Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation

Abstract

Conceptually, the simplest way to synthesize an organic molecule is to construct it one carbon at a time. The Wood-Ljungdahl pathway of CO(2) fixation involves this type of stepwise process. The biochemical events that underlie the condensation of two one-carbon units to form the two-carbon compound, acetate, have intrigued chemists, biochemists, and microbiologists for many decades. We begin this review with a description of the biology of acetogenesis. Then, we provide a short history of the important discoveries that have led to the identification of the key components and steps of this usual mechanism of CO and CO(2) fixation. In this historical perspective, we have included reflections that hopefully will sketch the landscape of the controversies, hypotheses, and opinions that led to the key experiments and discoveries. We then describe the properties of the genes and enzymes involved in the pathway and conclude with a section describing some major questions that remain unanswered.

Figure 1

The Wood-Ljungdahl pathway. “H₂” is used in a very general sense to designate the requirement for two electrons and two protons in the reaction.

Figure 2

Working model of the Wood-Ljungdahl pathway circa 1951.

Figure 3

The pathway of CO₂ fixation into acetyl-CoA circa 1966, modified from [58].

Figure 4

Scheme circa 1982 proposing roles for the corrinoid protein and CODH in anaerobic autotrophic CO₂ fixation, modified from Fig. 2 of Hu et al. [75].

Figure 5

Scheme circa 1983 after re-establishment of formate dehydrogenase and formyl-H₄folate synthetase in the pathway.

Figure 6

Scheme circa 1985 showing that CODH is ACS, the central enzyme in the pathway, and that the corrinoid enzyme is a methyl carrier. The red arrows designate the reactions involved in the CO/acetyl-CoA exchange. Modified from [83].

Figure 7

Arrangement of Wood–Ljungdahl pathway genes in the acs gene cluster and in the chromosome. A. Arrangement of Wood–Ljungdahl pathway genes on the circular chromosome of M. thermoacetica. The numbering shows kilobase pairs from the origin of replication. B. The acs gene cluster that contains core Wood–Ljungdahl pathway genes discussed in the text. From [98].

Figure 8

A. Structure of MeTr. Methyl-H₄folate and base-off cobalamin were modeled into the active site of MeTr, with the methyl group of methyl-H₄folate shown in green. From Fig. 5, [172]. B. The active site cavity of MeTr, based on the structure of the MeTr-methyl-H₄folate binding site. From Fig. 5, [173]. C. Hydrogen bonding network near the N-5 of methyl-H₄folate in the crystal structure of the binary complex of MeTr with methyl-H₄folate [173].

Figure 9

Structure of the CFeSP. (A) From Figure 1 of [187], AcsC and AcsD are the large and small subunits, respectively, and Cba is the corrinoid cofactor. This figure shows the middle and C-terminal domains of the large subunit, while the N-terminal domain that contains the [4Fe-4S] cluster was disordered and could not be modeled. An expanded view of the [4Fe4S] cluster is shown in the upper right hand corner. (B) Modified from Fig. 3 of [187], proposed conformational changes of the CFeSP during methyl transfer from methyl-H₄folate/MeTr to the corrinoid (MT-Conform 1) to a resting state (Cap-Conform shown in Fig. A), and then from methyl-corrinoid to the A cluster on ACS (MT-Conform 2). The reductive activation conformation is also depicted (Red-Conform).

Figure 10

From Figure 1 of [87].The two subunits are shown with light and dark wire tracings. Electrons generated by the oxidation of CO at the C and C’ clusters are transferred to the internal redox chain in CODH, consisting of the B (and B’) and D clusters. The D cluster, located at the interface between the two subunits, is proposed to transfer electrons to the electron transfer protein (CooF), which is coupled to hydrogenase.

Figure 11

A. The C-cluster of CODH and (B) the A-cluster of ACS. From [204].

Figure 12

Redox states of the CODH catalytic center, the C-cluster. From Figure 2 of [335].

Figure 13

Proposed mechanism of CO oxidation at the C-cluster of CODH, from Figure 4 of [222]. B₁ and B₂ designate active site bases. Recent information about early stages in CO oxidation was gleaned through NMR studies of a rapid reaction involving the interconversion between CO and bound CO₂ [222]. See the text for a detailed explanation of each step.

Figure 14

(A) Proposed mechanism of acetyl-CoA synthesis at the A-cluster of ACS, from Figure 3 of [206]. See the text for details.

Figure 15

Random mechanism of acetyl-CoA synthesis, from Figure 3 of [238]. See the text for details.

Figure 16

PFOR Mechanism showing the ylide nucleophile and the HE-TPP anionic and radical intermediates.

Figure 17

Incomplete TCA cycle allowing conversion of acetyl-CoA to cellular intermediates. Dashed arrows represent enzymes that not identified in the M. thermoacetica genome. From [98].

Figure 18

Coupling of various methyl donors to the Wood-Ljungdahl pathway. The methyltransferase systems involved in transferring the methyl groups from aromatic methyl ethers (Mtv) or methanol (Mta) to methyl-H₄folate have been identified by genomic and enzymatic studies. See the text for details. Ar-O-CH₃ designates the aromatic methyl ether that serves as the methyl donor, and Ar-OH signifies the alcohol, which is the demethylation product.

Figure 19

Redox couples that can be used by acetogens. Figure taken from [336]. CO₂ reduction to acetate is one of many possible electron-accepting processes.

Figure 20

Acetoclastic methanogenesis: coupling methanogenesis to the Wood-Ljungdahl pathway (reverse acetogenesis). MCR, methyl-SCoM reductase; HDR, heterodisulfide reductase

Figure 21

Coupling reverse acetogenesis to sulfate reduction.

Figure 22

Proposed electron transport chain from work done in Moorella species (modified from [98]). The specific proton translocating step and which specific electron carriers are coupled to the Wood-Ljungdahl pathway are not known. The cytochromes may be parts of larger protein complexes (i.e. cytochrome bd oxidase and formate dehydrogenase).

Figure 23

Protein complexes possibly involved in proton transfer in M. thermoacetica.