origin of genetic material: looking for the ancestral cradle
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Origin of genetic material: looking for the ancestral cradle. Enzo Gallori Department of Physics and Astronomy University of Florence, Italy Oparin 2014, Moscow, 24-26 September. “ On ne connaît pas complètement une science tant qu 'on n'en sait pas l' histoire . ” - PowerPoint PPT PresentationTRANSCRIPT
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
“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
ALEXANDER I. OPARIN (1894–1980)
“Proiskhozhdenie zhizny” 1924 “The Origin of Life” 1938
WHAT WAS THE PRIMORDIAL
HABITAT OF LIFE?
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
ERWIN SCHRÖDINGER
“What is Life?” (1944)
THE BASIC PRINCIPLE OF BIOLOGY
Replication
Transcription Translation
“…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
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
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
EARLY ATMOSPHERE (?)
• Composition H2O, CO2, N2, NH3, CH4
• Origin Volcanic outgassing
CLASSICAL RESEARCH: AQUEOUS SOLUTION CHEMISTRY
A.I. Oparin (~1924) - J.B.S. Haldane (~1930)
“The Primordial Soup”
STANLEY MILLER (1953)
Classical research: aqueous solution chemistry (primordial oceans)
In these conditions:hydrolysis and not polymerization!
THE “RNA WORLD”
JOHN D. BERNAL (1901-1971)
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)
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.
CLAY ON MARS
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)
JAMES FERRIS
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
Oligomerization of Nucleotides on
Montmorillonite
Mathew & Luthey-Schulten, OLEB (2010)
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)
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
+
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)
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)
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
ROLE OF CATIONS IN THE ADSORPTION
Franchi, Ferris and Gallori, OLEB (2003)
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)
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)
RNA-CLAY COMPLEXES
Clay minerals:montmorillonite (M)kaolinite (K)
ssRNAViroid
HammerheadRibozyme
RNA-ClayComplexes
16S RNA
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)
ENZYMATIC REPLICATION OF CLAY-ADSORBED RNA
Franchi and Gallori, Gene (2005)
Hammerhead Ribozymes
Hairpin Ribozymes
Could
Clay-RNA Complexes
Perform
Enzymatic Reaction??
HAMMERHEAD RIBOZYMEAVOCADO SUNBLOTCH VIROID (ASBVd) (FLORES,
1994)
ADENINE DEPENDENT HAIRPIN RIBOZYME (ADHR1)
ADHR1Meli et al., J. Biol. Chem (2003)
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)
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)
Phosphate (from apatite)
N-Base
Ribose
RADIATION
ProtectionInteraction Evolution
CLAY MICELLE
PROMETHEUS (Προμηθεύς, “THE ONE WHO THINK
OVER”)
• 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
THANK YOU MISHA!
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