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Biological conversion of carbon dioxide and hydrogen into liquid
fuels and industrial chemicals
Aaron S Hawkins1
, Patrick M McTernan2
, Hong Lian1
, Robert M Kelly1
and
Michael WW Adams2
Non-photosynthetic routes for biological fixation of carbon
dioxide into valuable industrial chemical precursors and fuels
are moving from concept to reality. The development of
‘electrofuel’-producing microorganisms leverages
techniques in synthetic biology, genetic and metabolic
engineering, as well as systems-level multi-omic analysis,
directed evolution, and in silico modeling. Electrofuel
processes are being developed for a range of
microorganisms and energy sources (e.g. hydrogen, formate,
electricity) to produce a variety of target molecules (e.g.
alcohols, terpenes, alkenes). This review examines the
current landscape of electrofuel projects with a focus on
hydrogen-utilizing organisms covering the biochemistry of
hydrogenases and carbonic anhydrases, kinetic and
energetic analyses of the known carbon fixation pathways,
and the state of genetic systems for current and prospective
electrofuel-producing microorganisms.
Addresses
1
Department of Chemical and Biomolecular Engineering, North Carolina
State University, Raleigh, NC 27695-7905, United States
2
Department of Biochemistry and Molecular Biology, University of
Georgia, Athens, GA 30602, United States
Corresponding author: Adams, Michael WW (adams@bmb.uga.edu)
Current Opinion in Biotechnology 2013, 24:376–384
This review comes from a themed issue on Energy biotechnology
Edited by Eric Toone and Han de Winde
For a complete overview see the Issue and the Editorial
Available online 16th March 2013
0958-1669/$ – see front matter, # 2013 Elsevier Ltd. All rights
reserved.
http://dx.doi.org/10.1016/j.copbio.2013.02.017
Introduction
There are intrinsic limitations to the production of biofuels
derived from photosynthetic organisms that impede the
development of a renewable liquid fuel industry at large-
scale. In particular, these include low efficiency of solar
energy conversion (Figure 1) and competition for agricul-
tural resources. Recent initiatives in the U.S. and else-
where have the objective of harnessing the molecular
mechanisms of non-photosynthetic organisms that can
utilize CO2 directly for the production of energy-dense
liquid fuels, which are now referred to as ‘electrofuels’
[1
,2,3
]. Electrofuel-producing microorganisms are being
developed that require the complementary expertise of
synthetic biologists, metabolic engineers, and microbiolo-
gists to equip native CO2-fixing species or autotrophs with
pathways fortargeted fuel production,or confer autotrophy
on heterotrophic host organisms, or both. The range of
possible sources currently being explored for low-poten-
tial, high-energy electrons to power an electrofuel process
includes hydrogen gas, formate, carbon monoxide and
electricity. This review will focus on electrofuel strategies
that use hydrogen gas as source of reducing power for CO2
fixation. Microorganisms that are able to use other sources
of electrons including electricity directly are discussed in
an accompanying review by Lovely [4]. A general scheme
for electrofuel productionfromhydrogenandCO2 isshown
in Figure 2.
CO2 fixation
The reduction of CO2, the most oxidized form of carbon,
into technologically useful organic compounds remains a
daunting task for abiological chemical catalysis. There
are, currently, six naturally occurring biological pathways
for carbon fixation, and these have been reviewed exten-
sively in recent years [5
,6,7,8]. Each pathway has
unique features arising from the ecological and molecular
context in which it evolved. Although there are many
examples of CO2-fixing carboxylases that are utilized for
metabolic purposes other than carbon assimilation, such
as energy conservation, anaplerosis, and redox-balancing
[1
,2,3
,9
,10], this review will focus on the autotrophic
CO2 fixation pathways that are relevant for electrofuel
production in addition to the primary host microorgan-
isms that are currently being considered that use hydro-
gen (Table 1).
The most ubiquitous CO2-fixation pathway is the Calvin–
Benson–Bassham (CBB) cycle found in plants, algae,
cyanobacteria, purple bacteria, and also in some proteo-
bacteria, such as Ralstonia eutropha. R. eutropha is a meta-
bolically diverse, facultatively autotrophic bacterium that
can grow on sugars, fatty acids, amino acids, triacylglycer-
ides as well as on H2/CO2 [5
,6,7,8,11
]. Previous work
on R. eutropha has focused on its ability to store excess
carbon as polyhydroxyalkanoates [12,13] (PHAs) and now
efforts seek to divert carbon flux away from PHA storage
and into other molecular targets. For example, R. eutropha
is a proposed host for isobutanol production via the 2-
ketoisovalerate pathway for branched chain amino acid
synthesis [11
] from H2 and CO2. This strategy has
already been successfully used in E. coli to produce
Available online at www.sciencedirect.com
Current Opinion in Biotechnology 2013, 24:376–384 www.sciencedirect.com
Biological conversion of carbon dioxide and hydrogen Hawkins et al. 377
Figure 1
(a)
(b)
CH2OH
H2/CO2
H2/CO2
OH
OH
OH
OH
O
CBP
TBD
TBD
0.18-0.2%c1.8-2.4%b
10-13%e,f
50-70%f
50-70%f
15-20%d
PV
PS
4.5-6%
a
70-85%f
Wet-milling, EH
WEHP
WEHP
WEHP
SMR
Current Opinion in Biotechnology
Electrofuel production from H2 and CO2. (a) Comparison of overall photon-to-fuel efficiency of biofuels versus electrofuels. Percentages represent the
cumulative efficiency of solar energy conversion at different stages. Although the conversion efficiency of an electrofuel process is currently unknown,
the improved efficiency of solar hydrogen compared to photosynthetic sugars indicates that a solar electrofuel process would require less land area
than current biofuels. (b) Hydrogen inputs for electrofuels are highly flexible and generation strategies can include electrolysis of water by renewable
wind power, electrolysis of water by conventional electricity (e.g. coal), or by steam reformation of methane, shown with conversion efficiencies for
each process. Abbreviations: PS – photosynthesis, EH – enzymatic hydrolysis, PV – photovoltaic, WEHP – Water Electrolysis Hydrogen Production,
SMR – steam methane reformation, TBD – To be determined. a
Zhu et al. [76], b
Assuming grain starch represents 40% of total corn biomass, c
Conrado
et al. [1
], d
Parida et al. [77], e
Assuming 65% overall electrolysis efficiency, f
Holladay et al. [78].
Figure 2
H
+
H
2 NADP
+
NADPH
(1) Generating Reducing Power (2) Incorporation of Inorganic Carbon
Acetyl-CoA
Pyruvate
CO2
Fixation
(3) Microbial Synthesis
n-butanol
farnesene
long chain alkenes
isobutanol
HCO
3
_
CO
2
Current Opinion in Biotechnology
Schematic drawing of the primary biochemical modules involved in electrofuel formation. Intracellular reducing power is generated from hydrogen gas
via hydrogenase enzymes. Carbon fixation cycle incorporates inorganic carbon into central metabolism via key intermediates. Microbial synthesis of
the target fuel molecule proceeds via endogenous and/or engineered metabolic pathways.
www.sciencedirect.com Current Opinion in Biotechnology 2013, 24:376–384
isobutanol and other higher alcohols from sugars [14,15],
as well as in Clostridium cellulolyticum to produce isobu-
tanol from cellulose [16]. R. eutropha can also use electro-
chemically generated formate as the electron donor for
the production of isobutanol and 3-methyl-1-butanol
[1
,2,3
,17
]. In addition, R. eutropha is being used, in
conjunction with in situ electrochemical generation of
hydrogen via molybdenum polypryridyl-oxo catalysts
tethered to the cell surface, for production of various
molecules including n-butanol (via PHA biosynthesis),
farnesene (via isoprenoid biosynthesis) and long chain
alkanes (via fatty acid biosynthesis) [1
,2,3
,4,18
].
Anaerobic microorganisms that are known to fix CO2
typically use either the reductive TCA (rTCA) cycle
or the Wood–Ljungdahl (W–L) pathway. The most
energetically efficient pathway for CO2 fixation is the
W–L pathway, which is found exclusively in anaerobic,
acetogenic bacteria and methanogenic archaea
[5
,6,7,8,14,15]. Acetogenic bacteria are well-known
for their ability to grow on H2/CO2 or synthesis gas
(CO/H2) and produce acetate, but various species also
naturally generate ethanol, butyrate, butanol and 2,3-
butanediol as end-products [1
,2,3
,9
,10,16,19,20].
These organisms are obvious hosts for electrofuel
development, and already butanol production
has been engineered into Clostridium ljungdahlii
[5
,6,7,8,11
,17
,21
]. Acetogens, such as Sporomusa
ovata, are also being explored for their ability to grow
directly on graphite cathodes and accept electrons for
microbial synthesis [12,13,22].
The most recently discovered pathways for biological
CO2 fixation involve the production of 3-hydroxypropio-
nate (3HP), dicarboxylates (DC) and/or 4-hydroxybuty-
rate (4HB). One version is found in members of the
thermoacidophilic archaeal order Sulfolobales, which
includes species in the genera Sulfolobus and Metallo-
sphaera [5
,6,7,8,11
,23]. One turn of the cycle converts
two molecules of CO2 to acetyl-CoA using NADPH as the
electron donor with 3HP and 4HB as intermediates,
although studies using isotopically labeled substrates
showed that most of the carbon flux enters central metab-
olism via succinyl-CoA rather than acetyl-CoA
[9
,10,14,15,24]. The enzymatic details of this pathway
have recently been completed with the biochemical
characterization of an epimerase and a mutase
[11
,16,25], and the identification of the gene encoding
a CoA-ligase [26]. The 3HP/4HB pathway is being engin-
eered into a hyperthermophilic host, Pyrococcus furiosus,
for the production of n-butanol from H2/CO2 [3
,12,13],
where the nearly 308C difference between the optimal
growth temperature of P. furiosus (Topt = 988C) and M.
sedula (Topt = 738C) is being exploited for a temperature-
dependent production strategy. Around 708C, where the
enzymes from M. sedula are most active, P. furiosus
metabolism is virtually quiescent, thereby minimizing
the maintenance energy requirements for the host.
Recently, this temperature-dependent strategy was used
to produce 3HP in P. furiosus using the first three enzymes
of the 3HP/4HB pathway [27
].
One important characteristic intrinsic to the various CO2-
fixing pathways is the tolerance of the enzymes and redox
carrier molecules to oxygen. The CBB cycle, the 3HP
bicycle, and the 3HP/4HB cycle (with the exception of a
single enzyme, 4-hydroxybutyryl-CoA dehydratase) are
all oxygen-tolerant pathways that operate in aerobic
organisms. The rTCA cycle, the W–L pathway, and
the DC/4HB cycle are all found in anaerobic organisms;
these all utilize oxygen-sensitive reduced ferredoxin as an
electron carrier and contain oxygen-sensitive enzymes,
for example, CO dehydrogenase/acetyl-CoA synthase and
pyruvate synthase [6]. Some species of aerobic H2-oxidiz-
ing bacteria, such as Hydrogenobacter thermophilus, utilize
the rTCA cycle; however, they have special biochemical
adaptations to protect against oxic conditions [28]. In
practical terms, the requirement of O2 to support
microbial growth presents explosion safety challenges
to large-scale electrofuel production using hydrogen gas
as substrate. There are some reactor designs that try to
minimize the risk with aerobic electrofuels hosts (such as
Ralstonia) by keeping oxygen and hydrogen gases separ-
ate [11
]. Utilizing anaerobic hosts, such as Clostridium
spp. and P. furiosus, avoids the issue altogether. However,
a recent study of oxygen detoxification in P. furiosus
showed that the organism is remarkably aero-tolerant
(up to 8% O2 vol/vol). This property would be advan-
tageous in bioprocessing, especially under conditions
where maintaining strict anoxia is costly [11
,29].
378 Energy biotechnology
Table 1
Electrofuel producing hosts in development. The organisms listed utilize hydrogen or formate for the delivery of low-potential electrons,
and have either been reported to produce an electrofuel or are currently in development. R = reported, D = development
Organism Type Electron donor(s) CO2 fixation cycle Target products Status References
Ralstonia eutropha H16 Betaproteobacteria Electrochemically
generated H2
CBB cycle PHB, butanol, farnesene,
long-chain alkenes
D [18
]
Ralstonia eutropha H16 Betaproteobacteria H2 CBB cycle Isobutanol D [11
]
Pyrococcus furiosus Archaeon H2 3HP/4HB cycle from
M. sedula
n-butanol D [3
]
Clostridium ljungdahlii Acetogenic bacteria H2 W–L pathway n-butanol, ethanol R [21
]
Current Opinion in Biotechnology 2013, 24:376–384 www.sciencedirect.com
Computational analyses of CO2 fixation
The growing interest in biological carbon fixation for
microbial production of fuels and commodity chemicals
has led to extensive analysis of the thermodynamic and
kinetic characteristics of the six known pathways. Boyle
and Morgan performed flux analysis to determine the
carbon flux and energy demand for biomass synthesis
from CO2, using maximum biomass production as the
objective function [30
]. They found that the energetic
cost of common core metabolites varied across the differ-
ent routes for fixing CO2, indicating that certain pathways
may be more efficient at producing a given product from a
single precursor. On average, they found that the W–L
pathway and the rTCA cycle were the most energy
efficient routes, followed by the DC/4HB cycle, the
3HP/4HB cycle, the 3HP-bicycle, and lastly the CBB
pathway. The same trend has been observed in other flux
balance analyses [31].
Another thermodynamic analysis of carbon fixation reac-
tions examined the ATP requirement and the reduction
potential of electron carriers, as well as other factors,
including the form and concentration of inorganic carbon,
and the associated effects of cellular pH and ionic
strength [32
]. Several possible explanations were put
forward to account for the differences in the ATP
required by the various pathways that are, in most cases,
higher than that required to make the net reaction ther-
modynamically feasible. One common explanation for
this is based on the different electron carriers used. For
example, ferredoxin (Eo’  À400 mV) has a lower
reduction potential than NAD(P)H (Eo’ = À320 mV),
but the extra energetic contribution of oxidizing two
ferredoxin molecules compared to one NADPH molecule
under standard conditions ($20 kJ molÀ1
) does not equal
the energy released by ATP hydrolysis (over 50 kJ molÀ1
)
[33]. Moreover, this effect is not enough to account for the
large differences in ATP cost for pyruvate formation
between, for example, the rTCA cycle (2 ATP) and
the 3HP bicycle (7 ATP) [5
].
A closer look at the thermodynamics of the individual
reactions in carbon fixation pathways helped to further
elucidate the local thermodynamic constraints that shape
the overall energetics and revealed a characteristic pat-
tern in the reaction profile of carbon fixation enzymes
[34
]. Inspection of the reduction potentials of half-
reactions in carbon fixation pathways reveals generalized
groupings of reactions based on reaction type. It is
specifically the carboxylation and carboxyl reduction
reactions that are the most energetically unfavorable in
the pathway and thus require most of the energetic push
to overcome. This is accomplished either directly by
coupling the reaction to energy release from ATP
hydrolysis, or indirectly by coupling hydrolysis of another
high-energy bond (e.g. thioester) to the energetically
unfavorable reaction. Almost all of the ATP investments
in each carbon fixation pathway are coupled directly or
indirectly to carboxylation and carboxyl reduction reac-
tions. Some pathways manage to reduce the ATP require-
ments of carbon fixation by coupling unfavorable
reactions to exergonic reactions other than ATP hydroly-
sis. In the case of the W–L pathway in acetogens, this
strategy is used to reduce the ATP investment to a single
ATP molecule during the formation of pyruvate [5
].
Synthetic pathways are not limited by the enzymatic
profile of naturally occurring pathways. Rather, the pro-
spect of combining enzymes in novel ways holds promise
for improving the efficiency of the pathway or reducing
the energetic cost. Using a constraint-based modeling
approach and drawing from the entire set of approxi-
mately 5000 known metabolic enzymes, Bar-Even et al.
predicted in silico pathways with faster kinetic rates than
naturally occurring ones [35]. They describe a family of
synthetic pathways that utilize PEP carboxylase and the
core of the C4 cycle in plants, which they term the ‘C4-
glyoxylate cycles’. These pathways all produce glyoxy-
late, which is assimilated to central metabolism via the
bacterial-like glycerate pathway, and are predicted to
have overall rates of CO2 to product formation that are
2–3 times faster than that of the CBB pathway. However,
these rates are still lower than those reported for the
rTCA, DC/4HB, and 3HP/4HB cycles.
In addition to the enzymes that catalyze carboxylations
and the carboxyl reduction reactions, the conversion of
CO2 and hydrogen to electrofuels is also dependent on
the two enzymes that activate these two gases, namely,
carbonic anhydrase and hydrogenase, respectively. In the
following the properties of these two enzymes relevant to
electrofuel production will be considered.
Hydrogen utilization
Hydrogen is used as a source of energy by microorganisms
from all three domains of life [36] and is activated by
hydrogenase, which catalyzes the reversible interconver-
sion of molecular hydrogen and protons in the presence of
a suitable electron carrier. Based on structural and bio-
chemical analysis, hydrogenases can be categorized by
the metal atoms in their active sites: [NiFe]-hydroge-
nases, [FeFe]-hydrogenases, and [Fe]-hydrogenases
[37,38]. Since electrofuel hosts containing CO2 fixation
pathways need to coordinate acquisition of reductant with
carbon flux, the types of hydrogenase present in the host
microorganism and the electron carriers that they use are
of paramount importance.
Extensive work on [NiFe]-hydrogenases from Desulfovi-
brio gigas [39–43] and the [FeFe]-hydrogenases from
Clostridium pasteurianum [44] and Desulfovibrio desulfuri-
cans [45] has shown that both enzyme types harbor deeply
buried active sites in which the site of H2 reactivity is a
single iron atom coordinated by diatomic ligands (carbon
Biological conversion of carbon dioxide and hydrogen Hawkins et al. 379
www.sciencedirect.com Current Opinion in Biotechnology 2013, 24:376–384
monoxide and cyanide). In the [NiFe]-enzymes, the iron
is also coordinated to a nickel atom, while in the [FeFe]-
hydrogenases it is bound by a second iron atom and linked
to a 4Fe-cluster. Both types of enzyme also contain
multiple [4Fe-4S] clusters, as well as hydrophobic gas
channels, that connect the catalytic sites to the molecular
surface [46]. These two enzymes differ with respect to
their distribution in nature, sensitivity to oxygen deacti-
vation, and in the assembly and maturation of their
catalytic sites [47]. For example, [NiFe]-hydrogenases
are widespread among bacteria and archaea, the [FeFe]-
enzymes are found in anaerobic bacteria and anaerobic
eukaryotes but not in the archaea, and the [Fe]-hydro-
genases are found only in certain methanogenic archaea.
The electrofuel production host R. eutropha H16 harbors
three [NiFe]-hydrogenases, all of which have been
characterized biochemically [48]. Two of them are used
to oxidize hydrogen, and thereby provide reducing
equivalents to the organism both for energy conservation
and biosynthesis, while the third type senses H2 in the
environment and serves a regulatory role. The cyto-
plasmic NAD(P)-reducing hydrogenase (SH) consists of
a heterodimeric H2-activating module (HoxHY) and a
heterodimeric NADH dehydrogenase module (HoxFU)
[49]. HoxH harbors the [NiFe] site, while HoxY contains
an iron–sulfur cluster. HoxF and HoxU contain multiple
iron–sulfur cluster and a flavin and these channel elec-
trons to NAD+
. SH also contains a fifth subunit (HoxI)
that is believed to be required for reducing NAD+
. The
NADH and NADPH generated by SH are primarily used
for biosynthetic processes, including autotrophic CO2
fixation. The other hydrogenase in R. eutropha used for
H2 activation is a heterodimeric membrane bound
[NiFe]-hydrogenase (MBH), which faces the periplasm
and is anchored to the membrane [50]. It oxidizes H2 and
feeds electrons to the quinone pool of the aerobic respir-
atory chain. MBH is made up of two subunits: HoxG is
the catalytic subunit while HoxK harbors three iron–
sulfur clusters. A di-heme b-type cytochrome HoxZ is
also part of the respiratory chain and it links MBH to the
quinone pool [48,50]. Hence, R. eutropha can efficiently
utilize H2 for carbon fixation both in terms of biosynthesis
via SH and in terms of ATP synthesis by aerobic respir-
ation via MBH.
P. furiosus is being engineered to fix CO2 via the 3HP/
4HB cycle and it contains three [NiFe]-hydrogenases, all
of which have been characterized biochemically [51].
Two of them are found in the cytoplasm (SHI, SHII)
and one is membrane bound (MBH). MBH is a respir-
atory complex encoded by 14 genes that oxidizes the
reduced ferredoxin generated from sugar fermentation
and evolves H2 and generates an ion gradient that is used
for ATP synthesis. SHI and SHII are thought to recycle
the H2 produced by MBH for biosynthetic purposes.
Each consists of four subunits that contain the [NiFe]
catalytic site, multiple iron–sulfur clusters, and flavin
adenine dinucleotide. SHI only uses NADP+
as an elec-
tron acceptor while SHII also uses NAD+
[52]. Hence,
even though P. furiosus is naturally a heterotroph, it does
have the capacity to utilize H2 and generate both
NADPH (via SHI and SHII) and NADH (via SHII) that
could be used to fix CO2 by a synthetic pathway. In the
case of the 3HP/4HB cycle, NADPH is the source of
reductant and, hence, SHI would be the key enzyme for
electrofuel generation. In this regard, the recently
reported ability to over-produce SHI by an order of
magnitude in an engineered P. furiosus strain [53] could
prove to be very useful for biofuel production.
In other organisms being considered for electrofuel pro-
duction, the situation is not so straightforward. For
example, there are five hydrogenases encoded in the
genome of Clostridium ljungdahlii [21
], but none have
been characterized biochemically. One is a [NiFe]-
enzyme that it is predicted to be membrane-bound, while
the other four are of the [FeFe] type, and all are predicted
to be cytoplasmic. Two of the [FeFe] hydrogenases
appear to be associated with other proteins that might
enable NAD+
reduction [21
]. The membrane-bound
[NiFe] hydrogenase is similar to the H2-oxidizing
MBH of R. eutropha discussed above, but the nature of
its physiological electron carrier is not known. Con-
sequently, it is not understood how C. ljungdahlii could
activate H2 and provide reducing power for CO2 fixation,
which is obviously required before the process could be
optimized through metabolic engineering.
Carbon dioxide capture
Any fuel or organic chemical produced from CO2 that
relies on biological carbon fixation depends on the con-
centration of CO2 in the environment. As such, mechan-
isms to concentrate CO2 have evolved to compensate for
the imbalance between the high demand of inorganic
carbon and low ambient CO2 concentration. It is well
known that some chemoautotrophs, various photoauto-
trophic microorganisms, green algae, and plants have
developed distinct mechanisms to increase the concen-
tration of CO2 in close proximity to ribulose-1,5-bispho-
sphate carboxylase/oxygenase (RubisCO), the CO2-fixing
enzyme of the CBB pathway [54,55]. This is necessary
because RubisCO has a low affinity for CO2 and does not
discriminate well between CO2 and the competing sub-
strate, O2. The O2-dependent oxygenase activity of
RubisCO is responsible for photorespiration, a wasteful
side reaction that leads to a net loss of carbon [56].
Carbonic anhydrase (CA), an essential component of CO2
concentrating mechanisms, catalyzes the reversible con-
version of CO2 and water to bicarbonate (HCO3
À
, the pKa
of carbonic acid is 6.4) [57,58]. CAs are both structurally
and functionally quite diverse, with five classes (a, b, g, d,
and z) widely distributed among plants, animals, fungi,
380 Energy biotechnology
Current Opinion in Biotechnology 2013, 24:376–384 www.sciencedirect.com
archaea, and bacteria, although the b-class are most
prevalent in CO2-fixing organisms [59,60
,61]. The cat-
alytic activity in CA relies on a metal cofactor, most
commonly zinc, which is coordinated by three histidine
residues (a, g, d) or two cysteines and a histidine (b and z).
The a, b, and g-classes all share a two-step zinc hydroxide
mechanism and are extremely fast enzymes (kcat/Km up to
108
MÀ1
sÀ1
).
Carbon concentrating mechanisms have only been
described for organisms that use the CBB cycle, however
exploitation of naturally occurring CO2-fixing pathways
for microbial electrofuels production may require engin-
eering of CA or attention to the molecular details for how
CO2 is fed to the carbon-fixing machinery in order to
optimize electrofuel production. The CO2-fixing
enzymes of 3HP, 3HP/4HB and DC/4HB cycles all use
bicarbonate rather than CO2 as substrate [32
], hence a
functional CA is likely a key requirement for an efficient
electrofuel production pathway. For example, the aceto-
genic C. acetobutylicum contains both b and g-types, while
the heterotrophic archaeon P. furiosus, which does not
naturally utilize CO2 as a carbon source but is the host for
an engineered 3HP/4HB pathway, appears to contain
only a g-type CA [58]. The extent to which the CA(s)
of the host might limit CO2-utilization by a heterologous
pathway is unclear at present. Moreover, as yet unchar-
acterized CO2-concentrating mechanisms might be pre-
sent in potential host organisms. In any case, the means
for concentrating and/or hydrating CO2 is obviously an
area that merits attention for electrofuel development.
Host development
The development of electrofuel hosts requires the avail-
ability of genetic tools, as well as a sound knowledge of
gene regulation and metabolism in the target host. Cur-
rent electrofuel projects are taking advantage of an estab-
lished body of knowledge for genetic manipulation in
well-studied organisms such as R. eutropha and Clostridium
spp., while others are working with newly developed
genetic systems (Table 2). There are two basic avenues
for electrofuel host development: engineer a natural
H2-utilizing autotroph to produce the desired electrofuel,
or engineer a suitable heterotroph to utilize CO2/H2 for
electrofuel production. In the latter case, choice of a
suitable host depends not only on the availability of a
genetic system but also tools for systems-level analysis
and the organism’s suitability for bioprocess production.
In the case of potentially suitable autotrophs, it may be
that these tools are not available or are still in the early
stages of development. Indeed, even though the
endogenous CO2-fixation machinery might be optimized,
diverting carbon flow to an electrofuel rather than to
native cellular metabolism may prove to be problematic.
The opposite is true for the heterotroph approach, where
preventing CO2-derived carbon from entering the host’s
native metabolism may be key to establishing an efficient
process. It is still too early to determine if the ‘auto-
trophic’ or the ‘heterotrophic’ strategy is better suited for
the generation of electrofuels.
R. eutropha serves as an example of the ‘autotrophic’
approach. A variety of tools and techniques exist for
genetic engineering of this H2-utilizing autotrophic
organism and there are both plasmid-based expression
systems [62] and chromosomal modifications via homolo-
gous recombination [63–66], as well as systems-level
analysis tools including microarrays [67]. While some
species of Clostridium are also natural H2-utilizing auto-
trophs, genetic tools for these organisms are still being
developed. So far they include plasmid-based and indu-
cible gene expression, antisense RNA knock-down, and
reporter systems [68,69], but techniques for chromosomal
modification have only recently emerged [70
]. These
efforts should enable clostridial hosts to be flexible elec-
trofuel producing platform organisms in the near future
[70
,71]. There is also a recent report of gene disruption
by cross-species complementation in the H2-oxidizing,
facultative autotroph, Metallosphaera sedula [72], although
the potential for metabolic engineering in this organism
will require continued development of its genetic system.
The second avenue for electrofuel development using
heterotrophs was recently demonstrated for the first time
Biological conversion of carbon dioxide and hydrogen Hawkins et al. 381
Table 2
Genetic tools for select electrofuels organisms. Current genetics tools for electrofuels organisms.
Organism Genome sequence Genetic tools
Ralstonia eutropha H16 Y Plasmid-based gene expression [62]
Gene knockout or deletion [63,65]
Chromosomal insertion [64]
Clostridium spp. Many Plasmid-based gene expression [68]
Anti-sense RNA silencing [68]
Expression reporter systems [68]
Chromosomal insertion [70
]
Pyrococcus furiosus Wild-type and COM1 Expression regulation [53]
Chromosomal insertion [27
,79]
Metallosphaera sedula Y Gene knockout or deletion [72]
www.sciencedirect.com Current Opinion in Biotechnology 2013, 24:376–384
in P. furiosus [27
]. Heterologous expression of the first
five genes from the 3HP/4HB pathway allowed P. furiosus
to utilize H2 and incorporate CO2 into 3HP, a crucial
intermediate in the carbon fixation pathway and a valu-
able industrial chemical building block. This was accom-
plished by using a highly competent strain that enables
chromosomal modification [73], the genome sequence of
which was recently reported [74]. The new genetic
system has also been successfully utilized for over-
expression of cytoplasmic hydrogenase I (SHI) [53],
thereby potentially allowing facile H2 oxidation and
NADPH production. Based on these promising prelimi-
nary results, efforts are underway for the construction of
the electrofuels production host utilizing the complete
M. sedula 3HP/4HB pathway for biological activation of
carbon dioxide into a variety of chemical and fuel mol-
ecules [3
].
Conclusion
Electrofuels are a promising paradigm that could improve
on the relatively poor efficiency of photosynthetically
produced biofuels and open up a program for scalable,
renewable liquid fuel production based on flexible energy
inputs. A handful of electrofuel organisms are in devel-
opment or have been recently reported, but opportunities
exist to expand the concept. The potential of harnessing
biological carbon fixation for production of key industrial
biomolecules holds great promise for displacing
petroleum-based feedstocks [75].
Acknowledgments
This work described here was supported in part by the US Department of
Energy Research through the ARPA-E Electrofuels Program (DE-
AR0000081 to RMK and MWA) and the Division of Chemical Sciences,
Geosciences and Biosciences, Office of Basic Energy Sciences (DE-FG05-
95ER20175 to MWA).
References and recommended reading
Papers of particular interest, published within the period of review,
have been highlighted as:
 of special interest
 of outstanding interest
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BiologicalGenerationLiquidFuelsReview

  • 1. Biological conversion of carbon dioxide and hydrogen into liquid fuels and industrial chemicals Aaron S Hawkins1 , Patrick M McTernan2 , Hong Lian1 , Robert M Kelly1 and Michael WW Adams2 Non-photosynthetic routes for biological fixation of carbon dioxide into valuable industrial chemical precursors and fuels are moving from concept to reality. The development of ‘electrofuel’-producing microorganisms leverages techniques in synthetic biology, genetic and metabolic engineering, as well as systems-level multi-omic analysis, directed evolution, and in silico modeling. Electrofuel processes are being developed for a range of microorganisms and energy sources (e.g. hydrogen, formate, electricity) to produce a variety of target molecules (e.g. alcohols, terpenes, alkenes). This review examines the current landscape of electrofuel projects with a focus on hydrogen-utilizing organisms covering the biochemistry of hydrogenases and carbonic anhydrases, kinetic and energetic analyses of the known carbon fixation pathways, and the state of genetic systems for current and prospective electrofuel-producing microorganisms. Addresses 1 Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States 2 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States Corresponding author: Adams, Michael WW (adams@bmb.uga.edu) Current Opinion in Biotechnology 2013, 24:376–384 This review comes from a themed issue on Energy biotechnology Edited by Eric Toone and Han de Winde For a complete overview see the Issue and the Editorial Available online 16th March 2013 0958-1669/$ – see front matter, # 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.copbio.2013.02.017 Introduction There are intrinsic limitations to the production of biofuels derived from photosynthetic organisms that impede the development of a renewable liquid fuel industry at large- scale. In particular, these include low efficiency of solar energy conversion (Figure 1) and competition for agricul- tural resources. Recent initiatives in the U.S. and else- where have the objective of harnessing the molecular mechanisms of non-photosynthetic organisms that can utilize CO2 directly for the production of energy-dense liquid fuels, which are now referred to as ‘electrofuels’ [1 ,2,3 ]. Electrofuel-producing microorganisms are being developed that require the complementary expertise of synthetic biologists, metabolic engineers, and microbiolo- gists to equip native CO2-fixing species or autotrophs with pathways fortargeted fuel production,or confer autotrophy on heterotrophic host organisms, or both. The range of possible sources currently being explored for low-poten- tial, high-energy electrons to power an electrofuel process includes hydrogen gas, formate, carbon monoxide and electricity. This review will focus on electrofuel strategies that use hydrogen gas as source of reducing power for CO2 fixation. Microorganisms that are able to use other sources of electrons including electricity directly are discussed in an accompanying review by Lovely [4]. A general scheme for electrofuel productionfromhydrogenandCO2 isshown in Figure 2. CO2 fixation The reduction of CO2, the most oxidized form of carbon, into technologically useful organic compounds remains a daunting task for abiological chemical catalysis. There are, currently, six naturally occurring biological pathways for carbon fixation, and these have been reviewed exten- sively in recent years [5 ,6,7,8]. Each pathway has unique features arising from the ecological and molecular context in which it evolved. Although there are many examples of CO2-fixing carboxylases that are utilized for metabolic purposes other than carbon assimilation, such as energy conservation, anaplerosis, and redox-balancing [1 ,2,3 ,9 ,10], this review will focus on the autotrophic CO2 fixation pathways that are relevant for electrofuel production in addition to the primary host microorgan- isms that are currently being considered that use hydro- gen (Table 1). The most ubiquitous CO2-fixation pathway is the Calvin– Benson–Bassham (CBB) cycle found in plants, algae, cyanobacteria, purple bacteria, and also in some proteo- bacteria, such as Ralstonia eutropha. R. eutropha is a meta- bolically diverse, facultatively autotrophic bacterium that can grow on sugars, fatty acids, amino acids, triacylglycer- ides as well as on H2/CO2 [5 ,6,7,8,11 ]. Previous work on R. eutropha has focused on its ability to store excess carbon as polyhydroxyalkanoates [12,13] (PHAs) and now efforts seek to divert carbon flux away from PHA storage and into other molecular targets. For example, R. eutropha is a proposed host for isobutanol production via the 2- ketoisovalerate pathway for branched chain amino acid synthesis [11 ] from H2 and CO2. This strategy has already been successfully used in E. coli to produce Available online at www.sciencedirect.com Current Opinion in Biotechnology 2013, 24:376–384 www.sciencedirect.com
  • 2. Biological conversion of carbon dioxide and hydrogen Hawkins et al. 377 Figure 1 (a) (b) CH2OH H2/CO2 H2/CO2 OH OH OH OH O CBP TBD TBD 0.18-0.2%c1.8-2.4%b 10-13%e,f 50-70%f 50-70%f 15-20%d PV PS 4.5-6% a 70-85%f Wet-milling, EH WEHP WEHP WEHP SMR Current Opinion in Biotechnology Electrofuel production from H2 and CO2. (a) Comparison of overall photon-to-fuel efficiency of biofuels versus electrofuels. Percentages represent the cumulative efficiency of solar energy conversion at different stages. Although the conversion efficiency of an electrofuel process is currently unknown, the improved efficiency of solar hydrogen compared to photosynthetic sugars indicates that a solar electrofuel process would require less land area than current biofuels. (b) Hydrogen inputs for electrofuels are highly flexible and generation strategies can include electrolysis of water by renewable wind power, electrolysis of water by conventional electricity (e.g. coal), or by steam reformation of methane, shown with conversion efficiencies for each process. Abbreviations: PS – photosynthesis, EH – enzymatic hydrolysis, PV – photovoltaic, WEHP – Water Electrolysis Hydrogen Production, SMR – steam methane reformation, TBD – To be determined. a Zhu et al. [76], b Assuming grain starch represents 40% of total corn biomass, c Conrado et al. [1 ], d Parida et al. [77], e Assuming 65% overall electrolysis efficiency, f Holladay et al. [78]. Figure 2 H + H 2 NADP + NADPH (1) Generating Reducing Power (2) Incorporation of Inorganic Carbon Acetyl-CoA Pyruvate CO2 Fixation (3) Microbial Synthesis n-butanol farnesene long chain alkenes isobutanol HCO 3 _ CO 2 Current Opinion in Biotechnology Schematic drawing of the primary biochemical modules involved in electrofuel formation. Intracellular reducing power is generated from hydrogen gas via hydrogenase enzymes. Carbon fixation cycle incorporates inorganic carbon into central metabolism via key intermediates. Microbial synthesis of the target fuel molecule proceeds via endogenous and/or engineered metabolic pathways. www.sciencedirect.com Current Opinion in Biotechnology 2013, 24:376–384
  • 3. isobutanol and other higher alcohols from sugars [14,15], as well as in Clostridium cellulolyticum to produce isobu- tanol from cellulose [16]. R. eutropha can also use electro- chemically generated formate as the electron donor for the production of isobutanol and 3-methyl-1-butanol [1 ,2,3 ,17 ]. In addition, R. eutropha is being used, in conjunction with in situ electrochemical generation of hydrogen via molybdenum polypryridyl-oxo catalysts tethered to the cell surface, for production of various molecules including n-butanol (via PHA biosynthesis), farnesene (via isoprenoid biosynthesis) and long chain alkanes (via fatty acid biosynthesis) [1 ,2,3 ,4,18 ]. Anaerobic microorganisms that are known to fix CO2 typically use either the reductive TCA (rTCA) cycle or the Wood–Ljungdahl (W–L) pathway. The most energetically efficient pathway for CO2 fixation is the W–L pathway, which is found exclusively in anaerobic, acetogenic bacteria and methanogenic archaea [5 ,6,7,8,14,15]. Acetogenic bacteria are well-known for their ability to grow on H2/CO2 or synthesis gas (CO/H2) and produce acetate, but various species also naturally generate ethanol, butyrate, butanol and 2,3- butanediol as end-products [1 ,2,3 ,9 ,10,16,19,20]. These organisms are obvious hosts for electrofuel development, and already butanol production has been engineered into Clostridium ljungdahlii [5 ,6,7,8,11 ,17 ,21 ]. Acetogens, such as Sporomusa ovata, are also being explored for their ability to grow directly on graphite cathodes and accept electrons for microbial synthesis [12,13,22]. The most recently discovered pathways for biological CO2 fixation involve the production of 3-hydroxypropio- nate (3HP), dicarboxylates (DC) and/or 4-hydroxybuty- rate (4HB). One version is found in members of the thermoacidophilic archaeal order Sulfolobales, which includes species in the genera Sulfolobus and Metallo- sphaera [5 ,6,7,8,11 ,23]. One turn of the cycle converts two molecules of CO2 to acetyl-CoA using NADPH as the electron donor with 3HP and 4HB as intermediates, although studies using isotopically labeled substrates showed that most of the carbon flux enters central metab- olism via succinyl-CoA rather than acetyl-CoA [9 ,10,14,15,24]. The enzymatic details of this pathway have recently been completed with the biochemical characterization of an epimerase and a mutase [11 ,16,25], and the identification of the gene encoding a CoA-ligase [26]. The 3HP/4HB pathway is being engin- eered into a hyperthermophilic host, Pyrococcus furiosus, for the production of n-butanol from H2/CO2 [3 ,12,13], where the nearly 308C difference between the optimal growth temperature of P. furiosus (Topt = 988C) and M. sedula (Topt = 738C) is being exploited for a temperature- dependent production strategy. Around 708C, where the enzymes from M. sedula are most active, P. furiosus metabolism is virtually quiescent, thereby minimizing the maintenance energy requirements for the host. Recently, this temperature-dependent strategy was used to produce 3HP in P. furiosus using the first three enzymes of the 3HP/4HB pathway [27 ]. One important characteristic intrinsic to the various CO2- fixing pathways is the tolerance of the enzymes and redox carrier molecules to oxygen. The CBB cycle, the 3HP bicycle, and the 3HP/4HB cycle (with the exception of a single enzyme, 4-hydroxybutyryl-CoA dehydratase) are all oxygen-tolerant pathways that operate in aerobic organisms. The rTCA cycle, the W–L pathway, and the DC/4HB cycle are all found in anaerobic organisms; these all utilize oxygen-sensitive reduced ferredoxin as an electron carrier and contain oxygen-sensitive enzymes, for example, CO dehydrogenase/acetyl-CoA synthase and pyruvate synthase [6]. Some species of aerobic H2-oxidiz- ing bacteria, such as Hydrogenobacter thermophilus, utilize the rTCA cycle; however, they have special biochemical adaptations to protect against oxic conditions [28]. In practical terms, the requirement of O2 to support microbial growth presents explosion safety challenges to large-scale electrofuel production using hydrogen gas as substrate. There are some reactor designs that try to minimize the risk with aerobic electrofuels hosts (such as Ralstonia) by keeping oxygen and hydrogen gases separ- ate [11 ]. Utilizing anaerobic hosts, such as Clostridium spp. and P. furiosus, avoids the issue altogether. However, a recent study of oxygen detoxification in P. furiosus showed that the organism is remarkably aero-tolerant (up to 8% O2 vol/vol). This property would be advan- tageous in bioprocessing, especially under conditions where maintaining strict anoxia is costly [11 ,29]. 378 Energy biotechnology Table 1 Electrofuel producing hosts in development. The organisms listed utilize hydrogen or formate for the delivery of low-potential electrons, and have either been reported to produce an electrofuel or are currently in development. R = reported, D = development Organism Type Electron donor(s) CO2 fixation cycle Target products Status References Ralstonia eutropha H16 Betaproteobacteria Electrochemically generated H2 CBB cycle PHB, butanol, farnesene, long-chain alkenes D [18 ] Ralstonia eutropha H16 Betaproteobacteria H2 CBB cycle Isobutanol D [11 ] Pyrococcus furiosus Archaeon H2 3HP/4HB cycle from M. sedula n-butanol D [3 ] Clostridium ljungdahlii Acetogenic bacteria H2 W–L pathway n-butanol, ethanol R [21 ] Current Opinion in Biotechnology 2013, 24:376–384 www.sciencedirect.com
  • 4. Computational analyses of CO2 fixation The growing interest in biological carbon fixation for microbial production of fuels and commodity chemicals has led to extensive analysis of the thermodynamic and kinetic characteristics of the six known pathways. Boyle and Morgan performed flux analysis to determine the carbon flux and energy demand for biomass synthesis from CO2, using maximum biomass production as the objective function [30 ]. They found that the energetic cost of common core metabolites varied across the differ- ent routes for fixing CO2, indicating that certain pathways may be more efficient at producing a given product from a single precursor. On average, they found that the W–L pathway and the rTCA cycle were the most energy efficient routes, followed by the DC/4HB cycle, the 3HP/4HB cycle, the 3HP-bicycle, and lastly the CBB pathway. The same trend has been observed in other flux balance analyses [31]. Another thermodynamic analysis of carbon fixation reac- tions examined the ATP requirement and the reduction potential of electron carriers, as well as other factors, including the form and concentration of inorganic carbon, and the associated effects of cellular pH and ionic strength [32 ]. Several possible explanations were put forward to account for the differences in the ATP required by the various pathways that are, in most cases, higher than that required to make the net reaction ther- modynamically feasible. One common explanation for this is based on the different electron carriers used. For example, ferredoxin (Eo’ À400 mV) has a lower reduction potential than NAD(P)H (Eo’ = À320 mV), but the extra energetic contribution of oxidizing two ferredoxin molecules compared to one NADPH molecule under standard conditions ($20 kJ molÀ1 ) does not equal the energy released by ATP hydrolysis (over 50 kJ molÀ1 ) [33]. Moreover, this effect is not enough to account for the large differences in ATP cost for pyruvate formation between, for example, the rTCA cycle (2 ATP) and the 3HP bicycle (7 ATP) [5 ]. A closer look at the thermodynamics of the individual reactions in carbon fixation pathways helped to further elucidate the local thermodynamic constraints that shape the overall energetics and revealed a characteristic pat- tern in the reaction profile of carbon fixation enzymes [34 ]. Inspection of the reduction potentials of half- reactions in carbon fixation pathways reveals generalized groupings of reactions based on reaction type. It is specifically the carboxylation and carboxyl reduction reactions that are the most energetically unfavorable in the pathway and thus require most of the energetic push to overcome. This is accomplished either directly by coupling the reaction to energy release from ATP hydrolysis, or indirectly by coupling hydrolysis of another high-energy bond (e.g. thioester) to the energetically unfavorable reaction. Almost all of the ATP investments in each carbon fixation pathway are coupled directly or indirectly to carboxylation and carboxyl reduction reac- tions. Some pathways manage to reduce the ATP require- ments of carbon fixation by coupling unfavorable reactions to exergonic reactions other than ATP hydroly- sis. In the case of the W–L pathway in acetogens, this strategy is used to reduce the ATP investment to a single ATP molecule during the formation of pyruvate [5 ]. Synthetic pathways are not limited by the enzymatic profile of naturally occurring pathways. Rather, the pro- spect of combining enzymes in novel ways holds promise for improving the efficiency of the pathway or reducing the energetic cost. Using a constraint-based modeling approach and drawing from the entire set of approxi- mately 5000 known metabolic enzymes, Bar-Even et al. predicted in silico pathways with faster kinetic rates than naturally occurring ones [35]. They describe a family of synthetic pathways that utilize PEP carboxylase and the core of the C4 cycle in plants, which they term the ‘C4- glyoxylate cycles’. These pathways all produce glyoxy- late, which is assimilated to central metabolism via the bacterial-like glycerate pathway, and are predicted to have overall rates of CO2 to product formation that are 2–3 times faster than that of the CBB pathway. However, these rates are still lower than those reported for the rTCA, DC/4HB, and 3HP/4HB cycles. In addition to the enzymes that catalyze carboxylations and the carboxyl reduction reactions, the conversion of CO2 and hydrogen to electrofuels is also dependent on the two enzymes that activate these two gases, namely, carbonic anhydrase and hydrogenase, respectively. In the following the properties of these two enzymes relevant to electrofuel production will be considered. Hydrogen utilization Hydrogen is used as a source of energy by microorganisms from all three domains of life [36] and is activated by hydrogenase, which catalyzes the reversible interconver- sion of molecular hydrogen and protons in the presence of a suitable electron carrier. Based on structural and bio- chemical analysis, hydrogenases can be categorized by the metal atoms in their active sites: [NiFe]-hydroge- nases, [FeFe]-hydrogenases, and [Fe]-hydrogenases [37,38]. Since electrofuel hosts containing CO2 fixation pathways need to coordinate acquisition of reductant with carbon flux, the types of hydrogenase present in the host microorganism and the electron carriers that they use are of paramount importance. Extensive work on [NiFe]-hydrogenases from Desulfovi- brio gigas [39–43] and the [FeFe]-hydrogenases from Clostridium pasteurianum [44] and Desulfovibrio desulfuri- cans [45] has shown that both enzyme types harbor deeply buried active sites in which the site of H2 reactivity is a single iron atom coordinated by diatomic ligands (carbon Biological conversion of carbon dioxide and hydrogen Hawkins et al. 379 www.sciencedirect.com Current Opinion in Biotechnology 2013, 24:376–384
  • 5. monoxide and cyanide). In the [NiFe]-enzymes, the iron is also coordinated to a nickel atom, while in the [FeFe]- hydrogenases it is bound by a second iron atom and linked to a 4Fe-cluster. Both types of enzyme also contain multiple [4Fe-4S] clusters, as well as hydrophobic gas channels, that connect the catalytic sites to the molecular surface [46]. These two enzymes differ with respect to their distribution in nature, sensitivity to oxygen deacti- vation, and in the assembly and maturation of their catalytic sites [47]. For example, [NiFe]-hydrogenases are widespread among bacteria and archaea, the [FeFe]- enzymes are found in anaerobic bacteria and anaerobic eukaryotes but not in the archaea, and the [Fe]-hydro- genases are found only in certain methanogenic archaea. The electrofuel production host R. eutropha H16 harbors three [NiFe]-hydrogenases, all of which have been characterized biochemically [48]. Two of them are used to oxidize hydrogen, and thereby provide reducing equivalents to the organism both for energy conservation and biosynthesis, while the third type senses H2 in the environment and serves a regulatory role. The cyto- plasmic NAD(P)-reducing hydrogenase (SH) consists of a heterodimeric H2-activating module (HoxHY) and a heterodimeric NADH dehydrogenase module (HoxFU) [49]. HoxH harbors the [NiFe] site, while HoxY contains an iron–sulfur cluster. HoxF and HoxU contain multiple iron–sulfur cluster and a flavin and these channel elec- trons to NAD+ . SH also contains a fifth subunit (HoxI) that is believed to be required for reducing NAD+ . The NADH and NADPH generated by SH are primarily used for biosynthetic processes, including autotrophic CO2 fixation. The other hydrogenase in R. eutropha used for H2 activation is a heterodimeric membrane bound [NiFe]-hydrogenase (MBH), which faces the periplasm and is anchored to the membrane [50]. It oxidizes H2 and feeds electrons to the quinone pool of the aerobic respir- atory chain. MBH is made up of two subunits: HoxG is the catalytic subunit while HoxK harbors three iron– sulfur clusters. A di-heme b-type cytochrome HoxZ is also part of the respiratory chain and it links MBH to the quinone pool [48,50]. Hence, R. eutropha can efficiently utilize H2 for carbon fixation both in terms of biosynthesis via SH and in terms of ATP synthesis by aerobic respir- ation via MBH. P. furiosus is being engineered to fix CO2 via the 3HP/ 4HB cycle and it contains three [NiFe]-hydrogenases, all of which have been characterized biochemically [51]. Two of them are found in the cytoplasm (SHI, SHII) and one is membrane bound (MBH). MBH is a respir- atory complex encoded by 14 genes that oxidizes the reduced ferredoxin generated from sugar fermentation and evolves H2 and generates an ion gradient that is used for ATP synthesis. SHI and SHII are thought to recycle the H2 produced by MBH for biosynthetic purposes. Each consists of four subunits that contain the [NiFe] catalytic site, multiple iron–sulfur clusters, and flavin adenine dinucleotide. SHI only uses NADP+ as an elec- tron acceptor while SHII also uses NAD+ [52]. Hence, even though P. furiosus is naturally a heterotroph, it does have the capacity to utilize H2 and generate both NADPH (via SHI and SHII) and NADH (via SHII) that could be used to fix CO2 by a synthetic pathway. In the case of the 3HP/4HB cycle, NADPH is the source of reductant and, hence, SHI would be the key enzyme for electrofuel generation. In this regard, the recently reported ability to over-produce SHI by an order of magnitude in an engineered P. furiosus strain [53] could prove to be very useful for biofuel production. In other organisms being considered for electrofuel pro- duction, the situation is not so straightforward. For example, there are five hydrogenases encoded in the genome of Clostridium ljungdahlii [21 ], but none have been characterized biochemically. One is a [NiFe]- enzyme that it is predicted to be membrane-bound, while the other four are of the [FeFe] type, and all are predicted to be cytoplasmic. Two of the [FeFe] hydrogenases appear to be associated with other proteins that might enable NAD+ reduction [21 ]. The membrane-bound [NiFe] hydrogenase is similar to the H2-oxidizing MBH of R. eutropha discussed above, but the nature of its physiological electron carrier is not known. Con- sequently, it is not understood how C. ljungdahlii could activate H2 and provide reducing power for CO2 fixation, which is obviously required before the process could be optimized through metabolic engineering. Carbon dioxide capture Any fuel or organic chemical produced from CO2 that relies on biological carbon fixation depends on the con- centration of CO2 in the environment. As such, mechan- isms to concentrate CO2 have evolved to compensate for the imbalance between the high demand of inorganic carbon and low ambient CO2 concentration. It is well known that some chemoautotrophs, various photoauto- trophic microorganisms, green algae, and plants have developed distinct mechanisms to increase the concen- tration of CO2 in close proximity to ribulose-1,5-bispho- sphate carboxylase/oxygenase (RubisCO), the CO2-fixing enzyme of the CBB pathway [54,55]. This is necessary because RubisCO has a low affinity for CO2 and does not discriminate well between CO2 and the competing sub- strate, O2. The O2-dependent oxygenase activity of RubisCO is responsible for photorespiration, a wasteful side reaction that leads to a net loss of carbon [56]. Carbonic anhydrase (CA), an essential component of CO2 concentrating mechanisms, catalyzes the reversible con- version of CO2 and water to bicarbonate (HCO3 À , the pKa of carbonic acid is 6.4) [57,58]. CAs are both structurally and functionally quite diverse, with five classes (a, b, g, d, and z) widely distributed among plants, animals, fungi, 380 Energy biotechnology Current Opinion in Biotechnology 2013, 24:376–384 www.sciencedirect.com
  • 6. archaea, and bacteria, although the b-class are most prevalent in CO2-fixing organisms [59,60 ,61]. The cat- alytic activity in CA relies on a metal cofactor, most commonly zinc, which is coordinated by three histidine residues (a, g, d) or two cysteines and a histidine (b and z). The a, b, and g-classes all share a two-step zinc hydroxide mechanism and are extremely fast enzymes (kcat/Km up to 108 MÀ1 sÀ1 ). Carbon concentrating mechanisms have only been described for organisms that use the CBB cycle, however exploitation of naturally occurring CO2-fixing pathways for microbial electrofuels production may require engin- eering of CA or attention to the molecular details for how CO2 is fed to the carbon-fixing machinery in order to optimize electrofuel production. The CO2-fixing enzymes of 3HP, 3HP/4HB and DC/4HB cycles all use bicarbonate rather than CO2 as substrate [32 ], hence a functional CA is likely a key requirement for an efficient electrofuel production pathway. For example, the aceto- genic C. acetobutylicum contains both b and g-types, while the heterotrophic archaeon P. furiosus, which does not naturally utilize CO2 as a carbon source but is the host for an engineered 3HP/4HB pathway, appears to contain only a g-type CA [58]. The extent to which the CA(s) of the host might limit CO2-utilization by a heterologous pathway is unclear at present. Moreover, as yet unchar- acterized CO2-concentrating mechanisms might be pre- sent in potential host organisms. In any case, the means for concentrating and/or hydrating CO2 is obviously an area that merits attention for electrofuel development. Host development The development of electrofuel hosts requires the avail- ability of genetic tools, as well as a sound knowledge of gene regulation and metabolism in the target host. Cur- rent electrofuel projects are taking advantage of an estab- lished body of knowledge for genetic manipulation in well-studied organisms such as R. eutropha and Clostridium spp., while others are working with newly developed genetic systems (Table 2). There are two basic avenues for electrofuel host development: engineer a natural H2-utilizing autotroph to produce the desired electrofuel, or engineer a suitable heterotroph to utilize CO2/H2 for electrofuel production. In the latter case, choice of a suitable host depends not only on the availability of a genetic system but also tools for systems-level analysis and the organism’s suitability for bioprocess production. In the case of potentially suitable autotrophs, it may be that these tools are not available or are still in the early stages of development. Indeed, even though the endogenous CO2-fixation machinery might be optimized, diverting carbon flow to an electrofuel rather than to native cellular metabolism may prove to be problematic. The opposite is true for the heterotroph approach, where preventing CO2-derived carbon from entering the host’s native metabolism may be key to establishing an efficient process. It is still too early to determine if the ‘auto- trophic’ or the ‘heterotrophic’ strategy is better suited for the generation of electrofuels. R. eutropha serves as an example of the ‘autotrophic’ approach. A variety of tools and techniques exist for genetic engineering of this H2-utilizing autotrophic organism and there are both plasmid-based expression systems [62] and chromosomal modifications via homolo- gous recombination [63–66], as well as systems-level analysis tools including microarrays [67]. While some species of Clostridium are also natural H2-utilizing auto- trophs, genetic tools for these organisms are still being developed. So far they include plasmid-based and indu- cible gene expression, antisense RNA knock-down, and reporter systems [68,69], but techniques for chromosomal modification have only recently emerged [70 ]. These efforts should enable clostridial hosts to be flexible elec- trofuel producing platform organisms in the near future [70 ,71]. There is also a recent report of gene disruption by cross-species complementation in the H2-oxidizing, facultative autotroph, Metallosphaera sedula [72], although the potential for metabolic engineering in this organism will require continued development of its genetic system. The second avenue for electrofuel development using heterotrophs was recently demonstrated for the first time Biological conversion of carbon dioxide and hydrogen Hawkins et al. 381 Table 2 Genetic tools for select electrofuels organisms. Current genetics tools for electrofuels organisms. Organism Genome sequence Genetic tools Ralstonia eutropha H16 Y Plasmid-based gene expression [62] Gene knockout or deletion [63,65] Chromosomal insertion [64] Clostridium spp. Many Plasmid-based gene expression [68] Anti-sense RNA silencing [68] Expression reporter systems [68] Chromosomal insertion [70 ] Pyrococcus furiosus Wild-type and COM1 Expression regulation [53] Chromosomal insertion [27 ,79] Metallosphaera sedula Y Gene knockout or deletion [72] www.sciencedirect.com Current Opinion in Biotechnology 2013, 24:376–384
  • 7. in P. furiosus [27 ]. Heterologous expression of the first five genes from the 3HP/4HB pathway allowed P. furiosus to utilize H2 and incorporate CO2 into 3HP, a crucial intermediate in the carbon fixation pathway and a valu- able industrial chemical building block. This was accom- plished by using a highly competent strain that enables chromosomal modification [73], the genome sequence of which was recently reported [74]. The new genetic system has also been successfully utilized for over- expression of cytoplasmic hydrogenase I (SHI) [53], thereby potentially allowing facile H2 oxidation and NADPH production. Based on these promising prelimi- nary results, efforts are underway for the construction of the electrofuels production host utilizing the complete M. sedula 3HP/4HB pathway for biological activation of carbon dioxide into a variety of chemical and fuel mol- ecules [3 ]. Conclusion Electrofuels are a promising paradigm that could improve on the relatively poor efficiency of photosynthetically produced biofuels and open up a program for scalable, renewable liquid fuel production based on flexible energy inputs. A handful of electrofuel organisms are in devel- opment or have been recently reported, but opportunities exist to expand the concept. The potential of harnessing biological carbon fixation for production of key industrial biomolecules holds great promise for displacing petroleum-based feedstocks [75]. Acknowledgments This work described here was supported in part by the US Department of Energy Research through the ARPA-E Electrofuels Program (DE- AR0000081 to RMK and MWA) and the Division of Chemical Sciences, Geosciences and Biosciences, Office of Basic Energy Sciences (DE-FG05- 95ER20175 to MWA). 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