitn

ess

Start of Walk

End of Walk

Random Drift Periods

Adaptive Periods

Evolution in genotype space sketched as a non-descending walk in a fitness landscape

Page 69: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Evolutionary design of RNA molecules

D.B.Bartel, J.W.Szostak, In vitro selection of RNA molecules that bind specific ligands. Nature 346 (1990), 818-822

C.Tuerk, L.Gold, SELEX - Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249 (1990), 505-510

D.P.Bartel, J.W.Szostak, Isolation of new ribozymes from a large pool of random sequences. Science 261 (1993), 1411-1418

R.D.Jenison, S.C.Gill, A.Pardi, B.Poliski, High-resolution molecular discrimination by RNA. Science 263 (1994), 1425-1429

Y.Wang, R.R.Rando, Specific binding of aminoglycoside antibiotics to RNA. Chemistry & Biology 2 (1995), 281-290

L.Jiang, A.K.Suri, R.Fiala, D.J.Patel, Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chemistry & Biology 4 (1997), 35-50

Page 70: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

yes

Selection Cycle

no

GeneticDiversity

Desired Properties? ? ?

Selection

Amplification

Diversification

Selection cycle used inapplied molecular evolutionto design molecules withpredefined properties

Page 71: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Retention of binders Elution of binders

Chr

omat

ogra

phic

col

umn

The SELEX technique for the evolutionary design of aptamers

Page 72: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Secondary structures of aptamers binding theophyllin, caffeine, and related compounds

Page 73: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

additional methyl group

Dissociation constants and specificity of theophylline, caffeine, and related derivatives of uric acid for binding to a discriminating aptamer TCT8-4

Page 74: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

tobramycin

A

AA

AA C

C C CC

C

CC

G G G

G

G

G

G

G U U

U

U

U U5’-

3’-

AAAAA UUUUUU CCCCCCCCG GGGGGGG5’- -3’

RNA aptamer

Formation of secondary structure of the tobramycin binding RNA aptamer

L. Jiang, A. K. Suri, R. Fiala, D. J. Patel, Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chemistry & Biology 4:35-50 (1997)

Page 75: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

The three-dimensional structure of the tobramycin aptamer complex

L. Jiang, A. K. Suri, R. Fiala, D. J. Patel, Chemistry & Biology 4:35-50 (1997)

Page 76: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

A ribozyme switch

E.A.Schultes, D.B.Bartel, One sequence, two ribozymes: Implication for the emergenceof new ribozyme folds. Science 289 (2000), 448-452

Page 77: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Two ribozymes of chain lengths n = 88 nucleotides: An artificial ligase (A) and a natural cleavage ribozyme of hepatitis-d-virus (B)

Page 78: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

The sequence at the intersection:

An RNA molecules which is 88 nucleotides long and can form both structures

Page 79: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Two neutral walks through sequence space with conservation of structure and catalytic activity

Page 80: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Reference for postulation and in silico verification of neutral networks

Page 81: RNA – Das Zaubermolekülpks/Presentation/leipzig-02.pdfEvolution of RNA molecules based on Qβphage D.R.Mills, R.L.Peterson, S.Spiegelman, An extracellular Darwinian experiment with

Coworkers

Peter Stadler, Universität Leipzig, GE

Walter Fontana, Santa Fe Institute, NM

Christian Reidys, Christian Forst, Los Alamos National Laboratory, NM

Ivo L.Hofacker, Christoph Flamm, Universität Wien, AT

Bärbel Stadler, Andreas Wernitznig, Universität Wien, ATMichael Kospach, Ulrike Langhammer, Ulrike Mückstein, Stefanie Widder

Jan Cupal, Kurt Grünberger, Andreas Svrček-Seiler, Stefan Wuchty

Ulrike Göbel, Institut für Molekulare Biotechnologie, Jena, GEWalter Grüner, Stefan Kopp, Jaqueline Weber