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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,
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.
Georges Cuvier, 1769 - 1832
Tornado, Cuvier’s metaphor for life: priority of energy flow
Morowitz, 1992
Nonequilibrium, - the flow of matter or energy,
can be the source of order and complexity
(Prigogine and Stengers, 2003)
Origin of life: physical approach
priority
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!
Wackett et al., 2004
1877-1932
В начале был единый Океан,
Дымившийся на раскаленном ложе.
И в этом жарком лоне завязался
Неразрешимый узел жизни: плоть,
Пронзенная дыханьем и биеньем.
Планета стыла.
Жизни разгорались.
Наш пращур, что из охлажденных вод
Свой рыбий остов выволок на землю,
В себе унес весь древний Океан
С 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 ensued
Insoluble knot of life: the flesh,
Pierced by breath and beat.
The planet cooled.
Lives flared.
Our ancestor that of chilled water
His fish skeleton dragged to the ground,
In itself carried all the ancient ocean
With the breath of the tides,
With the primary heat and salt of water Live blood flowing in his veins.
Concentration of metals
in human plasma and
in sea water (nm/l)
Fe
Zn
Cu
Mo
Cr
V
Mn
Ni
22300 / 0,5-20
17200 / 80
16500 / 10
10000 / 100
55 / 4
200 / 40
110 / 0,7
44 / 5
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)
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
Some specific metal ion catalysis
Frausto da Silva & Williams, 1997
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 1012 times!
 removal of the metals from protein molecule leads to
decrease or loss of its catalytic properties.
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?
At catalytic centres, metals increase acidity, electrophilicity
and/or nucleophilicity of reacting species, promote heterolysis,
or receive and donate electrons.
The protein’s primary and secondary metalcoordination spheres
tune the properties of the metal to optimize reactivity and
influence metal selection.
Donor ligands (S, O or N) can impart bias in favour of the
correct metal.
Crystal structure of the nitrogenase Mo-Fe protein.
Are the proteins the later addition to the primary
inorganic catalysts?
The elements used as cofactors by enzymes are shown in blue. The height
of each column represents the proportion of all enzymes with known
structures using the respective metal. A single enzyme uses cadmium
(Waldron et al., 2009).
The proportion of proteins
using the indicated metals
that occur in each of the six
Enzyme classes:
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
The abundances of Fe-, Zn-, Mn-, and CoB12-binding structural
domains in the proteomes of Archaea (black), Bacteria (red),
and Eukarya (blue). Dupont et al., 2009
Cu
Bacteria
Occurrence of Cu users and nonusers among bacteria
differing in their dependence on oxygen (Ridge et al., 2008).
Cu
Archaea
Occurrence of Cu users and nonusers among archaea
differing in their dependence on oxygen (Ridge et al., 2008).
 Taxonomic and ecological distribution of the
metals as activators of enzymes may be a
subject for geohistorical and evolutionary
interpretation.
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.
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.
Biological role of hydrogen
 Many microorganisms use H2 as an electron donor
in both catabolic and anabolic redox processes.
 H2 plays an important role as an intermediary
metabolite during microbial transformation of
organic matter.
 H2 is produced as a catabolic end product by a
variety of anaerobic bacteria or as a byproduct of
the nitrogenase reaction by nitrogen-fixing
bacteria.
Biological role of hydrogen
 Anaerobically, hydrogen oxidation is
coupled to CO2 reduction by methanogens
and acidogens, and to sulfate reduction by
sulfidogenic bacteria.
 Aerobically, the hydrogen bacteria use
hydrogen gas for both energy conservation
and autotrophic CO2 fixation.
 Phototrophic bacteria can either produce or
consume molecular hydrogen.
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).
Hydrogen metabolism in Bacteria
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).
Spear et al., 2006
Stetter, 1996
O2
Hyperthermophyles
H2
EUBACTERIA
ARCHAEOBACTERIA
EUKARYOTES
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)
catalysts
The prime role of hydrogen and its close interactions with other
established biogeochemical cycles (Williams & Ramsden 2007)
The role of hydrogen and the connection that
it forms between the geological world and the
biological world (Nealson, 2005)
The deep hydrogen-driven biosphere hypothesis
(Karsten, Pedersen, 2000)
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
1-10 bars CO2
CO2
ocean
400C springs
ocean
CO2
CO2
ocean
Mantle convection cells at 4.4Ga
Russell & Hall 2006 GSA Mem192, 1-32
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
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.
Russell, 2006
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.).
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
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.
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.
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
Schulte et al., 2006
Serpentinization: olivine and pyroxene are altered into serpentine minerals:
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 solidsolution end-members, and
Mg2SiO4 + MgSiO3 + 2H2O  Mg3Si2O5(OH)4
(2)
forsterite + pyroxene + water  serpentine
The reduced iron from the fayalite component of olivine (Reaction 1) may then be
Oxidized to magnetite through the reduction of water to molecular hydrogen
through the reaction
3Fe(OH)2  Fe3O4 + 2H2O + H2
iron hydroxide  magnetite + water + hydrogen
(3)
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).
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.
Hydrogenases
These enzymes catalyze the
simplest of chemical reactions:
the reversible reductive formation
of hydrogen from protons and
electrons:
2H+ + 2e-  H2
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.
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.
Iron hydrogenases:
Prosthetic group features
http://metallo.scripps.edu/PROMISE/MAIN.html
Nickel-iron hydrogenases
Prosthetic groups in large
subunits
Prosthetic groups in small
subunits
Similarity of the molecular
structures:
a - mineral greigite (Fe5NiS8),
b -thiocubane unite of the
ferredoxine protein,
c - the cuboidal complex in
the active site of the enzyme
acetyl-CoA synthasa/carbon
monoxide dehydrogenase
(shown simplified), and
d - A-cluster of the latter.
Atoms: Fe – red, Ni – green,
S – yellow, C – grey, N – blue.
R – links through sulfur to the
reminder of the protein.
After Russell, 2006
Metals in The Early Oceans
Abundant: Fe2+, Ni2+, Mn2+, Mo6+, V4+, W6+
etc.
(Frausto da Silva& Williams, 1997)
HOWEVER: The chemical and physical
parameters of biosphere irreversibly departed
from the initial conditions.
MAJOR CHANGES: Global temperature
decline, oxygenation, and decreasing
availability of hydrogen and some metals.
Geochemical evolution of magmatism
between 3.5 and 2.7 Ga:
At the early stage of their development, tholeiitic magmas were considerably
enriched in chalcophile and siderophile elements Fe, Mg, Cr, Ni, Co, V, Cu, and
Zn.
At the next stage, calc-alkaline volcanics of greenstone belts and syntectonic
TTG granitoids were enriched in lithophile elements Rb, Cs, Ba, Th, U, Pb, Nb,
La, Sr, Be and others (Samsonov, Larionova, 2006).
Lead isotope compositions of tungsten-bearing minerals occurrences worldwide
indicate that tungsten (W) of crustal mineralization was mainly supplied by the
mantle between 3.0 and 2.4 Ga (Chiaradia, 2003).
Ni
Konhauser et al., 2009
A decline of dissolved Ni concentrations in sea water through
time reduced the bioproduction of methane and affected other
kinds of hydrogen metabolism
Atmosphere history
(Kasting, Pavlov, 2001)
Availability change for
some elements in the
ocean due to its
oxygenation
(Williams,Frausto da Silva,
1996)
Range of MIF of sulphur over time. The great oxidation event occurred
~2.45 billion years ago. The pink bar shows the range of variability in
Δ33S that is due to mass-dependent effects, indicating only small
variations during the past 2.32 billion years (Kump, 2008).
Glass et al.,
2009
Solubility of some metal hydroxides and metal sulfides
in modern ocean (Di Toro et al., 2001)
Mn
Fe
Kirschvink J.L., 2004.
Largest ore deposits of Mn and Fe in Early Proterozoic
was causes by active oxygenation of ocean water due
to the photosynthesis of cyanobacteria and increasing
circulation of cooling waters.
Iron formation: the sedimentary
product of a complex interplay
among mantle, tectonic, oceanic,
and biospheric processes
Bekker et al., 2010
The age distribution of
relative volumes of juvenile
continental crust (Condie,
2005), and of crystallization
ages for over 7000 detrital
zircons (Campbell and
Allen, 2008).
The peaks in the zircon
crystallization ages are
similar to the ages
of supercontinents.
The crust generation rate
curve illustrates a model in
which the volume of new
crust generated decreases
with decreasing age.
Hawkesworth et al., 2010
Two major systems of nutrirent
supply in the ocean ecosystem
 First, mid-oceanic ridge where circulating
seawater transports nutrients from MORB
(mid oceanic ridge basalt) crust
 Second, the Earth's surface erosion that is
12
probably 10 times more powerful than the
first nutrient supply system (Maruyama et
al., 2013)
A)Temporal trends in Mo concentrations in anoxic organic rich
black shales. B) Temporal trends in Mo/TOC ratios in anoxic
black shales (Wallis, 2006; Och, 2011).
A) A compilation of Vanadium concentrations in black shales
B) V/TOC ratios greatly increase across the Precambrian–Cambrian
boundary whereby the highest values (exceeding 1000) are exclusively
from black shales sampled in South China (Och, Shields-Zhou, 2012)
Mn
The chemistry of manganese ores through time:
a signal of increasing diversity of Earth-surface environments
(Maynard, 2010)
METAL COFACTORS
OF ENZYMES
Hypothetical sequence of the
incorporation of the metals into
the enzymatic evolution in the
early history of the biosphere
(Fedonkin, 2003, 2005).
Oxygen
Oxygenation of the environments
dramatically reduced availability
of some metals (such as W, V, Ni,
Fe), while others (such as Mo, Cu,
Zn) became more readily available.
Replacement of the unavailable
metals with those available seems
to be a major way in early evolution
of enzymes.
Geological Time
H2-related evolution
 All sources of hydrogen declined in time.
 The subsequent evolution of life was in a
great extent driven by the competition for
access to hydrogen.
 Decline of the primary sources of hydrogen
made life to switch for the hydrogen
compounds such as H2S, CH4, NH3, and at
last, H2O in the oxygenic photosynthesis.
H2-related evolution
> 4 Ga ago
The length of the thick arrows
indicates the amount of energy
released.
Time
2.7 Ga ago ?
(Lane, 2006)
2006)
(Lane,
H2-related evolution
 By-products of the biochemical reactions
related to the hydrogen uptake could be the
factor of historical change in the atmosphere
chemistry, in particular, the rising content of
nitrogen and oxygen.
The biogeochemical cycles of macroelements (C, N, P and Si)
are modulated by trace metals (J.T.Cullen et al., 1995)
Biological consequences
Decreasing availability of hydrogen and some
metals as well as the oxygenation of the
habitats in the Archean-Proterozoic oceans
were the major driving forces for evolution of
the metabolic pathways and biological
complexity of the cell.
Biological consequences
 Compartmentalization of internal
environment in the cell (membranes,
vesicles, organelles) that keeps the
Archean biochemistry intact
 Mechanisms of scavenging, concentration
and storage of the metals internally
 Integration of the complementary
metabolic types in the cell
Biological consequences
 Symbiosis of the prokaryotic cells
mutually dependent on each others'
waste products gave the rise of the
eukaryotes
 Increasing rates of the biological
recycling of nutrients in the ecosystem
 Shift towards the heterotrophy
because of need to acquire nutrients in
chemically impoverished environment
Modern approach to the
symbiogenesis problem
follows the principles of
ecosystem ecology and
syntrophy:
Symbiogenetic origin
of the eukaryotic cell
was a long process of
a functional optimization
and structural
miniaturization of the
primary prokaryotic
ecosystems in response
to the irreversible
change of the
environmental
parameters.
O2 utilizing gene birth over time (David and Alm, 2010).
David and Alm, 2010
Acknowledgements:
Program of the Presidium of the Russian
Academy of Sciences (‘‘Problem of the
Origin of the Earth’s Biosphere and Its
Evolution’’), Russian Foundation for
Basic Research
Thank you for your attention!