The Stepwise Evolution of Early Life Driven by Energy Conservation
James G. Ferry* and Christopher H. House *Department of Biochemistry and Molecular Biology and Pennsylvania State Astrobiology Research Center, 205 South Frear
Laboratory, Pennsylvania State University; and Department of Geosciences and Pennsylvania State Astrobiology Research Center,
220 Deike Building, Pennsylvania State University
Two main theories have emerged for the origin and early evolution of life based on heterotrophic versus chemoautotrophic
metabolisms. With the exception of a role for CO, the theories have little common ground. Here we propose an alternative
theory for the early evolution of the cell which combines principal features of the widely disparate theories. The theory is
based on the extant pathway for conversion of CO to methane and acetate, largely deduced from the genomic analysis of the
archaeon Methanosarcina acetivorans. In contrast to current paradigms, we propose that an energy-conservation pathway
was the major force which powered and directed the early evolution of the cell. We envision the proposed primitive energyconservation pathway to have developed sometime after a period of chemical evolution but prior to the establishment of
diverse protein-based anaerobic metabolisms. We further propose that energy conservation played the predominant role in
the later evolution of anaerobic metabolisms which explains the origin and evolution of extant methanogenic pathways.
Introduction
The heterotrophic theory for the origin of life (Lazcano
and Miller 1999; Bada and Lazcano 2002) purports that life
arose from an ‘‘organic soup’’ of diverse preexisting compounds. The theory is supported experimentally by the abiotic synthesis of diverse biologically important compounds
starting from reduced gases (Miller 1998), including CO
(Pinto, Gladstone, and Yung 1980; Chameides and Walker
1981; Miyakawa et al. 2002), and the view that the earth’s
atmosphere at the time of the origin of life could have contained significant amounts of CO (Holland 1984; Kasting
1990; Kharecha, Kasting, and Siefert 2005), especially,
if the hydrogen escape rates were low (Tian et al. 2005;
Pavlov, Toon, and Feng 2006). The heterotrophic theory
is also derived from the metabolism of extant fermentative
organisms which metabolize reduced organic compounds
for the synthesis of adenosine triphosphate (ATP) by
substrate-level phosphorylation (SLP) (Lazcano and Miller
1999). A widely accepted challenge to this theory is that
life had a chemoautotrophic origin (Russell et al. 1988;
Wachtershauser 1988; Russell and Hall 1997) in which
the primary prebiotic initiation reaction for carbon fixation
was the surface-catalyzed synthesis of an acetate thioester
from CO and H2S driven by a geochemical energy source.
Central to the chemoautotrophic theory is the evolution
of biological CO2 fixation pathways in primitive cells
for which there are two views. One view is that a variation of the extant reduced citric acid cycle evolved first
(Wachtershauser 1990), whereas the other view suggests
a primitive form of the extant Wood-Ljungdahl pathway
(Wachtershauser 1997; Pereto et al. 1999; Martin and
Russell 2003; Russell and Martin 2004) in which 2CO2
molecules are reduced to acetyl-coenzyme A (CoA).
With the exception of a role for CO, the heterotrophic
and chemoautotrophic theories have little common ground.
Proponents of each theory continue to argue steadfastly for
the principles which separate them (Wachtershauser 2002).
In the debate, far less attention has been given to the role
Key words: Methanosarcina acetivorans, energy conservation, methanogenesis, acetate kinase, phosphotransacetylase.
E-mail: [email protected].
Mol. Biol. Evol. 23(6):1286–1292. 2006
doi:10.1093/molbev/msk014
Advance Access publication March 31, 2006
Ó The Author 2006. Published by Oxford University Press on behalf of
the Society for Molecular Biology and Evolution. All rights reserved.
For permissions, please e-mail: [email protected]
that energy conservation could have played in the early
stages for the evolution of life and metabolic pathways. Although inherent to the heterotrophic theory, a major role for
SLP in the chemoautotrophic theory has not been advanced.
It has been suggested that the earliest chemoautotrophic
organisms conserved energy by a chemiosmotic mechanism in which ATP synthesis was driven by a naturally occurring geochemical pH gradient (Russell and Hall 1997).
Here we propose a novel cyclic SLP energy-conserving
pathway that functioned in primitive cells. Further, the cells
feature a combination of principles that have separated the
two main contrasting theories for the origin of life (Lazcano
and Miller 1999; Martin and Russell 2003; Russell and
Martin 2004). Although our primitive cell requires the abiotic synthesis of diverse organic compounds for biosynthesis of cell material that is a tenet of the heterotrophic theory
(Miller and Bada 1988), the ‘‘primary’’ energy source is
geochemical that is also a feature of the chemoautotrophic
hypothesis (Wachtershauser 1988). Moreover, we propose
that the cyclic SLP energy-conserving pathway was the
main driving force directing the evolution of primitive
metabolisms and extant energy-yielding pathways, reshaping current theories for the early evolution of life.
Materials and Methods
Analysis of the Methanosarcina acetivorans strain
C2A genome (Galagan et al. 2002) was performed with
the sequence available at The Institute for Genomic
Research (TIGR) Web site (http://pathema.tigr.org/tigrscripts/CMR/CmrHomePage.cgi) using the Comprehensive Microbial Resource bioinformatics tools previously
described (Peterson et al. 2001). All annotations reported
were the primary annotations listed on the TIGR Web site.
Results and Discussion
The Pathway for CO Utilization by M. acetivorans C2A
A popular approach for development of theories for
the origins of metabolisms is the conceptual reconstruction
from extant pathways. Extant CO metabolisms of ancient
microbial lineages have the potential to reveal characteristics
of primitive metabolic pathways. Strictly anaerobic methaneproducing Archaea (methanoarchaea) are particularly attractive for predicting ancient pathways. Phylogenetic analysis
Stepwise Evolution of Early Life 1287
indicates that methanogenic Archaea are ancient (Bapteste, Brochier, and Boucher 2005), appearing prominent
among the deepest branching chemoautotrophs on the tree
of life (Kandler 1993) and dating to perhaps 3.8–4.1 billion years ago (Battistuzzi, Feijao, and Hedges 2004). The
phylogenetic analyses are supported by recent evidence
for biologically produced methane in 3.5 billion-yearold hydrothermal precipitates (Ueno et al. 2006).
Further, a few species of methanoarchaea utilize CO as
a growth substrate. It was recently reported that M. acetivorans C2A has a highly unusual energy-yielding metabolism producing methane, acetate, and formate during
CO-dependent chemoautotrophic growth (Rother and
Metcalf 2004).
Figure 1 shows the pathway proposed for conversion
of CO to acetate and methane based on the genomic analysis of M. acetivorans C2A and experimental results.
Step 1 involves oxidation of CO to CO2 providing electrons for the reduction of CO2 to CH3-tetrahydromethanopterin (THMPT) (steps 2–6) in analogy to the wellcharacterized pathway for CO2 reduction to methane with
electrons derived from the oxidation of H2 in species
other than M. acetivorans C2A (Ferry 1999). Methane
is produced from CH3-THMPT in steps 7–9, steps common to all known pathways for methanogenesis (Ferry
1999). The genomic sequence of M. acetivorans C2A
is annotated for genes encoding enzymes catalyzing steps
2–9 (table 1), supporting the proposed pathway. Genes
annotated to encode both the molybdenum and tungsten
forms of the formyl-methanofuran (MF) dehydrogenase
were identified in the genome. However, genes encoding
the H2-dependent methylene-THMPT reductase were not
found, consistent with the inability of M. acetivorans to
reduce CO2 to methane with H2. Further, proteomic analyses of CO-grown M. acetivorans C2A (in preparation)
has provided experimental evidence for abundant synthesis of enzymes catalyzing steps 2–9. The genome is
also annotated with genes encoding CooS (table 1),
a CO dehydrogenase with the potential to catalyze step 1;
however, the CO dehydrogenase/acetyl-CoA synthetase
proposed to catalyze step 10 (see below) could also function in step 1.
Acetate is produced from CH3-THMPT in the proposed pathway (steps 10–12, fig. 1) by reversal of the first
three steps in the well-characterized pathway for methane
formation from acetate in other Methanosarcina species
(Ferry 2003). In the acetate pathway, the five-subunit
CO dehydrogenase/acetyl-CoA synthetase (CdhABCDE)
reversibly cleaves acetyl-CoA producing CH3-THMPT,
a carbonyl group, and CoA. Indeed, it has been proposed
(Rother and Metcalf 2004) that the CdhABCDE complex
condenses the methyl group of CH3-THMPT with CO
and CoA to synthesize acetyl-CoA in step 10 (fig. 1). The
reported synthesis of acetyl-CoA from CO, CH3I, and
CoA by CdhABCDE from Methanosarcina thermophila
(Abbanat and Ferry 1990) further supports a role for this
complex in the proposed pathway (fig. 1). The acetylCoA is converted to acetate by phosphotransacetylase
(Pta) in step 11 and acetate kinase (Ack) in step 12 with
the synthesis of ATP by SLP. The genome is annotated with
pta, ack, and duplicate cdhABCDE operons (MA1011–
FIG. 1.—Proposed pathways for methane and acetate formation from
CO by Methanosarcina acetivorans C2A. MF, methanofuran; THMPT,
tetrahydromethanopterin; CoM, coenzyme M; and CoB, coenzyme B.
MA1016 and MA3860–MA3865, table 1). Further, proteomic analyses identify Pta, Ack, and subunits of both
CdhABCDE complexes in CO-grown M. acetivorans
C2A (in preparation). Finally, M. acetivorans C2A variants
with the ack and pta genes disrupted are unable to grow
with CO (Rother and Metcalf 2004), a result that further
supports a role for these enzymes in the proposed pathway
(fig. 1). Thus, the results suggest that Ack plays a prominent
role in the energy metabolism of CO-grown M. acetivorans.
Indeed, the energy available for ATP synthesis during conversion of CO to acetate (eq. 1) is comparable to that for
conversion of CO to methane (eq. 2).
4CO 1 2H2 O/2CO2
1 CH3 COOHðDG°# 5 165 kJ=molÞ:
ð1Þ
4CO 1 2H2 O/3CO2
1 CH4 ðDG°# 5 211 kJ=molÞ:
ð2Þ
A role for Ack in the energy-yielding metabolism of the
methanoarchaea is reinforced by the nonmethanogenic
growth of Methanosarcina barkeri with pyruvate for which
the sole mechanism of ATP synthesis is by SLP when
acetyl-CoA is converted to acetate by Pta and Ack (Bock
and Schonheit 1995). The finding that Ack and Pta function
in SLP pathways of chemolithoautotrophic methanoarchaea is consistent with a role for SLP in a chemoautotrophic
origin of life.
1288 Ferry and House
Table 1
Genes Identified in the Methanosarcina acetivorans Strain
C2A Genomic Sequence Encoding Enzymes and Proteins in
the Proposed Pathway for Acetate and Methane Formation
from Carbon monoxide
Gene
Symbol
Open
Reading
Frame
3
4
5
6
cooS
cooS
fmdE
fmdF
fmdA
fmdC
fmdD
fmdB
fwdE
fwdG
fwdC
fwdA
fwdB
fwdG
fwdB
fwdD
fwdA
fmdF
fmdA
fmdD
fmdB
fwdB
ftr
mch
mtd
mer
1309
3282
0304
0305
0306
0307
0308
0309
0381
0671
0832
0833
0834
2877
2878
2879
4174
4175
4176
4177
4178
4602
0010
1710
4430
3733
7
mtrH
0269
mtrG
0270
mtrF
0271
mtrA
0272
mtrB
0273
mtrC
0274
mtrD
0275
mtrE
0256
mcrA
mcrG
mcrB
hdrD
hdrE
hdrD
cdhE
4546
4547
4550
0526
0687
0688
1011
cdhD
1012
cdhC
1014
cdhB
1015
cdhA
1016
cdhA
3860
cdhB
3861
cdhC
3862
cdhD
3864
cdhE
3865
pta
ack
3607
3606
Stepa
1
2
8
9
10
11
12
a
See figure 1.
Annotation
CO dehydrogenase
CO dehydrogenase
(Mo) formyl-MF dehydrogenase, subunit E
(Mo) formyl-MF dehydrogenase, subunit F
(Mo) formyl-MF dehydrogenase, subunit A
(Mo) formyl-MF dehydrogenase, subunit C
(Mo) formyl-MF dehydrogenase, subunit D
(Mo) formyl-MF dehydrogenase, subunit B
(W) formyl-MF dehydrogenase, subunit E
(W) formyl-MF dehydrogenase, subunit G
(W) formyl-MF dehydrogenase, subunit C
(W) formyl-MF dehydrogenase, subunit A
(W) formyl-MF dehydrogenase, subunit B
(W) formyl-MF dehydrogenase, subunit G
(W) formyl-MF dehydrogenase, subunit B
(W) formyl-MF dehydrogenase, subunit D
(W) formyl-MF dehydrogenase, subunit A
(Mo) formyl-MF dehydrogenase, subunit F
(Mo) formyl-MF dehydrogenase, subunit A
(Mo) formyl-MF dehydrogenase, subunit D
(Mo) formyl-MF dehydrogenase, subunit B
(W) formyl-MF dehydrogenase, subunit B
Formyl-MF:THMPT formyl transferase
Methenyl-THMPT cyclohydrolase
Methylene-THMPT dehydrogenase
Methylene-THMPT reductase (coenzyme
F420-dependent)
Methyl-THMPT:HS-CoM methyl
transferase, subunit H
Methyl-THMPT:HS-CoM methyl
transferase, subunit G
Methyl-THMPT:HS-CoM methyl
transferase, subunit F
Methyl-THMPT:HS-CoM methyl
transferase, subunit A
Methyl-THMPT:HS-CoM methyl
transferase, subunit B
Methyl-THMPT:HS-CoM methyl
transferase, subunit C
Methyl-THMPT:HS-CoM methyl
transferase, subunit D
Methyl-THMPT:HS-CoM methyl
transferase, subunit E
Methyl-CoM reductase, subunit alpha
Methyl-CoM reductase, subunit gamma
Methyl-CoM reductase, subunit beta
Heterodisulfide reductase, subunit D
Heterodisulfide reductase, subunit E
Heterodisulfide reductase, subunit D
CO dehydrogenase/acetyl-CoA synthetase,
subunit epsilon
CO dehydrogenase/acetyl-CoA synthetase,
subunit delta
CO dehydrogenase/acetyl-CoA synthetase,
subunit gamma
CO dehydrogenase/acetyl-CoA synthetase,
subunit beta
CO dehydrogenase/acetyl-CoA synthetase,
subunit alpha
CO dehydrogenase/acetyl-CoA synthetase,
subunit alpha
CO dehydrogenase/acetyl-CoA synthetase,
subunit beta
CO dehydrogenase/acetyl-CoA synthetase,
subunit gamma
CO dehydrogenase/acetyl-CoA synthetase,
subunit delta
CO dehydrogenase/acetyl-CoA synthetase,
subunit epsilon
Phosphotransacetylase
Acetate kinase
A Primitive Cyclic SLP Pathway for an Early Cell
The pathway in figure 1 provides a unique perspective
for proposing an alternative to primitive metabolisms predicted by either of the two leading theories for the origin of
life (Martin and Russell 2003; Russell and Martin 2004).
We propose that a cyclic SLP pathway (fig. 2A), with combined features of the heterotrophic and chemoautotrophic
theories, evolved early and had a prominent role in the evolution of diverse metabolisms. We envision that this pathway evolved sometime after a period of chemical evolution
(possibly including an ‘‘RNA World’’; Joyce 2002) but before the establishment of diverse protein-based biochemistries. The pathway features the catalysis of steps B and C
(fig. 2A) by ancestors of extant Pta and Ack wherein ATP is
synthesized by SLP, although ATP could have been
replaced with pyrophosphate (de Duve 1991; de Zwart,
Meade, and Pratt 2004). Further, a one-step conversion
of CH3COSR to acetate and ATP catalyzed by an ancestor
of acetate thiokinase cannot be ruled out; nonetheless, the
major implications of the pathway are unchanged. We suggest that the SLP pathway was operative in primitive lipidencapsulated cells (fig. 2A), closely associated with sulfide
minerals. The acetic acid and R-SH excreted by the cell is
converted back to the CH3COSR thioester in an abiotic
reaction outside the lipid membrane (step A; fig. 2A).
The synthesis of CH3COSR from CO, R-SH, and CH3SH
(broken arrow, fig. 2A) is not part of the cyclic energyconserving pathway (steps A–C) and functions only to
prime the pathway and supply acetyl groups for biosynthesis. Step A and the priming reaction (broken arrow, fig. 2)
are grounded in the previously proposed geochemicaldriven surface-catalyzed synthesis of acetate thioesters
from CO and CH3SH, a primary tenet of the chemoautotrophic theory (Heinen and Lauwers 1996; Huber and
Wachtershauser 1997; Martin and Russell 2003). Thus,
Step A is proposed to occur adjacent to the cell membrane
on the surface of FeS/NiS minerals analogous to the Fe-SNi active site of the CdhABCDE complex (step 10, fig. 1)
where an acetyl group is condensed with CoA-SH to form
CH3COSCoA (Drennan, Doukov, and Ragsdale 2004). Our
model also uses geochemical energy, consistent with previously proposed abiotic acetate thioester synthesis driven
by an exergonic ‘‘pyrite-pulled’’ reaction in which FeS and
H2S are converted to FeS2 and H2 (Wachtershauser 1988,
1992). Thus, the pathway in figure 2A (steps A–C) is a biogeochemical cycle in which the primary energy source is
geochemical (step A), and primitive enzymes conserve
this energy by SLP (steps B and C). The cyclic pathway
would have circumvented the previously discussed problem of instability of the CH3COSR thioester (Huber and
Wachtershauser 1997; Russell and Martin 2004) by the ensuing enzyme-catalyzed conversion to acetyl-phosphate
and acetate (steps B and C). Further, the cyclic pathway
ensures a steady supply of substrates for pyrite-pulled abiotic synthesis of the thioester immediately outside the cell.
Support for this externally driven cycle can be found in the
extant archaeon Pyrodictium occultum that accumulates
pyrite outside the cell during growth by sulfur respiration
(Stetter, Konig, and Stackebrandt 1983). One explanation
previously offered is that P. occultum forms pyrite outside
Stepwise Evolution of Early Life 1289
FIG. 2.—Proposal for a cyclic energy-conserving pathway that functioned in the primitive (panel A) and chemoautotrophic cell independent of
surface-catalyzed reactions (panel B). The stippled areas represent the lipid membranes. Pi represents inorganic phosphate. Panel A: solid lines indicate
the cyclic pathway (steps A–C). The broken arrow indicates the priming reaction that is not part of the cyclic pathway. Panel B: THMPT, tetrahydromethanopterin.
the cell by reaction of Fe21 in the medium with the excreted
metabolic end product H2S to obtain additional energy for
growth (Stetter, Konig, and Stackebrandt 1983).
The cyclic energy-conserving pathway (steps A–C,
fig. 2A) is not dependent on oxidation of a preexisting reduced organic compound to generate ATP that is central to
extant fermentations and a precept of the heterotrophic theory for the origin of life. The pathway is also not dependent
on redox chemistry and chemiosmosis for energy conservation that has been suggested for the chemoautotrophic
theory (Martin and Russell 2003). Thus, the pathway incorporates SLP and surface-catalyzed reactions that are,
respectively, prominent features of the widely disparate heterotrophic and chemoautotrophic theories.
In our view, the proposed cyclic SLP pathway (fig. 2A)
was of major importance in evolution of the cell, and
evolved prior to autotrophic carbon fixation pathways,
which contrasts with currently proposed chemoautotrophic
theories (Wachtershauser 1990; Martin and Russell 2003;
Russell and Martin 2004). We suggest that the pathway
necessarily evolved early to supply an energy ‘‘currency’’
that drove and directed coevolution of primitive energydependent biosynthetic pathways utilizing the previously
proposed diversity of precursor compounds synthesized
in prebiotic reactions. We further suggest that the SLP pathway was the first protein-based energy-conserving metabolic cycle and was an early event in the evolution of
diverse primitive metabolisms. This view is supported by
the simplicity of the pathway involving only two enzymes
which is in contrast to the more complicated membrane-
bound electron transport chain and multisubunit ATPase
complex inherent in the chemiosmotic mechanism previously proposed to have evolved in primitive cells (Martin
and Russell 2003). Recent crystal structures establish that
Ack and Pta are simple homodimers with no prosthetic
groups (Buss et al. 2001; Iyer et al. 2004). Further, the secondary structure of Ack suggests an ancient origin and the
founding member of the ASKHA superfamily of phosphotransferases (Buss et al. 2001). Thus, the pathway could
have been necessary for the early establishment of phosphoryl group transfer that is essential for diverse metabolic processes fundamental to all extant life. It has been proposed
that acetyl phosphate served as the first metabolic handle for
activated phosphate (de Duve 1991). Indeed, Ack from
Escherichia coli also transfers phosphate from acetyl phosphate to enzyme I of the bacterial phosphotransferase system (Fox, Meadow, and Roseman 1986). Thus, Pta and Ack
could have been among the first enzymes to have evolved.
In fact, it has been demonstrated that steps B and C occur
without enzymes (Weber 1981, 1982) that may have preceded de novo evolution of primitive ancestors to Pta
and Ack. Finally, de Duve (1991) also has postulated a nonenzymatic phosphorolysis of the thioester bond leading to
formation of acetyl phosphate.
A Central Role for the Primitive SLP Pathway in
Evolution of Early Metabolic Pathways
The proposed early evolution of the SLP energyconserving pathway (fig. 2A) reshapes current proposals
1290 Ferry and House
for the continuing evolution of life and early metabolic pathways (Martin and Russell 2003; Russell and Martin 2004).
Key to this reshaping is the transition to a cell (fig. 2A) independent of abiotic surface-catalyzed reactions. The initial
event in this transition is the evolution of a primitive ancestor
to the extant CdhABCDE complex that evolved catalysis of
C-S bond formation to accelerate the geochemical-driven
synthesis of CH3COSR from acetic acid and R-SH (step
A, fig. 2A) as an energy source. It has been proposed (Huber
and Wachtershauser 1997) that CdhABCDE evolved to catalyze the synthesis of CH3COSCH3 from CO and CH3SH
for cell carbon, analogous to the priming reaction (broken
arrow, fig. 2A) in which both a C-C and C-S bond is formed.
Here we modify this concept to propose instead that a primitive Cdh at first evolved only catalysis of C-S bond formation to assist the condensation of acetic acid and R-SH to
provide CH3COSR as an energy source (step A, fig. 2A).
Further evolution of additional subunits permitted the
Cdh to catalyze both C-C and C-S bond formation required
for the priming reaction (broken arrow, fig. 2A) characteristic of the extant CdhABCDE complex. However, at this
juncture, the primitive cell is still dependent on geochemistry as the sole source of energy (step A, fig. 2A). Thus, the
next proposed event is the evolution of enzymes catalyzing
steps 1–6 in the extant pathway (fig. 1) which grafted onto
the CdhABCDE complex and completely released the primitive cell from dependence on geochemical energy and the
surface-catalyzed abiotic synthesis of CH3COSR (fig. 2B).
These events coincided with the evolution of enzymes for
the synthesis of compounds starting from CH3COSR, feeding the biosynthetic pathways that coevolved earlier with the
SLP pathway proposed in figure 2A. In the scenario presented here, this early cell (fig. 2B) was chemoautotrophic
which is in fundamental agreement with the chemoautotrophic theory, albeit with four important exceptions. First, the
driving force for evolution of the Wood-Ljungdahl pathway
was to supply an energy source and only later became essential to supply CH3COSR for chemoautotrophic growth that
is a tenet of the chemoautotrophic theory. Further, although
H2 has been proposed as the first electron donor in the WoodLjungdahl pathway (Russell and Martin 2004), CO is preferred based on the unfavorable thermodynamics (eqs. 3
and 4) with H2 for step 2 in the pathway (fig. 1).
1
CO2 1 MF 1 H2 /CHO-MF 1 H2 O 1 H
ðDG°# 5 1 16 kJ=molÞ:
1
CO 1 MF /CHO-MF 1 H
ðDG°# 5 4 kJ=molÞ:
1
ð3Þ
1
ð4Þ
Indeed, extant methanoarchaea require complex reverse
electron transport mechanisms to overcome the thermodynamic barrier with H2 as the electron donor (Stojanowic
and Hedderich 2004). Third, we propose that the chemoautotrophic cell inherited enzyme-catalyzed biosynthetic
pathways, which coevolved earlier with the primitive SLP
pathway, for the synthesis of complex cellular constituents.
Finally, in contrast to the more complex chemiosmotic mechanism espoused for the chemoautotrophic theory, we propose
that the first chemoautotrophic cell conserved energy by SLP
that drove biosynthesis. Thus, the early evolution of an SLP
FIG. 3.—Pathway for conversion of acetate to methane and carbon
dioxide.
energy-conserving pathway is proposed to have played a
previously unrecognized major role in early evolution.
At this juncture in the early evolution of life, it is proposed that the chemoautotrophic generation of complex
biomass would have provided growth substrates for the
evolution of primitive heterotrophic organisms that adopted
the conversion of acetyl-CoA to acetate for energy conservation. Indeed, the conversion of acetyl-CoA to acetate and
ATP is a staple of energy conservation in extant fermentative species from both the Archaea and Bacteria domains
(Gottschalk 1985). The vast majority of extant fermentation
pathways oxidize a variety of reduced substrates to acetylCoA as the common intermediate, consistent with the SLP
pathway of chemoautotrophic cells anchoring the evolution
of diverse extant fermentations. Included among these
fermentations is homoacetogenesis which employs the bacterial version of the Wood-Ljungdahl pathway. Although
similar to the archaeal version, the bacterial version
depends on ATP for the first step, employs different cofactors, and functions to dispose of electrons generated by oxidation of the substrate by reducing 2CO2 to acetyl-CoA
(Gottschalk 1985). Thus, we propose that the bacterial version of the Wood-Ljungdahl pathway evolved later for
a purpose different from the archaeal version. The next proposed event is the evolution of ATPase and membranebound electron transport from CO to one or more of the
reductive steps of the Wood-Ljungdahl pathway (steps 2,
5, or 6; fig. 1) which lead to a chemiosmotic mechanism
for ATP synthesis. The grafting of ancestral enzymes catalyzing steps 7–9 (fig. 1) onto steps 1–6 of the ancestral
Wood-Ljungdahl pathway are postulated to have evolved
the CO2 reduction pathway for methanogenesis (steps
1–9, fig. 1) that is strictly dependent on chemiosmosis
for ATP synthesis (Deppenmeier, Muller, and Gottschalk
1996). No longer dependent on SLP, the addition of hydrogenase and abandonment of Pta and Ack lead to the
H2-oxidizing CO2-reducing methanogenesis pathway typical of most extant methanoarchaea. Thus, the branched
pathway leading to both acetate and methane in figure 1
may represent a relic of evolution which existed at the time
of transition from SLP to chemiosmosis that was preserved
in the Methanosarcina. Finally, the simple reversal of steps
10–12 (fig. 1) coupled with steps 7–9 is postulated to have
evolved the pathway for methanogenesis from acetate
(fig. 3) that was produced by fermentative anaerobes
Stepwise Evolution of Early Life 1291
(Ferry 2003). Thus, the SLP energy-conserving pathway directed and powered the early evolution of anaerobic energyyielding pathways that also provided the foundation for
evolution of energy-yielding pathways in extant anaerobic
and aerobic organisms from all three domains of life.
In conclusion, an alternative for the early evolution
of life is offered that combines principles of the two most
popular albeit widely disparate theories. Further, in contrast
to both popular theories, it is proposed that the early evolution of a primitive energy-conserving cycle drove and directed the early evolution of fundamental metabolic
pathways. The alternative theory reshapes features of the
first chemoautotrophic cell predicted by popular theory
and explains the origin and evolution of extant methanogenic pathways.
Acknowledgments
This work was supported by Department of Energy
Grant No. DE-FG02-95ER20198 (J.G.F.), the National
Aeronautics and Space Administration (NASA) Astrobiology Institute (J.G.F. and C.H.H.), and NASA Grant No.
NNG05GN50G (C.H.H.).
Literature Cited
Abbanat, D. R., and J. G. Ferry. 1990. Synthesis of acetyl-CoA by
the carbon monoxide dehydrogenase complex from acetategrown Methanosarcina thermophila. J. Bacteriol. 172:7145–
7150.
Bada, J. L., and A. Lazcano. 2002. Origin of life. Some like it hot,
but not the first biomolecules. Science 296:1982–1983.
Bapteste, E., C. Brochier, and Y. Boucher. 2005. Higher-level
classification of the Archaea: evolution of methanogenesis
and methanogens. Archaea 1:353–363.
Battistuzzi, F. U., A. Feijao, and S. B. Hedges. 2004. A genomic
timescale of prokaryote evolution: insights into the origin of
methanogenesis, phototrophy, and the colonization of land.
BMC Evol. Biol. 4:44.
Bock, A. K., and P. Schonheit. 1995. Growth of Methanosarcina
barkeri (fusaro) under nonmethanogenic conditions by the fermentation of pyruvate to acetate: ATP synthesis via the mechanism of substrate level phosphorylation. J. Bacteriol.
177:2002–2007.
Buss, K. A., D. R. Cooper, C. Ingram-Smith, J. G. Ferry, D. A.
Sanders, and M. S. Hasson. 2001. Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases. J. Bacteriol. 183:680–686.
Chameides, W. L., and J. C. G. Walker. 1981. Rates of fixation by
lightning of carbon and nitrogen in possible primitive atmospheres. Origins Life 11:291.
de Duve, C. 1991. Blueprint for a cell. Neil Patterson,
Burlington, N.C.
Deppenmeier, U., V. Muller, and G. Gottschalk. 1996. Pathways
of energy conservation in methanogenic archaea. Arch. Microbiol. 165:149–163.
de Zwart, I. I., S. J. Meade, and A. J. Pratt. 2004. Biomimetic phosphoryl transfer catalyzed by iron(II)-mineral precipitates. Geochim. Cosmochim. Acta 68:4093–4098.
Drennan, C. L., T. I. Doukov, and S. W. Ragsdale. 2004. The metalloclusters of carbon monoxide dehydrogenase/acetyl-CoA
synthase: a story in pictures. J. Biol. Inorg. Chem. 9:511–515.
Ferry, J. G. 1999. Enzymology of one-carbon metabolism in methanogenic pathways. FEMS Microbiol. Rev. 23:13–38.
———. 2003. One-carbon metabolism in methanogenic anaerobes. Pp. 143–156 in L. G. Ljungdahl, M. W. Adams, L.
L. Barton, J. G. Ferry, and M. K. Johnson, eds. Biochemistry
and physiology of anaerobic bacteria. Springer-Verlag,
New York.
Fox, D. K., N. D. Meadow, and S. Roseman. 1986. Phosphate
transfer between acetate kinase and enzyme I of the bacterial
phosphotransferase system. J. Biol. Chem. 261:13498–
13503.
Galagan, J. E., C. Nusbaum, A. Roy et al. (55 co-authors). 2002.
The genome of M. acetivorans reveals extensive metabolic and
physiological diversity. Genome Res. 12:532–542.
Gottschalk, G. 1985. Bacterial metabolism. Springer-Verlag,
New York.
Heinen, W., and A. M. Lauwers. 1996. Organic sulfur compounds
resulting from the interaction of iron sulfide, hydrogen sulfide
and carbon dioxide in an anaerobic aqueous environment. Origins Life Evol. Biosph. 26:131–150.
Holland, H. D. 1984. Chemical evolution of the atmosphere and
oceans. Pp. 29–59. Princeton University Press, Princeton, N.J.
Huber, C., and G. Wachtershauser. 1997. Activated acetic acid
by carbon fixation on (Fe,Ni)S under primordial conditions.
Science 276:245–247.
Iyer, P. P., S. H. Lawrence, K. B. Luther, K. R. Rajashankar, H. P.
Yennawar, J. G. Ferry, and H. Schindelin. 2004. Crystal structure of phosphotransacetylase from the methanogenic archaeon
Methanosarcina thermophila. Structure 12:559–567.
Joyce, G. F. 2002. The antiquity of RNA-based evolution. Nature
418:214–221.
Kandler, O. 1993. The early diversification of life. Pp. 152–160 in
S. Bengtson, ed. Early life on earth. Nobel Symposium 84. Columbia University Press, New York.
Kasting, J. F. 1990. Bolide impacts and the oxidation state of carbon in the earth’s early atmosphere. Origins Life Evol. Biosph.
20:199–231.
Kharecha, P., J. Kasting, and J. Siefert. 2005. A coupled
atmosphere-ecosystem model of the early Archean Earth.
Geobiology 3:53.
Lazcano, A., and S. L. Miller. 1999. On the origin of metabolic
pathways. J. Mol. Evol. 49:424–431.
Martin, W., and M. J. Russell. 2003. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes
to nucleated cells. Philos. Trans. R. Soc. Lond. B Biol. Sci.
358:59–85.
Miller, S. L. 1998. The endogenous synthesis of organic compounds. Pp. 59–85 in A. Brack, ed. The molecular origins
of life: assembling pieces of the puzzle. Cambridge University
Press, Cambridge.
Miller, S. L., and J. L. Bada. 1988. Submarine hot springs and the
origin of life. Nature 334:609–611.
Miyakawa, S., H. Yamanashi, K. Kobayashi, H. J. Cleaves, and
S. L. Miller. 2002. Prebiotic synthesis from CO atmospheres:
implications for the origins of life. Proc. Natl. Acad. Sci. USA
99:14628–14631.
Pavlov, A. A., O. B. Toon, and T. Feng. 2006. Methane runaway
in the early atmosphere—two stable climate states of the Archean? Astrobiology Science Conference, Washington, D.C.
Pereto, J. G., A. M. Velasco, A. Becerra, and A. Lazcano. 1999.
Comparative biochemistry of CO2 fixation and the evolution of
autotrophy. Internatl. Microbiol. 2:3–10.
Peterson, J. D., L. A. Umayam, T. Dickinson, E. K. Hickey, and O.
White. 2001. The comprehensive microbial resource. Nucleic
Acids Res. 29:123–125.
Pinto, J. P., G. R. Gladstone, and Y. L. Yung. 1980. Photochemical production of formaldehyde in earth’s primitive atmosphere. Science 210:183–185.
1292 Ferry and House
Rother, M., and W. W. Metcalf. 2004. Anaerobic growth of Methanosarcina acetivorans C2A on carbon monoxide: an unusual
way of life for a methanogenic archaeon. Proc. Natl. Acad. Sci.
USA 101:16929–16934.
Russell, M. J., and A. J. Hall. 1997. The emergence of life from
iron monosulphide bubbles at a submarine hydrothermal redox
and pH front. J. Geol. Soc. Lond. 154:377–402.
Russell, M. J., A. J. Hall, A. G. Cairns-Smith, and P. S. Braterman.
1988. Submarine hot springs and the origin of life. Nature
336:117.
Russell, M. J., and W. Martin. 2004. The rocky roots of the acetylCoA pathway. Trends Biochem. Sci. 29:358–363.
Stetter, K. O., H. Konig, and E. Stackebrandt. 1983. Pyrodictium
gen. nov., a new genus of submarine disc-shaped sulphur reducing archaebacteria growing optimally at 105°C. Syst. Appl.
Microbiol. 4:535–551.
Stojanowic, A., and R. Hedderich. 2004. CO2 reduction to the
level of formylmethanofuran in Methanosarcina barkeri is
non-energy driven when CO is the electron donor. FEMS Microbiol. Lett. 235:163–167.
Tian, F., O. B. Toon, A. A. Pavlov, and H. De Sterck. 2005. A
hydrogen-rich early earth atmosphere. Science 308:1014–
1017.
Ueno, Y., K. Yamada, N. Yoshida, S. Maruyama, and Y.
Isozaki. 2006. Evidence from fluid inclusions for microbial
methanogenesis in the early Archaean era. Nature 440:
516–519.
Wachtershauser, G. 1988. Pyrite formation, the first energy source
for life: a hypothesis. Syst. Appl. Microbiol. 10:207–210.
———. 1990. Evolution of the first metabolic cycles. Proc. Natl.
Acad. Sci. USA 87:200–204.
———. 1992. Groundworks for an evolutionary biochemistry: the
iron-sulphur world. Prog. Biophys. Mol. Biol. 58:85–201.
———. 1997. The origin of life and its methodological challenge.
J. Theor. Biol. 187:483–494.
———. 2002. Discussing the origin of life. Science 298:747–749.
Weber, A. L. 1981. Formation of pyrophosphate, tripolyphosphate, and phosphorylimidazole with the thioester, n,
s-diacetyl-cysteamine, as the condensing agent. J. Mol. Evol.
18:24–29.
———. 1982. Formation of pyrophosphate on hydroxyapatite with thioesters as condensing agents. Biosystems 15:
183–189.
William Martin, Associate Editor
Accepted March 29, 2006