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