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Origin of genetic material: looking for the ancestral cradle

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 . ”

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Origin of genetic material: looking for the ancestral cradle

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  1. 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

  2. “On ne connaîtpascomplètement une science tantqu'on n'en saitpas l'histoire.” (To understand a science, it is necessary to know its history.) A. Comte

  3. Alexander I. Oparin (1894–1980) “Proiskhozhdenie zhizny” 1924 “The Originof Life” 1938

  4. Whatwas the primordial habitat of life?

  5. 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

  6. Erwin Schrödinger “What is Life?” (1944)

  7. Transcription Translation RNA Proteins The BasicPrincipleofBiology Replication DNA

  8. “…Currentbiologyindicatesthat life couldhavenotevolved in the absenceof a geneticreplicatingmechanism…” A. Lazcano, OLEB (2010) ↓ The presenceof a genetic system isabsolutelyessential

  9. Formation of Earth Prebiotic chemistry First DNA / protein life Diversification of life 4.5 4.0 3.5 3.0 The “appearance” of a nucleic acid-like polymer able to evolve marks the beginning of life MolecularEvolution

  10. How and Where?

  11. Building Code • Synthesis and accumulation of precursors (i.e.nucleotides) • Polymerizationof precursors. • Protectionfrom degradation • Expression of “biological”potentialityof the information molecule

  12. Early Atmosphere (?) • Composition • H2O, CO2, N2, NH3, • CH4 • Origin • Volcanic outgassing

  13. “The Primordial Soup” A.I. Oparin (~1924) - J.B.S. Haldane (~1930) Classicalresearch: AqueousSolutionChemistry

  14. Stanley Miller (1953)

  15. Classical research: aqueous solution chemistry (primordial oceans) In these conditions:hydrolysis and not polymerization!

  16. The “RNA World”

  17. John D. Bernal (1901-1971)

  18. The “Clay Honeycomb” “… Clays and other minerals were necessary to: Concentrate the organics present in a dilute ocean by adsorption Protect these organics from destruction by U.V. light Catalyze the polymerization of adsorbed organics…” J.D. Bernal (1951)

  19. Originof 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.

  20. Clay on Mars

  21. RoleofMinerals, mainly Clay Minerals, in the synthesisof: → Nucleic Acid Bases Saladino et al., CHEMBIOCHEM (2004), Costanzo et al., BMC EvolutionaryBiology(2007), Saladino et al., Physics Life Reviews(2012) → StabilizationofRibose Ricardo et al., Science (2004)

  22. James Ferris

  23. 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) G T C C C T A

  24. Oligomerization of Nucleotides on Montmorillonite Mathew & Luthey-Schulten, OLEB (2010)

  25. ProtectionofNucleicAcids DNA molecules adsorbed on clay minerals are protected to some extentagainst the action of different degrading agents, still maintaingtheir biological activities Stotzky & Gallori, Molecular Microbial Ecology, (1996)

  26. Trasformation + Replication + TAQ-Polymerase BiologicalCharacteristicsofNucleicAcid-ClayComplexes • 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)

  27. K-Chromosomal DNA (X 154,000) K-Plasmid DNA (X 271,500) Electron Microscopy (T.E.M.) Franchi et al., OLEB (1999)

  28. X-RayAnalysisofM-Nucleic acid complexes Franchi et al., OLEB (1999)

  29. FT-IR AnalysisofM-Nucleic Acid complexes B-Form A-Form Franchi et al., OLEB (1999)

  30. RoleofCations in the Adsorption Franchi, Ferris and Gallori, OLEB (2003)

  31. U.V. radiation Effects of UV and X-rays 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)

  32. 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)

  33. Hammerhead Ribozyme 16SRNA ssRNA Viroid RNA-ClayComplexes Clay minerals: • montmorillonite (M) • kaolinite (K) RNA-Clay Complexes

  34. C C C C G A G G A G A A A A A A U A U A A U U AnnealingofComplementary Single StrandedNucleicAcids Franchi and Gallori, Gene (2005)

  35. EnzymaticReplicationof Clay-Adsorbed RNA Franchi and Gallori, Gene (2005)

  36. Could Clay-RNA Complexes Perform Enzymatic Reaction?? Hammerhead Ribozymes Hairpin Ribozymes

  37. HammerheadRibozymeAvocado SunblotchViroid (ASBVd) (Flores, 1994)

  38. Adenine DependentHairpinRibozyme (ADHR1) ADHR1 Meli et al., J. Biol. Chem (2003)

  39. 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)

  40. ADHR1 self-cleavagekineticsafter5’ ofUV-irradiation Control + Mont Control in water UV + Mont UV in water Biondi et al., BMC Evolutionary Biology (2007)

  41. Phosphate (from apatite) N-Base Ribose

  42. RADIATION Interaction Protection Evolution

  43. Clay Micelle

  44. Prometheus(Προμηθεύς, “the onewhothinkover”)

  45. 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

  46. ThankyouMisha!

  47. Evolution on “Mineral Honeycomb” Real Mineral Structure Model Implementation of the theoretical model with a well defined spatial environment (i.e. a porous structure) Results Increase of information capacity of replicators in a mineral structured environment Branciamore et al., J Molec Evol (2010)

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