METHYL-VITAMIN B12 AS A SOURCE OF METHYL GROUPS FOR THE SYNTHESIS OF ACETATE BY CELL-FREE EXTRACTS OF CLOSTRIDIUM THERMOACETICUM

A life with acetogens, thermophiles, and cellulolytic anaerobes

Frankly, I was surprised to receive an invitation to write a prefatory chapter for the Annual Review of Microbiology. I have read several such chapters written by outstanding researchers, many of whom I know and admire. I did not think I belonged to such a preeminent group. In my view, my contributions to the physiology and biochemistry of anaerobic thermophilic bacteria and, more lately, to anaerobic fungi are modest compared to the contribution made by other authors of prefatory chapters. I am honored to write about my life and my work, and I hope that those who read this chapter will sense how exciting and rewarding they have been.

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

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.

Old acetogens, new light

Acetogens utilize the acetyl-CoA Wood-Ljungdahl pathway as a terminal electron-accepting, energy-conserving, CO(2)-fixing process. The decades of research to resolve the enzymology of this pathway (1) preceded studies demonstrating that acetogens not only harbor a novel CO(2)-fixing pathway, but are also ecologically important, and (2) overshadowed the novel microbiological discoveries of acetogens and acetogenesis. The first acetogen to be isolated, Clostridium aceticum, was reported by Klaas Tammo Wieringa in 1936, but was subsequently lost. The second acetogen to be isolated, Clostridium thermoaceticum, was isolated by Francis Ephraim Fontaine and co-workers in 1942. C. thermoaceticum became the most extensively studied acetogen and was used to resolve the enzymology of the acetyl-CoA pathway in the laboratories of Harland Goff Wood and Lars Gerhard Ljungdahl. Although acetogenesis initially intrigued few scientists, this novel process fostered several scientific milestones, including the first (14)C-tracer studies in biology and the discovery that tungsten is a biologically active metal. The acetyl-CoA pathway is now recognized as a fundamental component of the global carbon cycle and essential to the metabolic potentials of many different prokaryotes. The acetyl-CoA pathway and variants thereof appear to be important to primary production in certain habitats and may have been the first autotrophic process on earth and important to the evolution of life. The purpose of this article is to (1) pay tribute to those who discovered acetogens and acetogenesis, and to those who resolved the acetyl-CoA pathway, and (2) highlight the ecology and physiology of acetogens within the framework of their scientific roots.

Catalysis of methyl group transfers involving tetrahydrofolate and B(12)

This review focuses on the reaction mechanism of enzymes that use B(12) and tetrahydrofolate (THF) to catalyze methyl group transfers. It also covers the related reactions that use B(12) and tetrahydromethanopterin (THMPT), which is a THF analog used by archaea. In the past decade, our understanding of the mechanisms of these enzymes has increased greatly because the crystal structures for three classes of B(12)-dependent methyltransferases have become available and because biophysical and kinetic studies have elucidated the intermediates involved in catalysis. These steps include binding of the cofactors and substrates, activation of the methyl donors and acceptors, the methyl transfer reaction itself, and product dissociation. Activation of the methyl donor in one class of methyltransferases is achieved by an unexpected proton transfer mechanism. The cobalt (Co) ion within the B(12) macrocycle must be in the Co(I) oxidation state to serve as a nucleophile in the methyl transfer reaction. Recent studies have uncovered important principles that control how this highly reducing active state of B(12) is generated and maintained.

Characterization of a corrinoid protein involved in the C1 metabolism of strict anaerobic bacterium Moorella thermoacetica

The strict anaerobic, thermophilic bacterium Moorella thermoacetica metabolizes C1 compounds for example CO(2)/H(2), CO, formate, and methanol into acetate via the Wood/Ljungdahl pathway. Some of the key steps in this pathway include the metabolism of the C1 compounds into the methyl group of methylenetetrahydrofolate (MTHF) and the transfer of the methyl group from MTHF to the methyl group of acetyl-CoA catalyzed by methyltransferase, corrinoid protein and CO dehydrogenase/acetyl CoA synthase. Recently, we reported the crystallization of a 25 kDa methanol-induced corrinoid protein from M. thermoacetica (Zhou et al., Acta Crystallogr F 2005; 61:537-540). In this study we analyzed the crystal structure of the 25 kDa protein and provide genetic and biochemical evidences supporting its role in the methanol metabolism of M. thermoacetia. The 25 kDa protein was encoded by orf1948 of contig 303 in the M. thermoacetica genome. It resembles similarity to MtaC the corrinoid protein of the methanol:CoM methyltransferase system of methane producing archaea. The latter enzyme system also contains two additional enzymes MtaA and MtaB. Homologs of MtaA and MtaB were found to be encoded by orf2632 of contig 303 and orf1949 of contig 309, respectively, in the M. thermoacetica genome. The orf1948 and orf1949 were co-transcribed from a single polycistronic operon. Metal analysis and spectroscopic data confirmed the presence of cobalt and the corrinoid in the purified 25 kDa protein. High resolution X-ray crystal structure of the purified 25 kDa protein revealed corrinoid as methylcobalamin with the imidazole of histidine as the alpha-axial ligand replacing benziimidazole, suggesting base-off configuration for the corrinoid. Methanol significantly activated the expression of the 25 kDa protein. Cyanide and nitrate inhibited methanol metabolism and suppressed the level of the 25 kDa protein. The results suggest a role of the 25 kDa protein in the methanol metabolism of M. thermoacetica.

The Many Faces of Vitamin B12: Catalysis by Cobalamin-Dependent Enzymes

Vitamin B12 is a complex organometallic cofactor associated with three subfamilies of enzymes: the adenosylcobalamin-dependent isomerases, the methylcobalamin-dependent methyltransferases, and the dehalogenases. Different chemical aspects of the cofactor are exploited during catalysis by the isomerases and the methyltransferases. Thus, the cobalt-carbon bond ruptures homolytically in the isomerases, whereas it is cleaved heterolytically in the methyltransferases. The reaction mechanism of the dehalogenases, the most recently discovered class of B12 enzymes, is poorly understood. Over the past decade our understanding of the reaction mechanisms of B12 enzymes has been greatly enhanced by the availability of large amounts of enzyme that have afforded detailed structure-function studies, and these recent advances are the subject of this review.

Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?

The four decades of the now classic studies by Harland G. Wood and Lars G. Ljungdahl lead to the resolution of the autotrophic acetyl-CoA 'Wood/Ljungdahl' pathway of acetogenesis. This pathway is the hallmark of acetogens, but is also used by other bacteria, including methanogens and sulfate-reducing bacteria, for both catabolic and anabolic purposes. Thus, the pathway is wide spread in nature and plays an important role in the global turnover of carbon. Because most historical studies with acetogens focused on the biochemistry of the acetyl-CoA pathway, the metabolic diversity and ecology of acetogens remained largely unexplored for many years. Although acetogens were initially conceived to be a somewhat obscure bacteriological group with limited metabolic capabilities, it is now clear that acctogens are arguably the most metabolically diverse group of obligate anaerobes characterized to date. Their anaerobic metabolic arsenal includes the capacity to oxidize diverse substrates, including aromatic, C1, C2, and halogenated compounds, and engage a large number of alternative energy-conserving, terminal electron-accepting processes, including classic fermentations and the dissimilation of inorganic nitrogen. In this regard, one might consider acetogens on a collective basis as the pseudomonads of obligate anaerobes. By virtue of their diverse metabolic talents, acetogens can be found in essentially all habitats. This review evaluates the metabolic versatilities of acetogens relative to both the engagement (regulation) of the acetyl-CoA pathway and the ecological roles likely played by this bacteriogical group.

INCORPORATION OF C14 FROM CARBON DIOXIDE INTO SUGAR PHOSPHATES, CARBOXYLIC ACIDS, AND AMINO ACIDS BY CLOSTRIDIUM THERMOACETICUM

Ljungdahl, Lars (Western Reserve University, Cleveland, Ohio), and Harland G. Wood. Incorporation of C(14) from carbon dioxide into sugar phosphates, carboxylic acids, and amino acids by Clostridium thermoaceticum. J. Bacteriol. 89:1055-1064. 1965.-The mechanism of synthesis of acetate from carbon dioxide by Clostridium thermoaceticum was investigated by incubating cells with glucose or xylose in the presence of C(14)O(2). Sugar phosphates, amino acids, and carboxylic acids were isolated and the specific radioactivities were determined; the distributions of C(14) were also determined in some of the compounds. Only fructose-1,6-diphosphate, formate, and lactate had higher specific activities than the acetate. The specific activities and distribution of C(14) in the fructose-6-phosphate and ribose-5-phosphate were such that we conclude that the synthesis of acetate does not occur via a pathway involving the sugar phosphates as direct intermediates. Likewise, it is shown that pathways including lactate, aspartate, serine, glycine, malate, and succinate are not of importance in the synthesis of acetate from CO(2). The methyl group of free methionine was unlabeled and is not a precursor of the methyl group of acetate.

Effects of cobalt on in vitro fiber digestion of forages and by-products containing fiber

Cobalt glucoheptonate as a source of Co to enhance ruminal fiber digestion was evaluated in two in vitro digestibility experiments. In Experiment 1, Co supplementation (0, 5, and 10 ppm) of five substrates (leaf and stem fractions of alfalfa and orchardgrass hays and ground corn) was evaluated under two dietary conditions (ruminal fluid taken from steers fed alfalfa hay or a high concentrate diet) for 24 or 48 h of fermentation in a 3 x 5 x 2 x 2 factorial arrangement. In Experiment 2, four concentrations of Co (0, 10, 20, and 30 ppm) were added to five substrates (alfalfa hay, orchardgrass hay, corn cobs, recycled newsprint treated with HCl, and cellulose casings) and were incubated with ruminal fluid from steers fed alfalfa hay for 24 or 48 h of fermentation in a 4 x 5 x 2 factorial arrangement. No interactions among treatments were observed for digestibilities of DM, OM, or NDF in both experiments or for VFA concentrations in Experiment 1. Supplementation with Co did not increase digestibilities of DM, OM, or NDF in either experiment or concentrations of VFA in Experiment 1. In Experiment 1, in vitro digestibilities of DM, OM, and NDF were higher for inoculum from steers fed alfalfa versus concentrate. In Experiment 2, digestibilities of DM, OM, and NDF were highest for alfalfa hay and lowest for recycled newsprint treated with HCl. Cobalt concentrations that were above minimum requirements did not improve digestion of DM, OM, or fiber.

Metabolism of homocetogens

Homoacetogenic bacteria are strictly anaerobic microorganisms that catalyze the formation of acetate from C1 units in their energy metabolism. Most of these organisms are able to grow at the expense of hydrogen plus CO2 as the sole energy source. Hydrogen then serves as the electron donor for CO2 reduction to acetate. The methyl group of acetate is formed from CO2 via formate and reduced C1 intermediates bound to tetrahydrofolate. The carboxyl group is derived from carbon monoxide, which is synthesized from CO2 by carbon monoxide dehydrogenase. The latter enzyme also catalyzes the formation of acetyl-CoA from the methyl group plus CO. Acetyl-CoA is then converted either to acetate in the catabolism or to cell carbon in the anabolism of the bacteria. The homoacetogens are very versatile anaerobes, which convert a variety of different substrates to acetate as the major end product.

Enzymology of the acetyl-CoA pathway of CO2 fixation

We know of three routes that organisms have evolved to synthesize complex organic molecules from CO2: the Calvin cycle, the reverse tricarboxylic acid cycle, and the reductive acetyl-CoA pathway. This review describes the enzymatic steps involved in the acetyl-CoA pathway, also called the Wood pathway, which is the major mechanism of CO2 fixation under anaerobic conditions. The acetyl-CoA pathway is also able to form acetyl-CoA from carbon monoxide. There are two parts to the acetyl-CoA pathway: (1) reduction of CO2 to methyltetrahydrofolate (methyl-H4folate) and (2) synthesis of acetyl-CoA from methyl-H4folate, a carboxyl donor such as CO or CO2, and CoA. This pathway is unique in that the major intermediates are enzyme-bound and are often organometallic complexes. Our current understanding of the pathway is based on radioactive and stable isotope tracer studies, purification of the component enzymes (some extremely oxygen sensitive), and identification of the enzyme-bound intermediates by chromatographic, spectroscopic, and electrochemical techniques. This review describes the remarkable series of enzymatic steps involved in acetyl-CoA formation by this pathway that is a key component of the global carbon cycle.

The mechanism of cobalamin-dependent rearrangements

Adenosylcobalamin-dependent rearrangements are enzyme catalyzed reactions in which a hydrogen atom is transfered from one carbon atom to an adjacent one in exchange for a group X which migrates in the opposite direction. In the hydrogen transfer step, the mechanism of which is reasonably well understood, the cofactor serves as an intermediate hydrogen carrier. The transfer of hydrogen to the cofactor involves homolysis of the carbon-cobalt bond to generate cob(II) alamin and the 5'-deoxyadenos-5'-yl radical, followed by abstraction of a hydrogen atom from the substrate to form 5'-deoxyadenosine and the substrate radical. After migration of group X, the hydrogen atom is returned to the product radical by the reverse of the above reactions to generate the final product and reconstitute the cofactor. In contrast to the transfer of hydrogen, the mechanism of group X migration is poorly understood. Many reactions mechanisms have been proposed on chemical grounds, but there is insufficient biochemical evidence to permit a choice among these propsals. A quantity of negative evidence has accumulated suggesting that group X migration does not involve alkylation of the cobalt of cobalamin by the substrate, but in the absence of firm data supporting an alternative mechanism, even this weak conclusion must be regarded as provisional.

Total synthesis of acetate from CO 2 . V. Determination by mass analysis of the different types of acetate formed from 13 CO 2 by heterotrophic bacteria

Mass analysis was used to determine the amount of acetate which is totally synthesized from (13)CO(2) during fermentations by Clostridium formicoaceticum, C. acidiurici, C. cylindrosporum, Butyribacterium rettgeri, and Diplococcus glycinophilus. In the fermentation of fructose by C. formicoaceticum, 27% of the acetate was found to be totally synthesized from CO(2), and the remaining acetate was unlabeled, having been formed from fructose. Evidence is presented that the purine-fermenting organisms, C. acidiurici and C. cylindrosporum, totally synthesized about 9% of the acetate from CO(2), and that the methyl group of an additional 9% was formed from CO(2). The remaining acetate was formed from the carbons of the purine and not via CO(2). It has been postulated that the fermentation of the purines and synthesis of acetate from CO(2) both occur via derivatives of tetrahydrofolate. Evidence is presented that a compartmentalization of these folate intermediates is required if both the purine degradation and the CO(2) utilization involve identical intermediates. Neither B. rettgeri nor D. glycinophilus incorporated sufficient (13)CO(2) into acetate to allow determination of the types of acetate by mass analysis, although they did incorporate labeled (14)CO(2) in both positions of acetate.

Biochemical functions of corrinoid compounds. The sixth Hopkins memorial lecture

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