Something special about CO-dependent CO2 fixation

Abstract

Carbon dioxide enters metabolism via six known CO₂ fixation pathways, of which only one is linear, exergonic in the direction of CO₂ -assimilation, and present in both bacterial and archaeal anaerobes - the Wood-Ljungdahl (WL) or reductive acetyl-CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate. Here, we scan the major biochemical reaction databases for reactions involving CO and CO₂ . We identified 415 reactions corresponding to enzyme commission (EC) numbers involving CO₂ , which are non-randomly distributed across different biochemical pathways. Their taxonomic distribution, reversibility under physiological conditions, cofactors and prosthetic groups are summarized. In contrast to CO₂ , only 15 reaction classes involving CO were detected. Closer inspection reveals that CO interfaces with metabolism and the carbon cycle at only two enzymes: anaerobic carbon monoxide dehydrogenase (CODH), a Ni- and Fe-containing enzyme that generates CO for CO₂ fixation in the WL pathway, and aerobic CODH, a Mo- and Cu-containing enzyme that oxidizes environmental CO as an electron source. The CO-dependent reaction of the WL pathway involves carbonyl insertion into a methyl carbon-nickel at the Ni-Fe-S A-cluster of acetyl-CoA synthase (ACS). It appears that no alternative mechanisms to the CO-dependent reaction of ACS have evolved in nearly 4 billion years, indicating an ancient and mechanistically essential role for CO at the onset of metabolism.

Keywords: CODH/ACS; carbon dioxide; carbon monoxide; enzymatic reactions; metabolic networks.

Figure 1

Enzyme Commission (EC) numbers involving CO ₂ and CO in KEGG and BRENDA (only in vivo reactions) and their overlaps. The horizontal bars display the total of EC numbers for each molecule in each database. The vertical bars display the size of the overlaps (intersections) between the databases.

Figure 2

Functional analysis of EC numbers involving CO ₂ and CO. (A) EC numbers involving CO ₂ (dark and light blue for those in prokaryotes and in eukaryotes only, respectively) and CO (dark and light red, accordingly). (B) Enrichment analysis (Fisher's exact test with adjusted p‐values by the Bonferroni correction) for high‐level functional categories of EC numbers involving CO ₂ (prokaryotes only).

Figure 3

CO ₂ in a section of a global metabolic map (full map provided as Fig. S1). A portion of the KEGG map ‘01100 – metabolic pathways’ with reactions involving CO ₂ highlighted, portraying different directionality and reversibility assignments in BRENDA. In black, reactions not in BRENDA or where CO ₂ is a product in BRENDA but reversibility is unknown; in blue, reactions where CO ₂ is a substrate or it is a product and the reaction is classified as reversible in at least one study; in red, reactions classified as irreversible where CO ₂ is a product.

Figure 4

Metals and organic cofactors in reactions that consume CO or CO ₂. Percentage of entries of experimental evidence in BRENDA demonstrating the participation of different (A) metals and (B) cofactors in the catalytic activity of enzymes that use CO (red) or CO ₂ (blue) as substrates.

Figure 5

Phylogenomic analysis of CO‐interconverting enzymes. (A) Distribution of genes encoding the CODH and ACS reactions. The left part of the figure lists the taxonomic groups from 5655 completed sequenced genomes (212 archaeal and 5443 bacterial). The presence‐absence patterns (PAPs) represent the proportion of genomes within a taxonomic group where each gene is present according to the discrete grey scale‐bar of binned intervals (top right, value indicates upper value of each bin). Each column represents a different gene selected from a different query species capable of performing the aerobic CODH (oxidative) reaction, the anaerobic CODH or both the (anaerobic) CODH and the ACS reactions (Oligotropha carboxidovorans, Moorella thermoacetica, Carboxydothermus hydrogenoformans, Rhodospirillum rubrum, Archaeoglobus fulgidus, Candidatus Bathyarchaeota archaeon BA1, Methanothermobacter thermautotrophicus and Methanosarcina acetivorans). Homologous proteins were predicted by BLAST with an E‐value threshold of 10⁻⁵ and filtering for global amino acid identities of at least 20% with Powerneedle (see Materials and methods). (B) Phylogenetic trees of the query sequences of CODH (left) and ACS (right) used to BLAST the RefSeq Database to build the PAPs in (A), numbers at branches are bootstrap values. Metabolic modes of the different species are marked in front of the respective sequences with colored circles according to the legend (bottom right).

Figure 6

CO (A) and CO ₂ (B) bonding to transition metals. (A) CO binds to a transition metal (M) via the free electron pair of its carbon atom. The electron density in this orbital (red = positive phase, yellow = negative phase) can be placed into empty metal d orbitals forming a σ bond. Concurrently, a π bond is formed between an occupied d orbital and the antibonding empty π* orbital of CO (darker grey = positive phase, lighter grey = negative phase), so called ‘π backbonding’. (B) Different bonding modes between CO ₂ and transition metals include η¹‐C coordination, which mostly happens with electron‐rich metals (i.e. lower oxidation states), as they can transfer charge from the d_z ² orbitals to the antibonding π* orbitals of CO ₂. A double bond‐like interaction (dashed line) can also occur between a transition metal, carbon and oxygen, η²‐(C,O) bonding: an empty d_z ² orbital of a metal can take electron density from the π orbital of the CO ₂ orbital (red/yellow), while electron density can also be transferred from occupied d orbitals (blue) into the antibonding π* orbitals of CO ₂ (comparable to the backbonding of CO, but weaker).