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ISSN: 2167-7662

Research Article

Bioenergetics: Open Access

Marakushev and Belonogova, Bioenergetics 2016,
5:2
DOI: 10.4172/2167-7662.1000141

Open Access

The Emergence of Bioenergetics: The Formation of a Gluconeogenesis System
and Reductive Pentose Phosphate Pathway of CO2 Fixation in Ancient
Hydrothermal Systems

Sergey A. Marakushev* and Ol’ga V. Belonogova

Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region, Russia
*Corresponding author: Marakushev SA, Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Russia, Tel: 496-522-7772; E-mail:
marak@cat.icp.ac.ru

Rec date: Apr 18, 2016; Acc date: Nov 08, 2016; Pub date: Nov 11, 2016

Copyright: © 2016 Marakushev SA et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

The origin of phosphorus metabolism is one of the central problems in the context of the emergence of life on
Earth. It has been shown that the C–H–O system can be transformed into a four- component C–H–O–P system with
the formation of a gluconeogenesis path in a possible Archean hydrothermal condition under the influence of a
phosphorus chemical potential. This system became the energy supply basis for protometabolism, and facilitated the
formation of a new CO2 fixation cycle (the reductive pentose phosphate pathway).

The modular design of central metabolism in the C–H–O–P system is derived from the parageneses
(associations) of certain substances, and the emerging modules in turn associate with each other in certain physical
and chemical hydrothermal conditions. The assembly of malate, oxaloacetate, pyruvate, and phosphoenolpyruvate
is a reversible “turnstile – like” mechanism with a switching of reaction direction that determines the trend of specific
metabolic systems development.

Keywords: Origin of metabolism energetics; Autocatalytic cycles;
Gluconeogenesis; CO2 fixation; Modularity; Parageneses; Chemical
potentials

Introduction

in

life

One of the most important concepts in the theories of the
chemolithoautotrophic origin of
the Archean volcanic
hydrothermal environment is autocatalytic CO2 fixation [1-9]. It has
also been suggested that the last common ancestor (LCA) of all extant
cell lineages was a chemolithoautotrophic thermophilic anaerobe
[10-14] capable of synthesizing organic ‘building blocks’ from the
inorganic carbon. Thus, these microorganisms can serve as a model for
studying primordial metabolism. However, CO2 fixation requires
energy, which was provided by energy from high-energy intermediates,
organic phosphates in particular, that are presently involved in the
primary biochemical pathways.

In previous works we have considered the thermodynamic factors of
natural selection in the coupled autocatalytic cycles of CO2 fixation
(redundant modular constructions) in the three – component C-H-O
system [6,15]. It is rationalized that these systems are the primordial
metabolic autocatalytic reductive citrate (RC) cycle (reductive
tricarboxylic acid, Arnon-Buchanan cycles) and 3-hydroxipropionate
(3-HP) cycle. An important factor in the stability and subsequent
evolution of these coupled cycles is the reversibility of some key
chemical reactions such as succinate ↔ fumarate, malate ↔ fumarate
and others [16]. The further development of this system with negative
feedback involves increasing the number of independent components
by maintaining additional supply of phosphorus, nitrogen, and sulfur.
Adding phosphorus (forming a four – component C–H–O–P system)
leads to the development of the gluconeogenesis system, which

produces phosphorylated sugars, a basic source of energy for different
biosynthetic pathways. The nodal
intermediates and proposed
autocatalysts in this process are malate, pyruvate, and oxaloacetate, the
transformation of which into phosphoenolpyruvate permits the
formation of phosphorylated trioses, pentoses, and hexoses.

ancient

enzyme

The fundamental role of phosphorylated carbohydrates and the
universality of the few modern metabolic interconversions suggest
their origin at the earliest evolutionary stage. The possibility of
gluconeogenesis first originating as a precursor to phosphorus
metabolism in hyperthermophilic microorganisms was considered in
[17]. Gluconeogenesis starting with phosphoenolpyruvate uses the
unusual
aldolase/
phosphatase, which converts triose phosphates to fructose 1,6-
bisphosphate [18,13]. The ancient origin of gluconeogenesis with the
consequent origin of the ancestral Aquificae, Chloroflexi, and
Thermotogae taxa is postulated. Reactions converting triose phosphate
into fructose 1,6-bisphosphate are generally reversible, but the reaction
of fructose 1,6-bisphosphate into stable fructose 6-phosphate is
irreversible and substantially determines the unidirectionality of
gluconeogenesis, which precedes
the emergence of glycolysis
evolutionarily [17].

fructose 1,6-bisphosphate

–

catalyzed

the non-enzymatic metal

The early origin of gluconeogenesis is indirectly supported by data
formation of
from
phosphorylated three-carbon sugars and pyruvate [19,20], and the
widespread role of non-enzymatic catalysis in phosphate metabolism is
considered in ref. [21]. It should be noted that both non-enzymatic
and enzymatic reactions are based on the same fundamental
thermodynamic laws. Experimental analysis of the conditions required
for phosphorylated intermediate formation and stability in the pentose
phosphate pathway is given in ref. [22].

Bioenergetics, an open access journal
ISSN:2167-7662

Volume 5 • Issue 2 • 1000141

Citation: Marakushev SA, Belonogova OV (2016) The Emergence of Bioenergetics: The Formation of a Gluconeogenesis System and Reductive
Pentose Phosphate Pathway of CO2 Fixation in Ancient Hydrothermal Systems. Bioenergetics 5: 233. doi:10.4172/2167-7662.1000141

Page 2 of 6

1, which shows the development of coupled autocatalytic systems
(archaic RC and 3-HP cycles [26]) in the direction of phosphorus
metabolites – triose phosphates and phosphorylate d sugars. It is
assumed that these metabolic changes took place during of the orgin of
life energetics aspect.

Methodical Approach

The physicochemical analysis of parageneses

(associations,
assemblages) is widely used in geochemical researches of mineral
systems [27]. This approach is based on a generalization of the
thermodynamic and physical properties of minerals in order to detect
the conditions responsible for the formation of the parageneses
observed in rocks and ores. In this case, the thermodynamic potential
method [27,28], which allows one to develop a system of geochemical
mineral
is used. Our
preliminary calculations indicated that paragenetic analysis can be
extended to organic substances, which form the systems listed below
(the systems are
increasing complexity of chemical
composition and structure): C–H–O, C–H–O–N, C–H–O–N–P and
C–H–O–N–P–S [6,15,29].

facies (thermodynamic stability areas),

listed

in

The studies of organic substances assemblages (parageneses) and
areas of their thermodynamic stability (facies) is based on the Gibbs
phase rule, according to which the number of degrees of freedom for a
thermodynamic system in equilibrium is equal to the number of
system independent components plus two minus the number of
phases. In this case, the number of independent components is the
smallest number of chemical components; the compositions of all
possible phases of the system can be obtained by their combination.
The phase rule is not limited to consideration of the extensive
parameters of the system and, hence, is completely applicable to open
systems with chemical potential as an independent parameter [16,30].
Determining the total number of system independent parameters
(intensive and extensive), and using this number together with the
Gibbs phase rule provides a way to study the thermodynamic
properties of organic systems.

these organic compounds

The system state was calculated using free partial energy values for
organic substance formation (∆Go f,T), depending on external
conditions. The state diagrams, which reflect the facies of organic
compounds and their parageneses, are graphically presented. When
considering
in fluid and aqueous
hydrothermal systems, the points of major importance are shown with
diagrams: a) chemical composition – paragenesis (at constant pressure
(P), temperature (T), and chemical potential (µi)), b) chemical
potential – temperature (at constant P), c) the relationship between
chemical potentials of the components: µH2O – µCO2, µH2 – µO2, etc.
(at constant P and T).

The major equilibrium factors in the physicochemical analysis of
parageneses are the chemical potential (µi) of each component
(representing its partial energy). The value µi is expressed through
activity, αi, and fugacity, fi, as follows: (µi=(µºi)Т,р+RTln αi=(µºi)Т,р
+RTln fi.)

The aqueous constants used were derived using the electrostatic
model method, according to which the solvate constituent of a
substance plays an essential role in the chemical potential at different
electrostatic
temperatures,
interactions between the substance and solvent (H2O) [31-34].
Thermodynamic calculations of the Gibbs standard free energy and
analysis of the geochemical constraints showed that the abiotic

contribution

reflecting

from

the

Figure 1: Inferred coupling of the autocatalytic loops of the archaic
reductive citrate (RC) and 3-hydroxipropionate (3-HP) cycles with
the further development of phosphorus metabolism in the archaic
systems of gluconeogenesis and the reductive pentose phosphate
(RPP) pathway of CO2 fixation. The arrows show the direction of
reactions. The circular arrows show the direction of reactions in the
coupled RC and 3-HP cycles. In the RPP cycle, three molecules of
fructose-6-phosphate regenerate three molecules of ribulose-1,5-
bisphosphate and one molecule of 3-phosphoglycerate.

The reactions underlying the interconversion of phosphorylated
carbohydrates were examined under the conditions found in a putative
Archean ocean, which were determined based on the chemical
composition of sedimentary rocks in this time period. It was shown
that the simple inorganic ions (Fe (II), Co (II), Ni (II), Mo (IV)) found
in rocks from the Archean period could catalyze the reactions
observed in the extant metabolic pathways. It was also concluded that
iron (at concentrations of 20 µM to 5 mM) was the most effective
catalyst of metabolic reactions requiring substrate phosphorylation in
early anoxygenic Archean ocean. It is assumed that the ancient ocean
was enriched not only by ferro – ions but also phosphates [22-24] that
emanated from high-temperature alkaline hydrothermal fluids to the
surface of
some
it
thermodynamic analysis of
the possibility of phosphorylated
carbohydrates formation.

[25]. Nevertheless,

the Earth

requires

A simplified biomimetic image of primordial anaerobic central
carbon metabolism in the form of branching metabolic reactions with
the formation of gluconeogenesis and the reductive pentose phosphate
(RPP) CO2 fixation cycle (Calvin-Benson cycle) is presented in Figure

Bioenergetics, an open access journal
ISSN:2167-7662

Volume 5 • Issue 2 • 1000141

Citation: Marakushev SA, Belonogova OV (2016) The Emergence of Bioenergetics: The Formation of a Gluconeogenesis System and Reductive
Pentose Phosphate Pathway of CO2 Fixation in Ancient Hydrothermal Systems. Bioenergetics 5: 233. doi:10.4172/2167-7662.1000141

synthesis of organic compounds in hydrothermal systems is limited by
the metastable equilibrium that results from kinetic barriers, which
prevent the achievement of stable equilibrium [32,35-37]. Most of the
organic substances in condensed and dissolved phases are in a
metastable state, i.e., these substances do not reach the minimum
Gibbs free energy for the given composition of elements, and thus are
“kinetic” or “metastable” phases [38,39].

Previously, we calculated a diagram of composition – paragenesis for
the ternary C–H–O system [e.g., 6]. The addition of phosphorus to the
C–H–O system forms the quaternary system C–H–O–P, in which the
independent components – carbon, hydrogen, oxygen, and
phosphorus – are extensive parameters (fex). Figure 2 presents the
phase diagram of compositions for the compounds shown in Figure 1.
In this ternary C–H–O diagram, the phases of the phosphorylated
compounds are represented by the subtracting of orthophosphoric acid
(Н3РО4). If, in thermodynamic calculations, the chemical potential is

Page 3 of 6

determined for Н3РО4 (µH3PO4), and phosphorus becomes an
intensive parameter (fin), then the quaternary system becomes ternary
(C–H–O). If the chemical potential is calculated for hydrogen or
methane (µСН4, µН2), and hydrogen becomes intense parameter (fin),
then the ternary system becomes a binary system, C–O (Figure 2a and
b). The dashed conodes connect CH4 and H2 with substances phases,
which are represented by stars on the triangle side. The composition
diagram (Figure 2c) shows that, if the chemical potential is calculated
for CO2 (µСO2), and CO2 becomes an intensive parameter (fin), then
the ternary system becomes a binary system, C–H (dashed conodes
connect the CO2 point, and substance phases represented by rhombs
on the triangle base). The free energies of aqueous ionized phosphorus
substance formation were taken from ref. [40] and were designed for
non-ionized forms using the method described in refs., [40,41]. The
constants for substances in the C–H– O system were taken from [16].

Figure 2: C–H–O phase diagram representing the compositions of the compounds shown in the modular scheme (Figure 1). The two-
component C–O system is generated when the chemical potentials of CH4 and H2 (a and b) are used. The two-component C–H system (c) is
generated when the chemical potential of CO2 is used. Phosphorylated compounds are represented by the subtracting of orthophosphoric acid
(H3PO4) composition. Substances in the C–H–O system are indicated with filled triangles and substances in the C–H–O–P system are
indicated with empty boxes. Designations of the substances: 1 – fumarate (Fum), 2- succinate (Suc), 3 – acetate (Acet), 4 – pyruvate (Pyr), 5 –
malate (Mal), 6 – glyoxylate (Glx), 7 – oxaloacetate (Oxal), 8 – phosphoenolpyruvate (PEP), 9 – 3-phosphoglycerate (PG), 10 – glyceraldehyde –
3- phosphate (GAP), 11 – fructose 6-phosphate, 12 – ribulose 1,5 bisphosphate, 13 – fructose 1,6-bisphosphate (FBP).

Certainly, the hydrothermal systems are generally characterized by a
more high- pressure and high-temperature conditions. However, these
conditions cannot fundamentally change the character the diagrams of
chemical potentials – as a rule, the equilibria shifts in a direction of its
higher values.

hydrothermal systems, are the chemical potentials of molecular
and hydrocarbons. The predominant widespread
hydrogen
hydrocarbon is methane, the concentration of which (e.g., in volcanic
oceanic emissions) is usually more than two orders of magnitude
higher than the concentration of other hydrocarbons [44].

It is assumed that the anoxygenic Archean ocean saturated with
siliceous compounds and Fe (II) contained a higher level of dissolved
orthophosphate than the modern ocean [23,42,43]. These conditions
have primarily been determined with the use of the orthophosphate
chemical potential in thermodynamic calculations of the origin and
the evolution of protometabolic pathways related to the four
component C–H–O–P system.

The Chemical Potentials of Methane, Molecular
Hydrogen, and Carbon Dioxide

The most important energy factors in the generation of organic
compounds, which are intermediates of protometabolic pathways in

At the present time, the abiotic synthesis of organic compounds in
the hydrothermal systems of mid-ocean ridges has been confirmed in a
number of publications (e.g., [44-46]). Alkanes and carboxylic acids
represent some of the most abundant organic structure types found in
natural hydrothermal systems and sedimentary basin fluids.

The diagram in Figure 3 is based on aqueous constants at standard
conditions and shows the formation and development of coupled C–
H–O–P metabolic systems, Figure 1, under the influence of the
chemical potentials of methane (µCH4) and phosphoric acid
(μH3PO4).

Bioenergetics, an open access journal
ISSN:2167-7662

Volume 5 • Issue 2 • 1000141

Citation: Marakushev SA, Belonogova OV (2016) The Emergence of Bioenergetics: The Formation of a Gluconeogenesis System and Reductive
Pentose Phosphate Pathway of CO2 Fixation in Ancient Hydrothermal Systems. Bioenergetics 5: 233. doi:10.4172/2167-7662.1000141

Page 4 of 6

initiation) also

cycle
facies with
phosphoenolpyruvate – oxaloacetate paragenesis and further to facies
of 3-phosphoglycerate.

formation of

leads

the

to

According to [11], phosphoenolpyruvate and oxaloacetate are nodal
molecules of all anabolic networks (in addition to acetate, pyruvate,
and 2-oxoglutarate). From the diagrams in Figures 3 and 4, it is clear
that facies with phosphoenolpyruvate – oxaloacetate paragenesis are an
area of bifurcation (network node) that determines the development of
the primordial 3-HP (fumarate) and RC cycles (succinate), system of
gluconeogenesis (3-phosphoglycerate ↔ fructose 1,6-bisphosphate →
fructose 6-phosphate) and the RPP cycle (3-phosphoglycerate →
ribulose-1,5-bisphosphate → 3-phosphoglycerate). It is obvious that 3-
phosphoglycerate must be added to the five nodal molecules of
autotrophic anabolic networks mentioned above. Thus, the diagram in
Figure 3 and 4 represents a thermodynamic basis of “encrustation” of
the C-H-O system by a chemical “shell” of phosphorus under the
influence of a chemical potential of methane and/or hydrogen and
phosphorus. However, the autotrophic nature of the parageneses
formation of carboxylic acids and triose phosphates is manifested the
best with consideration of the chemical potential of carbon dioxide.

Figure 4: Diagram of the chemical potentials of H2 and H3PO4
(µH2=RTlnαH2, where α represents the activity of molecular
hydrogen in solution) at P=1 bar and T=298 K. The substance
designations correspond to the designations in Figure 2. The arrows
show the reversible reactions.

Figure 4 shows a diagram of the chemical potentials of hydrogen
and H3PO4. In general, this diagram is similar to Figure 3 (also see
Figures 2a and 2b), and the monovariant equilibria are three-phase or
degenerate two-phase. As we have shown previously [6,26], the
association of succinate with fumarate acts as a redox switch, turning
electron flow in the direction of archaic chemoautotrophic 3-HP and
RC cycles in the wide temperature range.

On the diagram of CO2 and H3PO4 chemical potentials (Figure 5), a
phosphoenolpyruvate – malate paragenesis is located in a sufficiently
limited range of the considered chemical potentials (center diagrams)
and develops in the direction of the discussed metabolic systems
(Figure 1) at varying chemical potentials. Thus, increasing the
chemical potential of phosphorus leads to the emergence of phases of
3-phosphoglycerate and glyceraldehyde phosphate (emerging at a low
chemical potential of CO2), and these compounds (phosphorylated
acid and aldehyde) are the initiators of gluconeogenesis and the RPP

Figure 3: Diagram of the chemical potentials of CH4 and H3PO4
(µCH4=RTlnαCH4, µH3PO4=RTlnαH3PO4, where α represents the
activities of the corresponding respective substances in aqueous
solution at standard conditions). The free energy of aqueous
substance formation values (∆G°298) are given in the table (values
are at standard conditions). The shaded field indicates the partially
overlapping facies of fumarate and succinate. The parageneses of
substances for each facies are shown in the linear diagram of the C–
O system. 3 HP and RC are the archaic 3-hydroxipropionate and
reductive citrate cycles. The substance designations correspond to
the designations in Figure 2.

in

the

According to the Gibbs phase rule, the diagram represents the four-
phase nonvariant equilibria in this two-component C–O system (see
Figure 2a), whereas the monovariant equilibria are three-phase,
separating divariant fields of phase stability and their parageneses and
are identified by linear diagrams in the system facies. Increasing the
H3PO4 chemical potential
stable paragenesis
results
phosphoenolpyruvate – oxaloacetate at a relatively low chemical
potential of methane (<-100 kJ/mol). Further development of the system leads to the facies formation of 3-phosphoglycerate and glyceraldehyde phosphate, permitting the development of the ancient pathway of substrate phosphorylation – gluconeogenesis and the reductive pentose phosphate (RPP) cycle of CO2 fixation. Attention should be drawn to the overlapping facies (shaded field) of succinate (RC-cycle) and fumarate (3-HP cycle) with oxaloacetate - succinate - fumarate - phosphoenolpyruvate paragenesis. This field is an area of thermodynamic stability of coupled RC + 3-HP bicycle [6] and the new metabolic pathways apparently originated at the beginning of these redundant autocatalytic metabolic systems. The chemical potential of H2 divides the lower region of the diagram (Figure 4) on the facies of the dicarboxylic acids (succinate ↔ fumarate) and thus fixes the phase areas of stability of the archaic autotrophic 3-HP and RC cycles of CO2 assimilation. With an increase in the chemical potential of H3PO4, facies of fumarate (3-HP cycle initiation) - oxaloacetate, and a further increase in the chemical potentials of H2 and H3PO4 leads to the decomposition of the metastable paragenesis with the formation of facies of 3-phosphoglycerate, which is a central metabolite (and autocatalyst [47]) in both gluconeogenesis and the RPP autocatalytic CO2 fixation cycle (see Figure 1). Similarly, increasing the H3PO4 chemical potential in facies of succinate (RC facies of phosphoenolpyruvate transform into Bioenergetics, an open access journal ISSN:2167-7662 Volume 5 • Issue 2 • 1000141 Citation: Marakushev SA, Belonogova OV (2016) The Emergence of Bioenergetics: The Formation of a Gluconeogenesis System and Reductive Pentose Phosphate Pathway of CO2 Fixation in Ancient Hydrothermal Systems. Bioenergetics 5: 233. doi:10.4172/2167-7662.1000141 cycle. It should be noted that glyceraldehyde phosphate is also one of the main centers of the ancient evolutionary development of the non- oxidative branch of the pentose phosphate pathway, which leads to the formation of a series of phosphorylated sugars [48]. Page 5 of 6 core metabolic pathways are derived from the parageneses of certain substances (micro modules - associations of chemical compounds which ultimately function together), and the resulting modules are in turn in paragenesis with each other in certain physical and chemical conditions. Malate, oxaloacetate, pyruvate, and phosphoenolpyruvate (Figure 1) form the reversible "turnstile - like" mechanism capable of switching reaction directions. A change in the external conditions shifts the coupled modular autocatalytic system toward developing in the direction that is most favorable to the formation of specific metabolic systems. The chemical C–H–O system acquired new "layers" from phosphorus, nitrogen, and sulfur. The present work investigated only the phosphorus "layer", which led to the development of new protometabolic energy systems. Thus, in early chemical protometabolic reactions of the CO2 fixation energetics, which primordially was provided by the partial energy of environmental chemical potentials (mainly due to the endogenous flow of hydrogen and hydrocarbons), was then replaced with energy from high-energy organic phosphates. Acknowledgments This study was supported by the program of the Presidium of the Russian Academy of Sciences on fundamental researches of the Evolution of Organic World and Planetary Processes. 1. Wächtershäuser G (1988) Before enzymes and templates: theory of surface metabolism. Microbiol Rev 52: 452-484. 2. Wächtershäuser G (1990) Evolution of the first metabolic cycles. Proc Natl Acad Sci USA 87: 200–204. 4. 3. Morowitz HJ, Kostelnik JD, Yang J, Cody GD (2000) The origin of intermediary metabolism. Proc Natl Acad Sci U S A 97: 7704-7708. 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Figure 5: Diagram of the chemical potentials of CO2 and H3PO4 (μCO2 = RTlnαCO2, where α represents the activity of CO2 in aqueous solution at standard conditions). The parageneses of substances for each facies are shown in the linear diagram of the C– H system. Abbreviations as above. References Decreasing the chemical potential of phosphorus leads to the disappearance of the phosphoenolpyruvate - malate paragenesis and the appearance of phosphoenolpyruvate - pyruvate (with decreasing µCO2) and phosphoenolpyruvate - oxaloacetate (with increasing µCO2) parageneses. In general, increasing the CO2 chemical potential leads to the carboxylation of compounds and their association with the formation of nodal facies - the center of phosphorus metabolism (malate - oxaloacetate – phosphoenolpyruvate). In this facies, as depicted in the diagram (Figures 3 and 4), the autocatalytic oxaloacetate - phosphoenolpyruvate paragenesis is also a "paragenesis bifurcation", meaning that this paragenesis determines the direction of natural selection of the primitive gluconeogenesis and CO2 fixation metabolic pathways. According to Figure 1, phosphoenolpyruvate, oxaloacetate, and pyruvate assemblage are "turnstile - like" chemical mechanisms, allowing the direction of development of metabolic systems to change. Conclusion it to assume is reasonable The energy processes within the living cells are chiefly determined by an element such as phosphorus, and phosphates play a crucial role in the activation of organic molecules through phosphorylation. Therefore, types of phosphorylated compounds also played a major role in the formation of the first protometabolic systems on the early Earth. 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