From self-organization to evolution of RNA molecules The origin of - PowerPoint PPT Presentation

From self-organization to evolution of RNA molecules The origin of biological information Peter Schuster Institut für Theoretische Chemie und Molekulare Strukturbiologie der Universität Wien Self-formation. Theory and application Vilnius, 26.– 28.11.2003

Web-Page for further information: http://www.tbi.univie.ac.at/~pks

1. Autocatalytic chemical reactions in the flow reactor 2. Replication, mutation, selection and Shannon information 3. Evolution in silico and optimization of RNA structures 4. Random walks and ‚ensemble learning‘ 5. Sequence-structure maps, neutral networks, and intersections

1. Autocatalytic chemical reactions in the flow reactor 2. Replication, mutation, selection and Shannon information 3. Evolution in silico and optimization of RNA structures 4. Random walks and ‚ensemble learning‘ 5. Sequence-structure maps, neutral networks, and intersections

Reaction Mixture Stock Solution p d e S T T dS env d S i � � � dS 0 dS 0 dS 0 Isolated system Closed system Open system � U = const., V = const., T = const., p = const., dS = dS env + dS 0 0 � � dS dG dU pdV TdS = - - 0 dS d S d S = + i e � d S 0 i Entropy changes in different thermodynamic systems

Stock Solution [a] = a0 Reaction Mixture [a],[b] A B A B A A A A B A B * � A A A � B A B A � Ø A A A � B - 1 Flow rate r = R B � A A B � Ø A A B A B A B B B B A A Reactions in the continuously stirred tank reactor (CSTR)

1.2 -1 Flow rate r [t ] ] 0 2.0 4.0 6.0 8.0 10.0 a [ 1.0 a n o i t a r t n e 0.8 c n o C k = 1 � A B 0.6 k = 1 � Reversible first order reaction in the flow reactor

1.2 -1 Flow rate r [t ] Concentration a [a ] 0 0.50 0.75 1.00 1.25 0.25 1.0 � = 0 � k = 1/(1+ ) � 0.8 A + B 2 B � k = 1/(1+ ) � � � k = /(1+ ) � A B 0.6 � � k = /(1+ ) � Autocatalytic second order reaction and uncatalyzed reaction in the flow reactor

1.2 -1 Flow rate r [t ] ] 0 0.50 0.75 1.00 1.25 0.25 a [ 1.0 a � n = 0 o i � t = 0.001 a r t n e � k = 1/(1+ ) � 0.8 c A + B 2 B n o C � k = 1/(1+ ) � � � k = /(1+ ) � A B 0.6 � � k = /(1+ ) � Autocatalytic second order reaction and uncatalyzed reaction in the flow reactor

1.2 -1 Flow rate r [t ] ] 0 0.50 0.75 1.00 1.25 0.25 a [ 1.0 a � n = 0 o i � t = 0.001 a r t � = 0.1 n e � k = 1/(1+ ) � 0.8 c A + B 2 B n o C � k = 1/(1+ ) � � � k = /(1+ ) � A B 0.6 � � k = /(1+ ) � � � = Autocatalytic second order reaction and uncatalyzed reaction in the flow reactor

1.2 -1 Flow rate r [t ] Concentration a [a ] 0 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 1.0 � = 0 0.8 � k = 1/(1+ ) � A +2 B 3B � k = 1/(1+ ) � � � k = /(1+ ) � A B 0.6 � � k = /(1+ ) � Autocatalytic third order reaction and uncatalyzed reaction in the flow reactor

1.2 -1 Flow rate r [t ] Concentration a [a ] 0 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 1.0 � = 0 � = 0.001 0.8 � k = 1/(1+ ) � A +2 B 3B � k = 1/(1+ ) � � � k = /(1+ ) � A B 0.6 � � k = /(1+ ) � Autocatalytic third order reaction and uncatalyzed reaction in the flow reactor

1.2 -1 Flow rate r [t ] Concentration a [a ] 0 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 1.0 � = 0 � = 0.001 � = 0.0025 0.8 � k = 1/(1+ ) � A +2 B 3B � k = 1/(1+ ) � � � k = /(1+ ) � A B 0.6 � � k = /(1+ ) � Autocatalytic third order reaction and uncatalyzed reaction in the flow reactor

1.2 -1 Flow rate r [t ] Concentration a [a ] 0 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 1.0 � = 0 � = 0.001 � = 0.0025 0.8 � = 0.007 � k = 1/(1+ ) � A +2 B 3B � k = 1/(1+ ) � � � k = /(1+ ) � A B 0.6 � � = � � k = /(1+ ) � Autocatalytic third order reaction and uncatalyzed reaction in the flow reactor

Autocatalytic third order reactions Multiple steady states � Oscillations in homogeneous solution Direct, A + 2 X 3 X , or hidden in the reaction mechanism Deterministic chaos (Belousow-Zhabotinskii reaction). Turing patterns Spatiotemporal patterns (spirals) Deterministic chaos in space and time Pattern formation in autocatalytic third order reactions G.Nicolis, I.Prigogine. Self-Organization in Nonequilibrium Systems. From Dissipative Structures to Order through Fluctuations . John Wiley, New York 1977

Autocatalytic second order reactions Chemical self-enhancement Combustion and chemistry � Direct, A + I 2 I , or hidden in of flames the reaction mechanism Selection of laser modes Selection of molecular or organismic species competing for common sources Autocatalytic second order reaction as basis for selection processes. The autocatalytic step is formally equivalent to replication or reproduction.

Stock Solution [A] = a 0 Reaction Mixture: A; I , k=1,2,... k k 1 A + I 2 I 1 1 d 1 k 2 A + I 2 I 2 2 d 2 k 3 A + I 2 I 3 3 d 3 k 4 A + I 2 I 4 4 d 4 k 5 A + I 2 I 5 5 d 5 Autocatalytic competition in the flow reactor P.Schuster & K.Sigmund, Dynamics of evolutionary optimization, Ber.Bunsenges.Phys.Chem. 89 : 668-682 (1985)

Concentration of stock solution a0 A + I 2 I 1 1 2 A + I + I A + I 2 I 2 2 1 A + I 1 A + I 2 I 3 3 A + I 2 I 4 4 A + I 2 I 5 5 A k > k > k > k > k 1 2 3 4 5 R-1 Flow rate r = � Selection in the flow reactor: Reversible replication reactions

Concentration of stock solution a0 A + I 2 I 1 1 A + I 2 I 2 2 A + I 1 A + I 2 I 3 3 A + I 2 I 4 4 A + I 2 I 5 5 A k > k > k > k > k 1 2 3 4 5 R-1 Flow rate r = � Selection in the flow reactor: Irreversible replication reactions

RNA as adapter molecule RNA is the catalytic subunit in RNA as scaffold for supramolecular RNA as transmitter of genetic information supramolecular complexes complexes DNA transcription ... CUG ... leu ...AGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUC... GAC messenger- RNA genetic code translation protein ribosome RNA as working copy of genetic information ? ? ? ? ? RNA as catalyst RNA RNA is modified by epigenetic control RNA editing Alternative splicing of messenger RNA ribozyme RNA as regulator of gene expression RNA as carrier of genetic information The RNA world as a precursor of RNA viruses and retroviruses the current DNA + protein biology RNA as information carrier in evolution in vitro and evolutionary biotechnology Functions of RNA molecules gene silencing by small interfering RNAs