Looking for the Cradle of Life Sergio Branciamore DBAG- University of Florence - Italy

Origin of Life: a multidisciplinary problem Chemical approach Biological approach Theoretical approach

Erwin Schrödinger “What is Life ?”, 1944

“What is Life today ?”

Pathways of supersystem evolution boundary template metabolism M BM B B TB T M TM T M B TM B T INFRABIOLOGICAL SYSTEMS

The Transition from the RNA to the DNA World

The recipe of rising life 1.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” S.L. Miller (1953)

Main problems of prebiotic chemistry in aqueous solution:  Dilution: concentration of reactants  Building blocks synthesis  Polymerization: Hydrolysis and not polymerization occurs !!

H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2OH2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O H2OH2O

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 the Suitable 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 C T G T C C Polymerization of precursors into larger molecules

Protection & Expression of Nucleic Acids Adsorbed on Minerals

RNA-Clay Complexes minerals ssRNA Viroid Hairpin Ribozyme RNA-mineral Complexes 16S RNA

Hammerhead Ribozymes Hairpin Ribozymes

Viroids Structural characteristics: –Single stranded, circular, 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 UA UA CG UA CG CG A U A A G C G U A A U G C G C U G C G CG C ’ 3’ A G A U C G II III C C G I A G U C A C A G UA GU A G CU C A AA HAMMERHEAD UA UA CG UA CG CG A U A A G C G U A A U G C G C U G C G CG C ’ 3’ A G A U C G II III C C G I A G U C A C A G UA GU A G CU C A AA 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. + montmorillonite Kobs= min-1 F∞= 0.58 free solution Kobs= min-1 F∞= 0.55

UV irradiation of ADHR1 hairpin ribozymes in the presence of Montmorillonite UV 254 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???

R1 R2 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

SEM image of etch-pit network near the surface of a weathered Shap alkali feldspar. (Scale bar 20 µm.) ribozymes resources nucleotides metabolism Pore Mineral environment

Evolution of an RNA population in a network of inorganic compartments

Phosphate (from apatite) N-Base Ribose

RADIATION ProtectionInteractionEvolution

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

Rolling Circle Replicative cycle 5’ OH 2’ P 3’ 5’ OH 2’ P 3’ Infective Viroid