Chemical replicating systems
1. Biological Replication Today
2. The Chemoton
3. Autocatalysis
4. Replication of Informational Molecules
5. Models for cell division and growth
Motivation
Self-replication as the central biological phenomenon
Emergence of life
Evolution = Replication + Variation + Selection
Technological aspects: Biosensors, Detection of
molecules (e.g., PCR, RCA, etc.)
Self-reproducing technical sytems
Biological replication
cell division in E. Coli
Biological replication
semi-conservative nature
of DNA replication
Biological replication
the replication fork
Molecular evolution
self-replicating molecules  populations of molecules in compartments
independent replicators  chromosomes
RNA as gene and enzyme (RNA world)  DNA and proteins
procaryotes  eucaryotes
asexual clones  sexual populations
protists  animals, plants, fungi (cell differentiation)
solitary individuals  colonies
primates  societies (language)
The major transitions according to
Maynard Smith & Szathmary
Molecular evolution
RNA world scenario
Molecular evolution
Evolution of compartments
The Chemoton
Autocatalysis
A
X
A
A+ X
2A
• autocatalytic systems catalyze their own production (feedback)
• autocatalysis: important step towards self-replication, but no evolution
Autocatalysis
exponential
growth
d[A]
= k[A]
dt
[A](t) = [A](0) × exp (kt)
• compensates for losses due to side-reactions
• exponential growth (in principle)  competition of replicators
Autocatalysis
A minimal self-replication model (self-complementary molecule)
Classification of replicators
Simple replicators
Hereditary replicators with limited
variation
Hereditary replicators with
unlimited variation
14
Prions as simple replicators
EWS
a
Conversion affected
by kinetic or
thermodynamic barriers
Amyloid fibre
+
Native
conformers
‘Seed’
Prion
conformers
De novo prion induction
by nucleation
b
Conformation conversion at fibre ends
Protein
Sup45
[ psi –]
Dissemination of prion fibres
by fragmentation
c
100
Sup35
Stop
Ribosome
High-fidelity
termination
Stop AAAA
Genotype: ade1–14
Phenotype: ade–
Sup35 prion aggregates
[PSI+]
Fibre assembley (%)
Start
75
15
50
25
Replication of informational molecules
A simple selfcomplementary
replicator
template-directed
formation of a
Schiff base
(Terfort, von Kiedrowski,
Angew. Chemie Int. Ed. Engl., 31,
654 (1992))
Replication of informational molecules
L. Orgel, Nature,
vol. 358, 203 (1992)
17
Replication of informational molecules
cross-catalytic self-replication
cross-catalysis
autocatalysis
© 1994 Nature Publishing Group
Sievers & v. Kiedrowksi, Nature, vol. 369, 221 (1994)
18
(E
= 80). The type of growth observed in curve b is, however,
an experimental novelty. We term it parabolic since the
growth of an autocatalyst with a reaction order of 112 in the
rate equation of its synthesis can be expressed as a second
order polynomial of time for early reaction times.
The reasoning behind the mechanism proposed for the
autocatalytic template production is the same as for the original system.12] It is generalized in Figure 2 to account for
Kinetics & Product inhibition
zA
??
• problem of product release
B
•no exponential growth observed
&
T
u.a
m,_._i
(24
• approximate square-root law
D
Fig. 2. General mechanism for a minimal self-replicating system. Constituent
A represents the activated form of trimer A* here. Large arrowheads at the
reaction arrows for the reversible reactions indicate the favored site of the
equilibrium.
71
6
5
similarities between the systems
known
I
d
so far. The following
d[A]
= α + β[A]p
dt
growth rate
C
b
should be noted:
4
1 ) The rate determining step is the irreversible formation of
cT3 lo4
a 3’-5’-phosphoamidate
3 linkage leading from the ternary
I m o L“I
~
complex M to the self-complementary duplex D which is
expressed by: d[D]/dt2 = k [ M ] .
2) The system is in dynamic equilibrium with respect to all
1
_ _ - - - a
single- and double-stranded
oligonucleotide constituents.
With K , = [MI [A]-’ [B]-’ [TJ-’and K2 = [D] [TI-’ it
0
follows for the formation
of duplex
molecules
that1.5d[D]/ 2.0
0
0.5
1.0
dt = k K , K z - 1 / 2[A] [B] [D]”’.
t Ihl
3) Under parabolic growth conditions ( K , K , $ I), and
Fig. 1. Time course for the formation of the hexameric 3’-5’-phosphoamidate
of complete activation, the apparent
for the special
T3 case
in the absence (curve b) and in the presence of template T’ (curves c-e) as
The data points shown
are averages
experimental
rate constantmeasured
k , canby HPLC.
be rationalized
in terms
offrom
thetheelecourses of A’, B3, T3. The set of theoretical curves b e represents the
mentary ratetime
and
equilibrium
constants:
k,
=
21/2
solution of differential equation (a) for the parameters given in Table 1 and the
k K 1 K 2 - ’ l 2 . experimental set of initial concentrations shown below. The yield ofT3is 50%
-
after 2 h (curve b). Curve a represents the theoretical time course if no auto-
and 75 times more efficient than Orgel’s and Rebek’s system,
respectively, in terms of k,. A low k, is necessary to achieve
sigmoidal growth. Thus, the quotient k,/k,, which defines
the factor by which the autocatalytic synthesis exceeds the
noninstructed process at a template concentration of 1 M,
must be large enough to observe sigmoidicity. With respect
to the autocatalytic excess factor E, as this quotient is termed
hereafter, the above system ( E = 420) is comparable to
Orgel’s system ( E = 340) but exceeds Rebek’s system
(E = 80). The type of growth observed in curve b is, however,
an experimental novelty. We term it parabolic since the
growth of an autocatalyst with a reaction order of 112 in the
rate equation of its synthesis can be expressed as a second
order polynomial of time for early reaction times.
The reasoning behind the mechanism proposed for the
autocatalytic template production is the same as for the original system.12] It is generalized in Figure 2 to account for
reaction order
p = 1/2
no autocatalysis
v. Kiedrowski,
Angew. Chem. Int. Ed. 30, 423 (1991)
zA
??
B
19
Kinetics & "Ecology"
• exponential growth, several species
with different growth rates, limited resources
one species will prevail
• subexponential growth, several species
with different growth rates, limited resources
growth limited by own copy number
(product inhibition !)
coexistence of species possible
20
A self-replicating ribozyme
5 discontinuous double-helical
sections improve product separation
Paul & Joyce, PNAS 99, 12733 (2002)
21
A self-replicating ribozyme
reaction order
p=1
Paul & Joyce, PNAS 99, 12733 (2002)
22
Published on Web 05/22/2002
Self-replicating peptides
ng Exponential Growth with a Self-Replicating Peptide
Roy Issac and Jean Chmielewski*
tment of Chemistry, Purdue UniVersity, West Lafayette, Indiana 47907
Received February 25, 2002
hold great promise for a wide
as well as to address fundamolecular origins of life.1 The
tors, however, requires high
pendent on the stability of the
optimum conditions and in the
licating systems should exhibit
nhibition causes growth to be
e design of self-replicating
ency has remained elusive,
workers reported the developalogue in which solid-phase
ition.3 Here we describe the
peptide self-replicator with a
o that of known enzymes.
alytic efficiency of the selft to destabilize its coiled coil
chieved dramatic decreases in
ptides by shortening the chain
rs found similar effects with
these precedents as a basis, a
ation, RI-26, that contains 3
ed coil, one shorter than the
tained the design principle of
ere positioned at the e and g
s to achieve pH-based control
RI-26b, therefore, correspond
ay undergo thioester mediated
7
was found to adopt a helical
shion; at pH 7.0 the helical
d by circular dichroism, and
owered to 4.0 as was observed
and RI-26b increased by 45%
e of RI-26 at pH 4.0, indicating
te for its fragments. Analytical
mine the aggregation state of
his peptide was found to exist
ists as a dimer under similar
p = 0.91
Figure 1. Helical wheel diagram (a) and sequence (b) of RI-26 and its
fragments. An arrow indicates the residues where chemical ligation occurs.
catalytic rate constant, ka, of 50.6 ( 0.5 M-1.91 s-1 and a
noncatalytic rate constant, kb, of 5.04 ( 0.03 × 10-4 M-1 s-1 with
a catalytic efficiency (! ) ka/kb) of 1.0 × 105. This is a remarkably
efficient system when compared to other self-replicating molecules;
self-replicating peptides and oligonucleotides have displayed catalytic efficiencies in the range of 24 to 3700.4,8 The efficiency
observed with RI-26 is comparable to that observed for some
enzymatic systems, such as glutathione transferases.9 The uninstructed noncatalytic or background reaction, presumably a result
of the association between the two fragments, is also much slower
in this peptide system than any of the other reported peptide selfreplication systems.4,8e-f This is most likely due to the presence of
fewer leucine residues in the shorter fragments, thereby reducing
the hydrophobic interactions between them.
chemical ligation of
α-helix forming peptides
Figure 2. RI-26 production from two fragments, RI-26a and RI-26b (500
µM each), at 23 °C in 100 mM MOPS buffer (with 1% 3-mercaptopropionic
acid) at pH 4.0 as a function of time with varying initial concentrations of
template: (]) no template, (0) 10 µM RI-26, (4) 20 µM RI-26, and (O)
40 µM RI-26. Error bars reflect standard deviations of two independent
experiments. Curves were generated with SimFit2 by simulations based on
the reaction model: RI-26a + RI-26b f RI-26 (kb); RI-26a + RI-26b +
0.91 RI-26 f 1.91 RI-26 (ka).
Issac & Chmielewski, JACS (2002)
23
Figure 4. Thermal
presence of 6 M Gd
efficiency for sel
minimum length
efficient self-repl
background reactio
occurring enzyme
size was a decrea
effective suppress
catalytic peptides
enhances their po
their consideration
Acknowledgme
NASA for suppor
Vesicle growth and division
replication of a non-informational structure
Szostak, Bartel & Luisi, Nature 409, 387 (2001)
24
Models for cellular compartments
• clay enhances vesicle
growth
montmorillonite
hydrated sodium calcium aluminium
magnesium silicate hydroxide
(Na,Ca)0.33(Al,Mg)2(Si4O10)(OH)2·nH2O
• RNA adsorbed to clay is
incorporated
Hanczyc, Fujikawa, Szostak, Science vol. 302, 618 (2003)
25
Towards a protocell
• RNA replicase (self-replicating
ribozyme)
• lipid vesicle compartment
• division of vesicles (feeding
with micelles)
• coupled replication cycles
26
Szostak, Bartel & Luisi, Nature 409, 387 (2001)
Evolution
27
Szostak, Bartel & Luisi, Nature 409, 387 (2001)
Eigen's error threshold
phenomenological rate equation
ẋi = k0 [Ai Qi − Di ]xi +
leads to (...)
Nmax
!
j!=i
wij xj − w0i xi
ln Qmin
=
1−q
maximum number of bases Nmax which can be stably maintained
with base copy fidelity q and minimum fidelity Qmin for "master
sequence"
⇨ Eigen's paradoxon
Eigen, Naturwissenschaften, vol. 58, 465 (1971)
28
The Hypercycle
• Eigen's paradoxon: impossible to store all
information necessary to ensure faithful replication
• Hypercycle: Coexistence of several cooperating
replicators - members of hypercycle better than
mutants; no competition between members; cycle
better than other cycles ...
autocatalytic replicators
29
gave a background rate constant
of von Kiedrowski
"1 "1
kb ¼ 0:072 ! 0:005 M s
and an apparent autocatalytic rate
" 3=2 " 1
constant ka ¼ 52 ! 1 M
s , making R2 more efficient
than its relative R1 (kb ¼ 0:063 M " 1 s " 1 and constant
ka ¼ 29:4 M " 3=2 s " 1 ).
A solution containing all three fragments E, N1 and N2 gave a
combinatorial synthesis of both replicators. A priori, one would
over the autocatalytic componen
desirable outcomes which assure
production of one species promot
an even greater degree. This parti
prevents one replicator from over
the two to reproduce as a single c
To verify that R1 and R2 cataly
A hypercyclic network of peptide replicators
Table 1 Initial rates of product formati
Product
autocatalysis
R
cross-catalysis
R
1
I
E
N1
2
II
IV
III
E
N2
autocatalysis
Figure 1 Schematic diagram of a minimal hypercycle based on two selfreplicating peptides. Cycles I and III show the self-producing cycles of replicators
R (dark grey/light grey) and R (dark grey/striped) respectively, which precatalysis more
efficient in the presence of partner replicator !
organize their constituent fragments thereby promoting peptide ligation. Cycle
1
4.8
5.8
........................................................................................
The data in this table (in units of 10!8 M min!1) a
fragments in the absence and presence of ad
R1
R2
cross-catalysis
No replicators added
........................................................................................
2
II, where R1 promotes R2 formation, and cycle IV, where R2 promotes R1 formation,
comprise the catalytic components of the hypercycle and allow the replicators to
positively regulate each others’ production. The mechanistic details of the
Lee, Severin,Yokobashi, Ghadiri, Nature 390, 591 (1997)
present hypercyclic network may be more complex than the minimal system
depicted here. Detailed kinetic analyses of the replicator sequences have shown
that the autocatalytically productive intermediates involve, at least in part, qua-
30
coexistence, rather it is one of ultimate
ing to them the Hoogsteen mode of binding and so can
orking
together
within
this symbiotic
still self-replicate or catalyze the formation of the original
mbers of a hypercycle may compete better
replicator. In separate reactions, the original replicator
491
This ‘principle of self-organization’
was
could promote production
of the mutants as well as
ved
by Eigen [l], who later went on
itself. Similarly, Achilles and von Kiedrowski [24] observed
demonstrate
hypercyclic
organization
reciprocal catalysis
between
self-replicating
Autocatalytic
networks:
the transition
from pentameric
molecular
ge DNA and its replicase apparatus [Zl]. self-replication
and hexameric oligonucleotides
which may have included
to molecular ecosystems
hypercyclic network was constructed out David
a hypercyclic
component.
H Lee, Kay
Severin and M Reza Ghadiri*
ating
peptides that share one common
from inanimate to animate chemistry is
concepts of non-equilibrium
physics [l-3]. In general,
Figure 5). At first glance one might The transition
Conclusions
thought to involve self-organised networks of molecular
they provide plausible descriptions
of the early stages
l-of-the-fittest
situation where the more speciesIn whose
this collective
reviewemergent
we property
have gives
discussed
how
self-organization
of self-organize to form
rise to
of biogenesis
wherein biopolymers
characteristics of living systems. In the past,
autocatalytic networks. Although the main conclusions of
or would commandeer
all the resources. the overall
catalytic
molecules into simple networks
with nonlinear
simple autocatalytic networks have been constructed that
these theories are generally accepted, there have been
d,
however, that not only could each displaygrowth
basic forms kinetics
of cooperative behaviour.
very fewemergence
experimental
results
results These
in include
the rapid
of that
a support their tenets.
reciprocal catalysis, autocratic, and hypercyclic networks.
In this review we summarize
recent attempts
to fill
icate
but that they collaborate in each The design
robustness
[ZS] and functional innovation
that would be
and emergent properties of these novel molecular
this gap. We will focus on multicomponent
enzyme-free
are reviewed
the constituents
of which are interconnected
as well! Control experiments verified the networks
difficult,
if here.
not impossible, to achieve systems,
through
the gradual
via autocatalytic
and/or catalytic cycles. Thus far only
ocatalytic abilities of these two peptides.
accumulation of mutations in any single
molecule.
a
three very
simple typesEven
of autocatalytic
networks have
Addresses
been realized experimentally:
cross-catalytic,
autocratic,
e catalytic coupling that contributed
to Departments
cursory
examination
of
the
internal
organization
of
living
of Chemistry and Molecular Biology and the Skaggs
and
hypercyclic.
These
systems
are
all
based
on
molecular
Institute for Chemical Biology, The Scripps Research Institute, La
of a given peptide was stronger than the Jolla, things
species that
can directly
(or indirectly) catalyze their own
makes it clear that this transition
from
individual
CA 92037, USA
*e-mail: [email protected]
formation.
utocatalytic component of the hypercycle
self-replicating
molecules to the next level in the hierarchy
Current Opinion in Chemical Biology 1997, 1:491-496
was more efficient than autocatalysis. This http://biomednet.com/elecref/1367593100100491
of self-organized
systems should Molecular
be further
explored.
Replication
In the most basic form of molecular
self-replication
ant in that this pattern of coupling is 0 Current
What
forms of self-organization a reaction
are possible?
How
Biologyother
Ltd ISSN 1367-5931
product serves as a specific catalyst for its
The requirement
ecessary for a hypercycle to remain stable.
can several networks be productivelyown synthesis.
associated?
What of a specific recognition
event during the catalytic transformation
distinguishes
emergent
might these systems
496
Model properties
systems
Introduction
self-replication display?
from plain The
autocatalytic
reactions, and
Livingcurrent
systems are
autonomous
self-reproducing
information
to be transferred
to the molecular
challenge
is to design‘molecand allows
characterize
new
and
explicitly
stated, other multicomponent
ular ecosystems’ defined as a collective of self-organized
offspring. The first enzyme-free
replication
system-a
more complex
in time, palindromic
even large
molecular
ve formed hypercycles too. For instance, communities
of dynamic, networks,
interdependent, and,
interacting,
hexanucleotide
sequencewas reported in
computing
molecular
species. One hallmark
of
1986
by von Kiedrowski
[4*]. Since then a series of other
ecosystems,
in order
to answer
these
questions.
Ultimately
nd co-workers [23] triacid-based replicators and
living systems is their ability to translate
molecular
self-replicating
molecules have been designed and characinteractions and chemical reactions into complex animate
terized (for reviews see [.5”,6,7,8]), including abiological
Von Kiedrowski G: Minimal replicator theory
we
hope
that
in
designing
such
self-instructed
chemical
12.
characteristics
that far exceed the simple sum of the
organic molecules
[5”,9] and most recently
peptides
exponential
growth. Bioorg Chem front 1993
individual
propertiesweof will
their glean
molecular some
constituents.
The autocatalytic
systems
processes
insights[lO”,ll*].
into how
life cameprocess forionthese
Kiedrowski
discusses
various aspects of empirical
These animate characteristics are macroscopic properties
is based on template-directed
condensation
reactions
cating structures
systems.
that to
arisebe.
as a result of nonlinear
dynamic interactions
induced by assembly of self-complementary
and the passage, growth, and change of information
(Figure 1). For replicators containing nucleobases, molec13.
Reinhoudt DN, Rudkevich DM, de Jong F: Kin
within the molecular ecosystem. Understanding
how such
ular recognition
is mediated by a well defined pattern
.
Rebek self-replicating system: is there a co
self-organized
systems may have established
themselves
of hydrogen
bond donor and acceptor groups. In the
Chem Sot 1996,i 18:6880-6889.
in the ‘beginning’,
how they might have evolved and
case of peptide
self-replication
however, hydrophobic
‘I‘he
authors
would
hkc
to
thank
Krishna
Kumar,
Alan
Kennan,
Yohei
Reinhoudt
and coworkers demonstrate the utility of
grown in complexity, and how they result in the emergent
interactions-assisted
by electrostatic
interactions -are
Yokobayashi
and Jose
for many
brainstorming
the self-replicating system of Rebek.
properties
that distinguish
livingAntonio
systems hlartinez
from inanimate
the productive
main recognition
driving force. studying
Detailed
kinetic
sessions
grateful
to Juansuch
R Granja
matter,
remainsand a their
major enthusiasm.
experimental The
and authors
theoretical are also
analyses
of several
systems, complemented
by a
14.
Bohler C, Nielsen PE, Orgel LE: Template sw
for invaluable
discussions
and help with some of
the figures.
challenge.
‘minimal
replicator theory’ [12], have revealed a linear
PNA and RNA oligonucleotides. Nature 1995
relationship between the initial rate of product formation
Thisconcentration.
manuscript describes the non-enzymatic transit
and the square root of the initial template
It is widely believed
that inanimate
chemistry
eminformational
barked on its path towards ‘living chemistry’
via the
The corresponding
parabolic growth profile
reflects anbiopolymer to another, providing some c
sibility
of a that
pre-RNA genetic material.
formation
of self-replicating
molecules.
Now that a
intrinsic shortcoming of current replication
systems,
of particular
interest,
published
annual
period of
review, of the catalysts (products)
few Papers
enzyme-free
self-replicating
molecular
systems within
have the
is the
self-inhibitory
tendencies
Acknowledgements
Current Opinion in Chemical Biology 1, 491 (1997)
31
References
and recommended
readings
Self-reproducing machines
32