32.16: Fixing Carbon Fixation

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Carbon Fixation

Nature has produced many enzymes that can fix atmospheric CO₂, and, of course, everyone knows that photosynthesis is the source of most fixed CO₂ in the biosphere.  Plankton, cyanobacteria, algae, and plants are key in removing atmospheric CO₂ through photosynthesis.  Yet we can't plant enough trees to reduce CO₂ in the atmosphere in the next decade to avoid some of the worst consequences of anthropogenic climate change.  Old-growth trees (mostly gone or under significant stress) are best at removing CO₂.  New trees would take decades of growth before their effect on carbon drawdown would be consequential.  We also need to fix carbon dioxide not only to decrease atmospheric CO₂ but also to make more food!

A lot of carbon (about 100 petagrams) is sequestered each year in net primary production (fixation of carbon into biomolecules). This is split almost equally between land and ocean organisms.  The key enzyme in this process is Rubisco in the C3 (Chapter 20.4) and C4/CAM (Chapter 20.5) pathways.  The enzyme is big containing many large subunits and an equivalent number of small ones.  A chaperonin is required for folding.  It is also a very slow enzyme with a k_cat of around 2-10 CO₂/sec. In addition, it can bind another substrate, O₂, and engage in a competing reaction of photorespiration as described in Chapter 20.4.   

Figure \(\PageIndex{1}\) shows an interactive iCn3D model of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301 (1RBL)

Figure \(\PageIndex{1}\): Ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301 (1RBL) (Copyright; author via source). Click the image for a popup or use this external link (long load time): https://structure.ncbi.nlm.nih.gov/i...pxLGgEKR5gCYK8

This structure is a hetero 16-mer of 8 small chains and 8 large chains. The small chains are in gray and the large ones in differing colors.  Each large subunit contains a bound reaction intermediate analog 2-carboxyarabinitol 1,5-bisphosphate.

This chapter section will focus on improving and designing new ways to capture carbon dioxide as one way to reduce its concentration in the atmosphere.  Don't lose sight of the fact that the best way to deal with anthropogenic climate change is to stop putting CO₂ in the atmosphere from burning fossil fuels.

Naturally occurring pathways to fix carbon

(Much of this immediate section derives from the following reference: Natural carbon fixation. Sulamita Santos et al.,  Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways, Journal of Advanced Research, Volume 47, 2023, Pages 75-92, ISSN 2090-1232, https://doi.org/10.1016/j.jare.  Creative Commons license

There are six naturally occurring pathways that fix carbon. These are illustrated in Figure \(\PageIndex{2}\) below.  

Figure \(\PageIndex{2}\):  Natural carbon fixation. Sulamita Santos et al.,ibid.

Panel (A) shows the CBB cycle which we discussed in great detail in Chapter 20.4.  Here are the enzymes: ribulose-1,5-bisphosphate carboxylase/oxygenase, 3-phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, ribulose-phosphate epimerase.

Panel (B) shows the reverse (reductive)-TCA cycle which we discussed in Chapter 16.4 in the section on the α-ketoacid pathway - A primordial, prebiotic anabolic "TCA-like" pathway.  The enzymes include ATP-citrate lyase, malate dehydrogenase, succinyl-CoA synthetase, ferredoxin (Fd)-dependent-2-oxoglutarate synthase, isocitrate dehydrogenase, PEP carboxylase. 

Panel (C) shows the Wood–Ljungdahl (or reductive Acetyl-CoA) cycle which we discussed in Chapter 30.1.  At the top of the pathway are the acetogens Archaea and at the bottoms are the methanogens Archaea.  The enzymes include MPT-methylene tetrahydromethopterin, MFR-methanofuran, THF, tetrahydrofolate. 

Panel (D) shows the 3-hydroxypropionate (3HP) cycle.  The enzymes include acetyl-CoA carboxylase, propionyl-CoA carboxylase, methylmalonyl-CoA epimerase, succinyl-CoA:(S)-malate-CoA transferase, trifunctional (S)-malyl-CoA, -methylmalyl-CoA, mesaconyl-CoA transferase, mesaconyl-C4-CoA hydratase. 

Panel (E) shows the hydroxypropionate/4-hydroxybutyrate (HP/HB) and the dicarboxylate/4-hydroxybutyrate (DC/HB) cycles.  The enzymes include pyruvate synthase, PEP-carboxylase, malate dehydrogenase, fumarate hydratase/reductase, acetyl-CoA/propionyl-CoA carboxylase, 3-hydroxypropionate-CoA ligase/dehydratase, methylmalonyl-CoA mutase, succinyl-CoA reductase, 4-hydroxybutyrate-CoA ligase, crotonyl-CoA hydratase, acetoacetyl-CoA-ketothiolase.

Table \(\PageIndex{1}\) below shows a comparative description of the natural and synthetic carbon fixation pathways.

Pathway	Organisms	Energy Source	Input	Output	Reductants	Key Enzyme
Calvin-Benson (N)	Plants, Algae, Cyanobacteria, Aerobic Proteobacteria, Purple bacteria	Light	3 CO2, 9 ATP,6 NAD(P)H	Glyceraldehyde-3- phosphate	NAD(P)H	RuBisCO
rTCA (N) *	Green sulfur bacteria, Proteobacteria, Aquificae,  Nitrospirae	Light and Sulfur	2 CO2, 2 ATP,4 NAD(P)H	Pyruvate	NAD(P)H & ferredoxin	2-Oxoglutarate synthase, Isocitrate dehydrogenase
Wood–Ljungdahl (N) *	Acetogenic, Methanogenic Archaea, Planctomycetes, Sulfate. Archaeoglobales,	Hydrogen	2 CO2, 1 ATP, 4 NAD(P)H	Acetyl-CoA	Ferredoxin	NAD-independent formate dehydrogenase, Acetyl-CoA synthase-CO dehydrogenase
3-HP (N)	Chloroflexaceae	Light	3 HCO, 5 ATP, 5 NAD(P)H	Pyruvate	NAD(P)H	Acetyl-CoA carboxylase, Propionyl-CoA carboxylase
HP/HB (N)	Aerobic Sulfolobales	Hydrogen/sulfur	2 HCO, 4 ATP, 4NAD(P)H	Acetyl-CoA	NAD(P)H	Acetyl-CoA-Propionyl-CoA carboxylase
DC/HB (N) *	Anaerobic Thermoproteale,Desulfurococcales	Hydrogen/sulfur	1 CO2, 1 HCO, 3ATP, 4 NAD(P)H	Acetyl-CoA	NAD(PH &Ferredoxi	Pyruvate synthase, PEP carboxylase
RHP (CN)	Methanospirillum  hungatei	Hydrogen	CO2, 3 ATP, 2 NAD(P)H	Gluconeogenesis and glycolysis	NAD(P)H	RuBisCO
Natural Reductive Glycine (CD)	Candidatus  phosphitivorax, anaerolimiDesulfovibrio  desulfuricans	Phosphite	CO2, ATP, NAD(P), H	Formate/ Pyruvate	NAD(P)H &Ferredoxi	CO2-reducing formate dehydrogenase(fdhAB)
Reverse Otca (CD)	Desulfurella  acetivorans	Hydrogen	CO2, ATP, NAD(P) H	Acetyl-CoA	Ferredoxin	Citrate synthase
CETCH (S)	Theoretical	–	2 CO2, 2 ATP, 3 NAD(P)H	Glyoxylate	NAD(P)H	CoA- dependent carboxylase
Reductive Glycine (S)	Demonstrated in E.  coli  as host	–	CO2, NADH	Pyruvate	Ferredoxin	Glycine cleavage system
Synthetic malyl-CoA- glycerate (S)	Demonstrated in E.  coli  and Synechococcus  elongatus  PCC7942 host	–	CO2, 3 ATP, 3 NADH	Acetyl-CoA	NAD(P)H	PEP-carboxylase, RuBisCO
SACA Pathway (S)	Demonstrated in E.  coli  as host	–	CO2	Acetyl-CoA	–	NAD-independent formate dehydrogenase
Formolase pathway (S)	Theoretical	–	CO2, NADH, ATP	Dihydroxyacetone- phosphate	NADH	NAD-independent formate dehydrogenase

Sulamita Santos et al.,  Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways, Journal of Advanced Research,
Volume 47, 2023, Pages 75-92, ISSN 2090-1232, https://doi.org/10.1016/j.jare.  Creative Commons license

Plants and microorganisms that are photoautotrophic fix CO₂ by the Calvin cycle using NADPH and ATP and produce O₂.  Some anerobic photosynthetic bacteria don't produce O₂.  In chemolithoautotrophic microorganisms, energy sources (i.e. electron donors like H₂, H₂S, sulfur, Fe²⁺, nitrite and NH₃ found in bedrock - the lithosphere) other than NADPH, ATP and light can be used to drive CO₂ uptake. For chemoorganotropic microbes, reduced organic molecules such as sugars and amino acids serve as electron (donor) sources.  

Genetic engineering and synthetic biology are now employed to improve preexisting enzymes and to create whole new pathways for carbon capture.

As a simple example, people are trying to engineer carbonic anhydrase, used to convert CO₂ to HCO₃^- for transport to the lung where it is converted back to CO₂ and released.  It is a diffusion-controlled enzyme with a k_cat/K_M reported as high as 8 x 10⁷ M^-1s^-1, so how can it be made better?  One way is to engineer thermal stability into the enzyme. A critical problem for the forward reaction is that the enzyme is readily reversible so bicarbonate, HCO₃^-, is a competitive inhibitor of the forward reaction. In addition, the enzyme can be engineered to be more stable at higher pH to allow product (HCO₃^-) removal by the addition of OH^- in a process of mineralization, as shown in the equation below,

HCO₃^- + OH^- →  CO₃^2- + H₂O

where the carbonate anion can precipitate in the presence of divalent cations like  Ca²⁺, Mg²⁺ and Fe²⁺.  Here is a link to a Literature-based Guided Assessment on thermoengineering of carbonic anhydrase.  

Now let's explore the use of new pathways created by synthetic biology to capture carbon.  Some of these pathways are engineered to produce reactants (feedstocks) for biofuels, which we discussed in-depth in previous Chapter 32 sections, and chemical synthesis.  We'll focus on three:  the CETCH pathway, the reductive glyoxylate and pyruvate synthesis (rGPS) cycle, and the malyl-CoA-glycerate (MCG) pathway.

CETCH (Crotonyl-CoA-EThylmalonyl-CoA-4Hydorxybutyl-CoA) pathway

To engineer a new pathway, Swander et al identified efficient carboxylases from known ones (acetyl-CoA carboxylase, Rubisco, propionyl-CoA carboxylase, PEP carboxykinase, 2-oxoglutarate carboxylase, and pyruvate carboxylase), all of which we have discussed in previous chapters.  They created new pathways, calculated free energy and ATP/NADPH requirements, and then optimized the pathways.  They chose CoASH–dependent carboxylases and enoyl-CoA carboxylases/reductases.  Figure \(\PageIndex{3}\) below shows the reaction of one key carboxylase.  

Figure \(\PageIndex{3}\): Carboxylase used in the CETCH pathways to fix CO₂  

The pathway was named CETCH (Crotonyl-CoA-EThylmalonyl-CoA-4Hydorxybutyl-CoA) which catalyzes this next reaction in cell lysates (in vitro):

2CO₂ + 3NAD(P)H + 2ATP + FAD → glycolate + 3NAD(P) + 2ADP +2P_i + FADH₂

The rate of CO_2­ fixation by the CETCH pathways was similar to the rate of the Calvin cycle rates in cell lysates. 

In a more expansive approach, Gleizer used synthetic biology to change E. Coli from a heterotroph to an autotroph in which its biomass (carbon reservoir) came from CO₂.  Formate (HCO₂^-) was used as a source of reducing power (electrons) as it was oxidized by an added formate dehydrogenase to produce NADH for the autotropic fixation of CO₂ through the addition of Calvin cycle enzymes.  Using isotopically labeled ¹³CO₂ to follow carbon flow, after 10 generations and evolution, the cells were completely autotrophic through fixation of CO₂.  To accomplish this, they knocked out genes for phosphofructokinase (glycolysis) and glucose-6-phosphate-dehydrogenase (pentose-phosphate pathway) to impair these main metabolic pathways, and added carbonic anhydrase (to interconvert CO₂ and HCO₃^-) as well as Rubisco and phosphoribulokinase.  As formate was ultimately converted to CO₂, the net effect was not exactlycarbon neutral but could be if atmospheric CO₂ was used to make formate (for a feedstock) by electrochemical reduction.

Figure \(\PageIndex{4}\) below shows the next reactions in the synthetic E. Coli autotrophs.

Figure \(\PageIndex{4}\):  Schematic Representation of the Engineered Synthetic Chemo-autotrophic E. coli.  Shmuel Gleizer et al., Conversion of Escherichia coli to Generate All Biomass Carbon from CO2, Cell, 179 (2019). https://doi.org/10.1016/j.cell.2019.11.009.   Creative Commons license.  

CO₂ (green) is the only carbon source for all the generated biomass. The fixation of CO₂ occurs via an autotrophic carbon assimilation cycle. Formate is oxidized by a recombinant formate dehydrogenase (FDH) to produce CO₂ (brown) and NADH. NADH provides the reducing power to drive carbon fixation and serves as the substrate for ATP generation via oxidative phosphorylation (OXPHOS in black). The formate oxidation arrow is thicker than the CO₂ fixation arrow, indicating a net CO₂ emission even under autotrophic conditions.

Figure \(\PageIndex{5}\) shows that almost 100% of carbon atoms after many generations are labeled with ¹³C (detected by mass spec analysis) derived from ¹³CO₂.   

Figure \(\PageIndex{5}\): Isotopic Labeling Experiments Using ¹³C Show that All Biomass Components Are Generated from CO₂ as the Sole Carbon Source.  Gleizer  et al., ibid.

(A) Values are based on LC-MS analysis of stable amino acids and sugar-phosphates. The fractional contribution of ¹³CO₂ to various protein-bound amino acids and sugar-phosphates of evolved cells grown on ¹³CO₂ and naturally labeled formate showed almost full ¹³C labeling of the biosynthesized amino acids. The numbers reported are the ¹³C fraction of each metabolite, taking into account the effective ¹³CO₂ fraction out of the total inorganic carbon (which decreases due to unlabeled formate oxidation to CO₂). The numbers in parentheses are the uncorrected measured values of the ¹³C fraction of the metabolites. 

Synthetic reductive glyoxylate and pyruvate synthesis (rGPS) cycle and the malyl-CoA-glycerate (MCG) pathways

These pathways were created to synthesize acetyl-CoA, pyruvate, and malate from CO₂ in cell-free systems to free the system from cell growth and regulation requirements, and to make it insensitive to oxygen.  These molecules are also intermediates in the created cycle, which could operate continuously for hours at the same or greater rates of CO₂ fixation compared to photosynthesis. The cycle is shown in Figure \(\PageIndex{6}\) below.

Figure \(\PageIndex{6}\):  The rGPS–MCG cycle with acetyl-CoA as the end product. Luo, S., Lin, P.P., Nieh, LY. et al. A cell-free self-replenishing CO₂-fixing system. Nat Catal 5, 154–162 (2022). https://doi.org/10.1038/s41929-022-00746-x .  Creative Commons Attribution 4.0 International License, http://creativecommons.org/licenses/by/4.0/

The rGPS cycle consists of the reductive glyoxylate sythesis (rGS) pathway (blue) and the reductive pyruvate synthesis (rPS) pathway (green). The malyl-CoA-glycerate (MCG) pathway (orange) consists of the rGS pathway and the glycerate pathway. The red arrow indicates the carboxylation reaction. Gcl, glyoxylate carboligase; Tsr, tartronate semialdehyde reductase; Gk, glycerate 2-kinase; Eno, enolase and 2PG, 2-phospho-d-glycerate

 

Microbial electrosynthesis from CO₂

We mentioned above that if the formate used in the CETCH pathway could be synthesized through electrochemistry from CO₂, then the pathway would be truly carbon neutral. In fact, new microbial electrochemical methods are being designed to synthesize a variety of small molecules that could serve as feedstocks for chemical synthesis in industry.  The carbon in CO₂ has an oxidation number of +4 while the carbon in formic acid has an oxidation number of +2.  Hence two electrons must be added by electrochemically to make the CETCH pathway truly carbon neutral.  Bigger electrochemical reductants of CO₂ require more electrons.  Figure \(\PageIndex{7}\) below shows how key feedstocks could be made electrochemically from CO₂ and how they are usually made in industry.  

Figure \(\PageIndex{7}\) below.  :  Overview of the Main Products Formed from Microbial Electrosynthesis (MES) From CO₂, Along With the Main Industrial Methods to Manufacture These Products.  Jourdin et al., Trends in Biotechnology, April 2021, Vol. 39, No. 4 https://doi.org/10.1016/j.tibtech.2020.10.014.  Creative Commons Attribution (CC BY 4.0)

These feedstocks could be made by reductive electrosynthesis using electrons from the oxidation of water though electrolysis.  Released electrons  (oxidation number of O in water is -2 and 0 in O₂) move to a biocathode to reduce CO₂, as illustrated in Figure \(\PageIndex{8}\) below. 

Figure \(\PageIndex{8}\):  Reactor configurations for MES-based CO₂ conversion: (a) H-type, (b) single chamber, (c) dual chamber, (d) continuous stirred tank, and (e) schematic of electron transfer mechanism.  G. S. Lekshmi et al., Microbial electrosynthesis: carbonaceous electrode materials for CO₂ conversion.  Mater. Horiz., 2023, 10, 292-312.  DOI: 10.1039/D2MH01178F.  Creative Commons Attribution-Non Commercial 3.0 Unported Licence

The biocathode consists of a biofilm of cells printed onto a graphene, graphite, or carbon nanotube-laden support (all carbonaceous).