Looking for the Cradle of Life Sergio Branciamore DBAG- University of Florence - Italy.
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Transcript of Looking for the Cradle of Life Sergio Branciamore DBAG- University of Florence - Italy.
Looking for the Cradle of Life
Sergio BranciamoreDBAG- University of Florence - Italy
Origin of Life: a multidisciplinary
problem
Chemicalapproach
Biologicalapproach
Theoreticalapproach
Erwin Schrödinger
“What is Life ?”, 1944
“What is Life today ?”
Pathways of supersystem evolution
boundary
template
metabolism M B
B T
M T M B T
INFRABIOLOGICAL SYSTEMS
The Transition from the RNA to the DNA World
The recipe of rising life1. Synthesis and accumulation of precursors
(nucleotides)
2. Joining of precursors into larger molecules
3. Protection of biomolecules from degradation
4. Expression of “biological” potentiality of the informational molecules
Classical research: Aqueous Solution Chemistry (primordial oceans)
A.I. Oparin (~1920) - J.B.S. Haldane (~1930)
““The Primordial Soup”The Primordial Soup”
S.L. Miller (1953)
Main problems of prebiotic chemistry in aqueous solution:
Dilution: concentration of reactants
Building blocks synthesis
Polymerization:
( ) ( 1) 2n M n MM P P H O ( ) ( 1) 2n M n MM P P H O
Hydrolysis and not polymerization occurs !!
H2 O
H2 O
H 2O H
2O
H 2O H
2O
H 2O H
2O
H 2O
H 2O
H 2O
H2O
H 2O
H2O
H2O
H2O
H2 O
H 2O
H2O
H 2O H
2O
H 2O H
2O
H 2O H
2O
H 2O
H 2O
H2O
H 2O
H2O
H2O
H2O
( ) ( 1) 2n M n MM P P H O
Main problems of prebiotic chemistry in aqueous solution:
Dilution: concentration of reactants
Building blocks synthesis
Polymerization:
Hydrolysis and not polymerization occurs !!
Polymers eventually formed are very susceptible to degradation (environmental persistence)
Looking for theSuitable Environment
for the Emergence of Life
Possible Physical Settings
The snowball hypothesis(L.E. Orgel, A.V. Vlassov)
Hydrothermal vent & pyrite
(G. Wächtershäuser M.J. Russel )
Mineral environment
It is necessary a protected confined environment where the primordial genetic
molecule, could originate and express its biological potential to self-replicate
and evolve
The “Mineral Honeycomb”
“. . . clays and other minerals were necessary to:
1) Concentrate the organics present in a dilute ocean by adsorption;
2) Protect these organics from destruction by U.V. light;
3) Catalyze the polymerization of adsorbed organics . . . ”
J.D. Bernal (1951)
The mechanism of accumulation is driven by heat in a twofold way. Thermal convection shuttles the molecules vertically up and down and thermophoresis pushes the molecules horizontally to the right. The result is a strong molecular accumulation from the top to the bottom (linear concentration color scale).
Heat-driven molecular accumulation in hydrothermal pores.
Section through aragonite (CaCO3) from the submarine hydrothermal vent field at Lost City
Formation of sugar-phosphates in the presence of mineral particles, Pitsch et al., OLEB (1995)
Stabilization of ribose in the presence of borate
minerals, Ricardo et al., Science (2004)
Synthesis of Nucleobases by Formamide in the
Presence of Montmorillonite, Saladino et al.,
ChemBioChem (2004)
Synthesis of building blocks
\
Montmorillonite catalyzes the formation of oligonucleotides up to 50-mer long
Ertem and Ferris Nature (1996)
Ferris et al. Nature (1996)
A CT G
TCC
Polymerization of precursors into larger molecules
Protection & Expressionof Nucleic Acids
Adsorbed on Minerals
RNA-Clay Complexes
minerals
ssRNAViroid
HairpinRibozyme
RNA-mineralComplexes
16S RNA
Hammerhead Ribozymes
Hairpin Ribozymes
Viroids
Structural characteristics:– Single stranded, circular, 250-400 nt long– Mostly, self-complementary (double helix)– Not coding– “Nude” (without capside)– Replication by rolling circle– Smallest and simplest autonomous infective agents
Viroids Could be Relics of the RNA World
Cleavage Site
U AU AC GU AC GC GA UAAGC
GUA
AU
GC
GC
U
GC
GCG
C
53 3925’3’
AG
AU
CG
II
III
CCG
IAGU
C
ACAG
U A
GU A
GC UC
AAA
HAMMERHEAD
U AU AC GU AC GC GA UAAGC
GUA
AU
GC
GC
U
GC
GCG
C
53 3925’3’
AG
AU
CG
II
III
CCG
IA
GUC
ACAG
U A
GU A
GCUC
AAA
Cleavage Site
HAMMERHEAD
Interactions of Hammerhead and Hairpin Ribozymes with Clay Particles
Increase self-cleavage kinetics of ribozymes (“natural prebiotic chaperon”);
Protect RNA from degradation.
0 50 100 150 200 2500
10
20
30
40
50
60
70
Time
% s
elf-cl
eava
ge
+ montmorillonite
Kobs= 0.343 min-1
F∞= 0.58
free solution
Kobs= 0.027 min-1
F∞= 0.55
UV irradiation of ADHR1 hairpin ribozymes in the presence of Montmorillonite
UV254 nm
Self-cleavage
The UV inactivation of hairpin ribozyme is strongly reduced by the presence of clay minerals
Early replication is still a problem: Eigen’s paradox (1971)
• Early replication must have been error-prone
Quasispecie
Error catastrophe
No genome without enzymes, and no enzyme without genomes
Eigen’s paradox
Early replication is still a problem: Eigen’s paradox (1971)
• Early replication must have been error-prone
• Error threshold sets the limit of maximal genome size to <100 nucleotides
• Not enough for several genes• Unlinked genes will compete• Genome collapses• Resolution???
R1R2
R3
R4
R5
HYPERCYCLE MODEL
R6
autocatalysis
heterocatalytic aid
short circuit
parasite
Population structure is necessary!
Good-bye to the well-stirred flow reactor !!!
The evolutionary processes need adhesion to
surface or compartmentation
The stochastic corrector model
Hypercycle in a (mineral) surface
Hypercycles (with more than 4 members) spiral on the surface and resist to some type of parasites
Metabolism
R1
R4 R2
R3
The metabolic model
nn
ii
iii
xM
Mkxdt
dx
/1
1
)(
)()(
x
xx
SEM image of etch-pit network near the surface of a weathered Shap alkali feldspar. (Scale bar 20 µm.)
ribozymes
resources
nucleotidesmetabolism
Pore
Mineral environment
Evolution of an RNA population in a network of inorganic compartments
Phosphate (from apatite)
N-Base
Ribose
RADIATION
ProtectionInteraction Evolution
Conclusions
The formation of a “close” association between prebiotic genetic molecules – whatever they were – and mineral surfaces could have represented a crucial step in the origin, persistence and activity of genetic material in primeval terrestrial habitats, opening the way to the biochemical evolution on Earth suggesting the possibility of a…..Mineral-Mediated Life
RollingCircle
Replicative cycle
5’ OH
2’
P
3’
5’ OH
2’
P
3’
InfectiveViroid