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Role of hydrogen and metals in the formation and evolution metabolic systems

Oparin-2014 The problem of the origin of life Moscow, September 22-26, 2014. Role of hydrogen and metals in the formation and evolution metabolic systems. Mikhail Fedonkin Geological Institute, Russian Academy of Sciences, Moscow. Alexander Ivanovich Oparin, 1894-1980,

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Role of hydrogen and metals in the formation and evolution metabolic systems

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  1. Oparin-2014 The problem of the origin of life Moscow, September 22-26, 2014 Role of hydrogen and metals in the formation and evolution metabolic systems Mikhail Fedonkin Geological Institute, Russian Academy of Sciences, Moscow

  2. Alexander Ivanovich Oparin, 1894-1980, biochemist, author of the theory of the origin of life: Oparin, A. I. The Origin of Life. Moscow: Moscow Worker publisher, 1924. According to Oparin the early Earth had a strongly reducing atmosphere, containing hydrogen, water vapor, methane, and ammonia. These elements and simple compounds were the raw materials for complex organic molecules subjected to natural selection and evolution.

  3. Georges Cuvier, 1769 - 1832

  4. Tornado, Cuvier’s metaphor for life: priority of energy flow

  5. Morowitz, 1992 Nonequilibrium, - the flow of matter or energy, can be the source of order and complexity (Prigogine and Stengers, 2003)

  6. Origin of life: physical approachpriority In the contrast to the chemical approach focused on the origin of “building blocks” of the living cell (RNA, DNA, proteins etc.), the physical approach concentrates on the origin of energy flow common for all living organisms: proton gradients and electron transfer. Central place should belong to hydrogen and metals!

  7. Wackettet al., 2004

  8. 1877-1932 В начале был единый Океан,Дымившийся на раскаленном ложе.И в этом жарком лоне завязалсяНеразрешимый узел жизни: плоть,Пронзенная дыханьем и биеньем.Планета стыла.Жизни разгорались.Наш пращур, что из охлажденных водСвой рыбий остов выволок на землю,В себе унес весь древний ОкеанС дыханием приливов и отливов,С первичной теплотой и солью вод —Живую кровь, струящуюся в жилах. In the beginning there was a single ocean,That was smoking on the heated bed.And in this hot lap ensuedInsoluble knot of life: the flesh,Pierced by breath and beat.The planet cooled.Lives flared.Our ancestor that of chilled waterHis fish skeleton dragged to the ground,In itself carried all the ancient oceanWith the breath of the tides,With the primary heat and salt of water -Live blood flowing in his veins.

  9. Concentration of metals in human plasma and in sea water(nm/l) Fe22300/0,5-20 Zn17200/80 Cu16500/10 Mo10000/100 Cr55/4 V 200/40 Mn110/0,7 Ni44/5

  10. Phytoplankton vs sea water chemistry Fe – 87 000 Zn – 65 000 Al – 25 000 N – 19 000 P – 15 000 Cu – 17 000 Mn – 9 400 Cd – 910 S – 1.7 Mg – 0.69 Na – 0.14 Ratio of the concentration of elements in phytoplankton to concentration of elements in sea water reflects the degree of biological need and, on the other hand, the degree of depletion of the particular elements from the seawater Bowen (1966)

  11. Biologically relevant metals • Na, K, Ca, Mg, Mn, Zn, Cu, Fe, V, Cr,Co, Ni, Mo, W Metals in the living cell serve as • electron-transfer agents • oxygen carriers • cellular messengers • structural components of proteins • nucleophiles • catalysts

  12. Some specific metal ion catalysis Frausto da Silva & Williams, 1997

  13. Transition metals as catalysts • over 30% of known enzymes contain metal ions as a cofactor of an active site • metal activators increase the rate of reactions catalysed by enzymes up 1012times! • removal of the metals from protein molecule leads to decrease or loss of its catalytic properties.

  14. Could the metals ions or their simple compounds be the first catalysers that, due to fast reactions segregated life, first dynamically and then structurally, from the mineral realm?

  15. At catalytic centres, metals increase acidity, electrophilicity and/ornucleophilicity of reacting species, promote heterolysis, or receiveand donate electrons. The protein’s primary and secondary metalcoordinationspheres tune the properties of the metal to optimizereactivity and influence metal selection. Donor ligands (S, O or N) canimpart bias in favour of the correct metal.

  16. Crystal structure of the nitrogenase Mo-Fe protein. Are the proteins the later addition to the primary inorganic catalysts?

  17. The elements used ascofactors by enzymes are shown inblue. The height of each columnrepresents the proportion of allenzymes with known structures usingthe respective metal. A single enzymeuses cadmium (Waldron et al., 2009).

  18. The proportion of proteins using the indicated metals that occur in each of the six Enzymeclasses: oxidoreductases (EC 1), blue; transferases (EC 2), yellow; Hydrolases(EC 3), purple; lyases (EC 4), pink; isomerases (EC 5), green; Ligases(EC 6), grey. EC, Enzyme Commission. After Waldron et al., 2009

  19. The abundances of Fe-, Zn-, Mn-, and CoB12-binding structural domains inthe proteomes of Archaea (black), Bacteria (red), and Eukarya (blue). Dupont et al., 2009

  20. Cu Bacteria Occurrence of Cu users and nonusers among bacteria differing in their dependence on oxygen (Ridge et al., 2008).

  21. Cu Archaea Occurrence of Cu users and nonusers among archaea differing in their dependence on oxygen (Ridge et al., 2008).

  22. Taxonomic and ecological distribution of the metals as activators of enzymes may be a subject for geohistorical and evolutionary interpretation.

  23. Hydrogen role in the energetic metabolism • Hydrogen, the most abundant chemical element in the Universe, well could be the primary fuel for early life. • Biological role of hydrogen is related not only to the domination of H2O in the mass of the living cell. • The soft hydrogen bonds provide stability and versatility of the macromolecules. • Many recent microorganisms use H2 as a source of energy.

  24. Hydrogen role in the energetic metabolism • Various microbial enzymes perform the H+ transfer. • The H+ gradients are used in the process of ATP generation. • Negative ion of hydrogen H- is known as an energy currency of the cell (an equivalent of two electrons). • H2 as a key intermediate product of anaerobic metabolism makes a universal trophic (energetic) connection between the microorganisms that live on different substrates – a key ecosystem factor.

  25. Biological role of hydrogen • Many microorganisms use H2as an electron donor in both catabolic andanabolic redox processes. • H2 plays an important role asan intermediary metabolite during microbialtransformation of organic matter. • H2is produced as a catabolic end product by avariety of anaerobic bacteria or as a byproductof the nitrogenase reaction by nitrogen-fixingbacteria.

  26. Biological role of hydrogen • Anaerobically, hydrogenoxidation is coupled to CO2 reduction bymethanogens and acidogens, and to sulfatereduction by sulfidogenic bacteria. • Aerobically, the hydrogen bacteriause hydrogen gas for both energy conservationand autotrophic CO2 fixation. • Phototrophicbacteria can either produce or consumemolecular hydrogen.

  27. Biological role of hydrogen • Hydrogen as a source of energy and free electrons is easy to take up by various chemosynthesizing organisms. • The near universality of hydrogen metabolism among microorganisms and high similarity between all the Ni-Fe hydrogenase operons suggests that the microbial ability to metabolize hydrogen is of great importance and ancient origin (Casalot, 2003).

  28. Hydrogen metabolism in Bacteria

  29. Proportions of the H2 oxidizing methanogenic Archaea (99%) and Bacteria in groundwater from Lidy Hot Spring (Beaverhead Mts, Idaho).Depth 200 m, temperature 58.5 °C, anoxic, very low dissolved Corg and high concentration of H2 (Chapelle et al., 2002).

  30. Spear et al., 2006

  31. Stetter, 1996 O2 H2 Hyperthermophyles

  32. EUBACTERIA Fundamental difference between prokaryotic and eukaryotic physiology from the standpoint of energy metabolism may indicate chemoautotrophic origin of life. Large part of the reactions in the prokaryotes involves hydrogen and its volatile compounds that must be the primary feature. Redox reactions involving inorganic donors and acceptors after Amend & Shock, 2001, Doeller et al. 2001 (see refs. in Martin & Russell, 2002) ARCHAEOBACTERIA EUKARYOTES

  33. catalysts The prime roleof hydrogen and its close interactions with other established biogeochemical cycles (Williams & Ramsden 2007)

  34. The role ofhydrogen and the connection that it forms between the geological world and the biological world (Nealson, 2005)

  35. The deep hydrogen-driven biosphere hypothesis (Karsten, Pedersen, 2000)

  36. Early Earth (> 4 Ga) • Radiogenic heat was over 10 times higher than at present • Contribution of close Moon into the mechanical heating of the Earth interior was high • Intensive volcanism • Full recycling of the earth crust • Low relief • Global shallow ocean

  37. 1-10 bars CO2 CO2 CO2 400C springs CO2 ocean ocean ocean Mantle convection cells at 4.4Ga Russell & Hall 2006 GSA Mem192, 1-32

  38. Early Earth (> 4 Ga) • Low luminosity of Sun (30% below present) • Dense green-house atmosphere • High temperature of the planet surface • Rapid formation of the metal core of the planet (during the first 100 Ma) • Magnetic field was established early as well • Reducing atmosphere • Anoxia, no protective ozone screen

  39. Iron sulfide bubbles around alkaline vents in the Hadean ocean. Fe-Ni sulfides catalyzed synthesis of simple organic molecules that formed more complex peptides. The peptides have coated the inside surfaces of the bubbles, the first step towards cellular autonomy. Hydrothermal mounds were key to life’s origin. Alkaline fluids from such vents carried hydrogen, sulfide and ammonia. Water was enriched with the heavy metals (Fe, Ni etc.). Russell, 2006

  40. From the physical point of view • the onset of life by the hydrothermal systems or in the hot ocean seems to be a plausible hypothesis because of the factors such as: • - electron-rich environment • electrochemical gradients • abundance of metal ions • - molecular hydrogen and its volatile compounds

  41. Sources of hydrogen on early Earth • Kadik A.A. & Litvin Yu.A. (2007): … the first stages of the core growth took place under reduced conditions imposed by the pristine terrestrial materials and was accompanied by the emission of CH4, H2, NH3 and minor H2O into the atmosphere. • According to Galimov (1985, 2004) the great bulk (95%) of the metal core was formed during the first 100 Ma after the accretion of the planet.

  42. Sources of hydrogen on early Earth • the degassing of the mantle that released the neutral or slightly acidic fluids saturated with H2, CH4, H2S, and CO2; • the serpentinization, reaction of the rocks, rich with olivine and pyroxene, with water. • photolysis of water by UV light • radiolysis, radiation-induced dissociation of H2O (background radiation on early Earth could be much higher than at present, mostly due to the decay of the short-lived isotopes.

  43. Serpentinization — the reaction of olivine- and pyroxene-rich rocks with water at temperature 200-400°С— produces magnetite, hydroxide, and serpentine minerals, and liberates molecular hydrogen, a source of energy and electrons that can be readily utilized by a broad array of chemosynthetic organisms. Schulte et al., 2006

  44. Schulte et al., 2006 Serpentinization: olivine and pyroxene are altered into serpentineminerals: Fe2SiO4 + 5Mg2SiO4 + 9H2O 3Mg3Si2O5(OH)4 + Mg(OH)2 + 2Fe(OH)2. (1) fayalite +forsterite + water  serpentine + brucite +iron hydroxide where fayalite and forsterite are the olivine solidsolutionend-members, and Mg2SiO4 + MgSiO3 + 2H2O Mg3Si2O5(OH)4(2) forsterite + pyroxene + water  serpentine The reduced iron from the fayalite component ofolivine (Reaction 1) may then be Oxidizedto magnetite through the reduction of waterto molecular hydrogen through the reaction 3Fe(OH)2 Fe3O4 + 2H2O + H2 (3) iron hydroxide magnetite + water + hydrogen

  45. Sources of hydrogen on early Earth • Calculations by Tian F. et al. (2005) demonstrate that hydrogen could make up to 30% of ancient atmosphere. • The concentration of H2 in the prebiotic atmosphere was 3-4 orders of magnitude higher than at present (Hoehler, 2005).

  46. Sources of hydrogen on early Earth • Concentration of hydrogen could be even greater among the dissolved gases in the fluids going through the rocks and sediments due to slow migration of the fluids. • Abundance of hydrogen gave an easy access to the protons and electrons, the very motor of the cellular energy machine.

  47. Hydrogenases These enzymes catalyze thesimplestof chemical reactions: the reversible reductive formation of hydrogen from protons and electrons: 2H+ + 2e- H2

  48. Ragsdale, 2004 The water-gas shift reaction, an organometallic reaction sequence that is catalysed by Fe-Ni dehydrogenase, may also be one of the oldest on Earth.

  49. The structure of CpI hydrogenase from Clostridium pasteurianum with its naturally embedded metallo-clusters. Arrows show the pathways for the electrons, hydrogen ions, and the hydrogen product to and from the active H-cluster.

  50. Iron hydrogenases: Prosthetic group features http://metallo.scripps.edu/PROMISE/MAIN.html

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