Origin of genetic material: looking for the ancestral cradle
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Origin of genetic material: looking for the ancestral cradle
Enzo GalloriDepartment of Physics and Astronomy
University of Florence, Italy
Oparin 2014, Moscow, 24-26 September
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“On ne connaît pas complètement une science tant qu'on n'en sait pas l'histoire.”
(To understand a science, it is necessary to know its history.)
A. Comte
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ALEXANDER I. OPARIN (1894–1980)
“Proiskhozhdenie zhizny” 1924 “The Origin of Life” 1938
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WHAT WAS THE PRIMORDIAL
HABITAT OF LIFE?
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CHARLES DARWIN (1809-1882)
“… But if (and oh what a big if!) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity &c present, that a protein compound was chemically formed, ready to undergo still more complex changes, …”Letter to J. D. Hooker, 1 Feb 1871
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ERWIN SCHRÖDINGER
“What is Life?” (1944)
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THE BASIC PRINCIPLE OF BIOLOGY
Replication
Transcription Translation
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“…Current biology indicates that life could have not evolved in the absence of a genetic
replicating mechanism…”A. Lazcano, OLEB (2010)
↓The presence of a genetic system is
absolutely essential
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MOLECULAR EVOLUTION
Formation of Earth
4.5
Prebiotic chemistry
4.0
First DNA / protein life
3.5
Diversification of life
3.0
The “appearance” of a nucleic acid-like polymer able to evolve marks the beginning of life
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BUILDING CODE
1. Synthesis and accumulation of precursors (i.e. nucleotides)
2. Polymerization of precursors.
3. Protection from degradation
4. Expression of “biological”potentiality of the information molecule
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EARLY ATMOSPHERE (?)
• Composition H2O, CO2, N2, NH3, CH4
• Origin Volcanic outgassing
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CLASSICAL RESEARCH: AQUEOUS SOLUTION CHEMISTRY
A.I. Oparin (~1924) - J.B.S. Haldane (~1930)
“The Primordial Soup”
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STANLEY MILLER (1953)
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Classical research: aqueous solution chemistry (primordial oceans)
In these conditions:hydrolysis and not polymerization!
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THE “RNA WORLD”
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JOHN D. BERNAL (1901-1971)
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THE “CLAY 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)
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ORIGIN OF CLAY MINERALS
Clay minerals originated by weathering of volcanic glass and rocks. The Mars investigation indicates the occurrence of clay minerals with an age of ≥ 3.5 Ga. By analogy, clay minerals would have formed on the early Earth.
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CLAY ON MARS
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Role of Minerals, mainly Clay Minerals, in the synthesis of:
→ Nucleic Acid Bases Saladino et al., CHEMBIOCHEM (2004), Costanzo et al., BMC
Evolutionary Biology (2007), Saladino et al., Physics Life Reviews (2012)
→ Stabilization of Ribose Ricardo et al., Science (2004)
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JAMES FERRIS
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Clay minerals catalyze the formation of oligonucleotides up to 50-mer long
Ertem and Ferris, Nature (1996); Ferris et al., Nature (1996)
Ertem, OLEB (2004)
A CT G
TCC
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Oligomerization of Nucleotides on
Montmorillonite
Mathew & Luthey-Schulten, OLEB (2010)
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PROTECTION OF NUCLEIC ACIDS
DNA molecules adsorbed on clay minerals are protected to some extent against the action of different degrading agents, still
maintaing their biological activities
Stotzky & Gallori, Molecular Microbial Ecology, (1996)
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BIOLOGICAL CHARACTERISTICS OF NUCLEIC ACID-CLAY
COMPLEXES
• DNA bound on clay is still able to transform bacterial competent cells
Gallori et al., FEMS Microbiol Ecol (1994)
• DNA adsorbed on clay can be replicated and amplified by PCR
Vettori et al., FEMS Microbiol Ecol (1996)
Replication
TAQ-Polymerase
+
Trasformation
+
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ELECTRON MICROSCOPY (T.E.M.)
K-Chromosomal DNA(X 154,000)
K-Plasmid DNA(X 271,500)
Franchi et al., OLEB (1999)Franchi et al., OLEB (1999)
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X-RAY ANALYSIS OF M-NUCLEIC ACID COMPLEXES
2 7 12 17 22 27 32 37 42 472
M
M-DNA
M-RNA
Franchi et al., OLEB (1999)Franchi et al., OLEB (1999)
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B-Form
A-Form
Franchi et al., OLEB (1999)
0
0,05
0,1
0,15
0,2
0,25
0,3
0,35
0,4
0,45
0,5
1800
1750
1700
1650
1600
1550
1500
1450
1400
1350
1300
1250
(cm-1)
Abs
orba
nce
free DNAK-adsorbed
DNA
kaolinite
FT-IR ANALYSIS OF M-NUCLEIC ACID COMPLEXES
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ROLE OF CATIONS IN THE ADSORPTION
Franchi, Ferris and Gallori, OLEB (2003)
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EFFECTS OF UV AND X-RAYS RADIATION
U.V. radiation
DNA adsorbed on clay minerals is protected from both UV and X-ray radiation
Ciaravella et al., Astrobiology (2004); Scappini et al., Astrobiology (2004)
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EXPERIMENTS ON BOARD INTERNATIONAL SPACE STATION (ISS)
Free and clay-adsorbed DNA in space environment (16-30/05/2011)
De Sio et al., Microgravity Sci Technol (2012)
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RNA-CLAY COMPLEXES
Clay minerals:montmorillonite (M)kaolinite (K)
ssRNAViroid
HammerheadRibozyme
RNA-ClayComplexes
16S RNA
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ANNEALING OF COMPLEMENTARY SINGLE STRANDED NUCLEIC ACIDS
AA A A A A A AU U U U
GG G G
AA A
CC C C
Franchi and Gallori, Gene (2005)
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ENZYMATIC REPLICATION OF CLAY-ADSORBED RNA
Franchi and Gallori, Gene (2005)
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Hammerhead Ribozymes
Hairpin Ribozymes
Could
Clay-RNA Complexes
Perform
Enzymatic Reaction??
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HAMMERHEAD RIBOZYMEAVOCADO SUNBLOTCH VIROID (ASBVd) (FLORES,
1994)
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ADENINE DEPENDENT HAIRPIN RIBOZYME (ADHR1)
ADHR1Meli et al., J. Biol. Chem (2003)
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INTERACTIONS OF RIBOZYMES
WITH CLAY PARTICLES
Tightly adsorbed RNA molecules are able:
• To perform self-cleavage reactions
• To resist to the action of various degradative agents (biotic and abiotic)
Franchi & Gallori, Gene (2005); Biondi et al., Gene (2007)
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Control + MontControl in water
UV in water
UV + Mont
ADHR1 SELF-CLEAVAGE KINETICS AFTER 5’ OF UV-
IRRADIATION
Biondi et al., BMC Evolutionary Biology (2007)
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Phosphate (from apatite)
N-Base
Ribose
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RADIATION
ProtectionInteraction Evolution
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CLAY MICELLE
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PROMETHEUS (Προμηθεύς, “THE ONE WHO THINK
OVER”)
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• Prof. J. P. Ferris, Department of Chemistry and Chemical Biology, New York Center for Studies on the Origins of Life
• Prof. R. Flores, Universidad Politecnica Valencia, Spain
• Prof. M.-C. Maurel, Centre des Acides Nucléiques et Biophotonique, UPMC Paris VI , Paris, France
• Prof. G. Stotzky, Department of Biology, New York University, USA
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THANK YOU MISHA!
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Real Mineral Structure
Implementation of the theoretical model with a well defined spatial environment (i.e. a porous structure)
Increase of information capacity of replicators in a mineral structured environment
Results
EVOLUTION ON “MINERAL HONEYCOMB”
Branciamore et al., J Molec Evol (2010)
Model