THE ROLE OF TRANSCARBOXYLATION IN PROPIONIC ACID FERMENTATION

Metabolic energy conservation for fermentative product formation

Microbial production of bulk chemicals and biofuels from carbohydrates competes with low-cost fossil-based production. To limit production costs, high titres, productivities and especially high yields are required. This necessitates metabolic networks involved in product formation to be redox-neutral and conserve metabolic energy to sustain growth and maintenance. Here, we review the mechanisms available to conserve energy and to prevent unnecessary energy expenditure. First, an overview of ATP production in existing sugar-based fermentation processes is presented. Substrate-level phosphorylation (SLP) and the involved kinase reactions are described. Based on the thermodynamics of these reactions, we explore whether other kinase-catalysed reactions can be applied for SLP. Generation of ion-motive force is another means to conserve metabolic energy. We provide examples how its generation is supported by carbon-carbon double bond reduction, decarboxylation and electron transfer between redox cofactors. In a wider perspective, the relationship between redox potential and energy conservation is discussed. We describe how the energy input required for coenzyme A (CoA) and CO2 binding can be reduced by applying CoA-transferases and transcarboxylases. The transport of sugars and fermentation products may require metabolic energy input, but alternative transport systems can be used to minimize this. Finally, we show that energy contained in glycosidic bonds and the phosphate-phosphate bond of pyrophosphate can be conserved. This review can be used as a reference to design energetically efficient microbial cell factories and enhance product yield.

From Glucose to Lactate and Transiting Intermediates Through Mitochondria, Bypassing Pyruvate Kinase: Considerations for Cells Exhibiting Dimeric PKM2 or Otherwise Inhibited Kinase Activity

A metabolic hallmark of many cancers is the increase in glucose consumption coupled to excessive lactate production. Mindful that L-lactate originates only from pyruvate, the question arises as to how can this be sustained in those tissues where pyruvate kinase activity is reduced due to dimerization of PKM2 isoform or inhibited by oxidative/nitrosative stress, posttranslational modifications or mutations, all widely reported findings in the very same cells. Hereby 17 pathways connecting glucose to lactate bypassing pyruvate kinase are reviewed, some of which transit through the mitochondrial matrix. An additional 69 converging pathways leading to pyruvate and lactate, but not commencing from glucose, are also examined. The minor production of pyruvate and lactate by glutaminolysis is scrutinized separately. The present review aims to highlight the ways through which L-lactate can still be produced from pyruvate using carbon atoms originating from glucose or other substrates in cells with kinetically impaired pyruvate kinase and underscore the importance of mitochondria in cancer metabolism irrespective of oxidative phosphorylation.

Underground isoleucine biosynthesis pathways in E. coli

The promiscuous activities of enzymes provide fertile ground for the evolution of new metabolic pathways. Here, we systematically explore the ability of E. coli to harness underground metabolism to compensate for the deletion of an essential biosynthetic pathway. By deleting all threonine deaminases, we generated a strain in which isoleucine biosynthesis was interrupted at the level of 2-ketobutyrate. Incubation of this strain under aerobic conditions resulted in the emergence of a novel 2-ketobutyrate biosynthesis pathway based upon the promiscuous cleavage of O-succinyl-L-homoserine by cystathionine γ-synthase (MetB). Under anaerobic conditions, pyruvate formate-lyase enabled 2-ketobutyrate biosynthesis from propionyl-CoA and formate. Surprisingly, we found this anaerobic route to provide a substantial fraction of isoleucine in a wild-type strain when propionate is available in the medium. This study demonstrates the selective advantage underground metabolism offers, providing metabolic redundancy and flexibility which allow for the best use of environmental carbon sources.

Evolutionary engineering in Saccharomyces cerevisiae reveals a TRK1-dependent potassium influx mechanism for propionic acid tolerance

BACKGROUND

Propionic acid (PA), a key platform chemical produced as a by-product during petroleum refining, has been widely used as a food preservative and an important chemical intermediate in many industries. Microbial PA production through engineering yeast as a cell factory is a potentially sustainable alternative to replace petroleum refining. However, PA inhibits yeast growth at concentrations well below the titers typically required for a commercial bioprocess.

RESULTS

Adaptive laboratory evolution (ALE) with PA concentrations ranging from 15 to 45 mM enabled the isolation of yeast strains with more than threefold improved tolerance to PA. Through whole genome sequencing and CRISPR-Cas9-mediated reverse engineering, unique mutations in TRK1, which encodes a high-affinity potassium transporter, were revealed as the cause of increased propionic acid tolerance. Potassium supplementation growth assays showed that mutated TRK1 alleles and extracellular potassium supplementation not only conferred tolerance to PA stress but also to multiple organic acids.

CONCLUSION

Our study has demonstrated the use of ALE as a powerful tool to improve yeast tolerance to PA. Potassium transport and maintenance is not only critical in yeast tolerance to PA but also boosts tolerance to multiple organic acids. These results demonstrate high-affinity potassium transport as a new principle for improving organic acid tolerance in strain engineering.

Shifting the balance of fermentation products between hydrogen and volatile fatty acids: microbial community structure and function

Fermentation is a key process in many anaerobic environments. Varying the concentration of electron donor fed to a fermenting community is known to shift the distribution of products between hydrogen, fatty acids and alcohols. Work to date has focused mainly on the fermentation of glucose, and how the microbial community structure is affected has not been explored. We fed ethanol, lactate, glucose, sucrose or molasses at 100 me- eq. L^-1, 200 me- eq. L^-1 or 400 me- eq. L^-1 to batch-fed cultures with fermenting, methanogenic communities. In communities fed high concentrations of electron donor, the fraction of electrons channeled to methane decreased, from 34% to 6%, while the fraction of electrons channeled to short chain fatty acids increased, from 52% to 82%, averaged across all electron donors. Ethanol-fed cultures did not produce propionate, but did show an increase in electrons directed to acetate as initial ethanol concentration increased. In glucose, sucrose, molasses and lactate-fed cultures, propionate accumulation co-occurred with known propionate producing organisms. Overall, microbial communities were determined by the substrate provided, rather than its initial concentration, indicating that a change in community function, rather than community structure, is responsible for shifts in the fermentation products produced.

Which way does the citric acid cycle turn during hypoxia? The critical role of α-ketoglutarate dehydrogenase complex

The citric acid cycle forms a major metabolic hub and as such it is involved in many disease states involving energetic imbalance. In spite of the fact that it is being branded as a "cycle", during hypoxia, when the electron transport chain does not oxidize reducing equivalents, segments of this metabolic pathway remain operational but exhibit opposing directionalities. This serves the purpose of harnessing high-energy phosphates through matrix substrate-level phosphorylation in the absence of oxidative phosphorylation. In this Mini-Review, these segments are appraised, pointing to the critical importance of the α-ketoglutarate dehydrogenase complex dictating their directionalities.

HPLC assay for methylmalonyl-CoA epimerase

Methylmalonyl-CoA epimerase (MCE) is broadly distributed in nature and has diverse cellular roles. Many MCE homologues are represented in public databases, but the biochemical function and physiological roles of the majority of these putative proteins have not been investigated. Here, a simplified assay for MCE is described. In this assay, MCE converted (2S)-methylmalonyl-CoA to (2R)-methylmalonyl-CoA which in turn was converted to succinyl-CoA by methylmalonyl-CoA mutase, an enzyme specific for the 2 R isomer. MCE activity was quantified by measuring the disappearance of methylmalonyl-CoA by HPLC. To obtain the methylmalonyl-CoA mutase which was required as a reagent for the assay, an Escherichia coli strain was constructed that expressed high levels of this enzyme as a fusion protein with an 8x histidine tag. This allowed purification of the mutase in a single affinity chromatography step. Previously reported MCE assays required radioactive substrates and/or multiple reagent enzymes that were difficult to obtain. The assay reported here overcomes these difficulties and hence will facilitate studies of MCEs. Such enzymes play important roles in the metabolism of both prokaryotes and higher eukaryotes including humans.

THE GENUS VEILLONELLA . II. NUTRITIONAL STUDIES

Rogosa, M. (National Institute of Dental Research, U.S. Public Health Service, Bethesda, Md.), and Ferial S. Bishop. The genus Veillonella. II. Nutritional studies. J. Bacteriol. 87:574-580. 1964.-A medium is described for the study of the vitamin, hypoxanthine, putrescine, or cadaverine requirements of 86 Veillonella isolates from man, rabbit, rat, and hamster. No organism required riboflavine or folic acid for growth. Niacin and calcium pantothenate were often stimulatory, but in nearly all cases were dispensable. Biotin and p-aminobenzoic acid were frequently stimulatory and sometimes indispensable for continued growth. V. parvula (antigenic group VI) required pyridoxal and thiamine and did not require putrescine or cadaverine. V. alcalescens (antigenic group IV) required pyridoxal, generally required thiamine, and also required putrescine or cadaverine. Of the isolates, 25 from the rat and 3 from the hamster (antigenic group II) generally behaved like V. parvula, except that a putrescine or cadaverine requirement was often observed. Spermine, spermidine, and agmatine could not replace putrescine or cadaverine. Although succinate is metabolized by resting cells, the organisms could not grow with succinate as an energy source.

PURIFICATION AND PROPERTIES OF ENZYMES INVOLVED IN THE PROPIONIC ACID FERMENTATION

Allen, S. H. G. (Western Reserve University, Cleveland, Ohio), R. W. Kellermeyer, R. L. Stjernholm, and Harland G. Wood. Purification and properties of enzymes involved in the propionic acid fermentation. J. Bacteriol. 87:171-187. 1964.-Chromatographic procedures are described for the separation and purification of phosphotransacetylase, acetyl kinase, malic dehydrogenase and coenzyme A (CoA) transferase. Purity of the enzymes was judged by homogeneity in an ultracentrifuge and by specific activity. Phosphotransacetylase was obtained 85% pure with a specific activity of 27.1. The preparation of acetyl kinase was a homogeneous protein with a specific activity of 531. The malic dehydrogenase likewise was homogeneous with a specific activity of 938. The CoA transferase, which was about 56% pure with a specific activity of 42.6, is the purest preparation of this enzyme yet described. The pH optimum was 6.5 to 7.8, and the K(m) for succinyl-CoA in the transfer of CoA to acetate was found to be 1.3 x 10(-4)m; for acetate, in the same transfer, the K(m) was 7.0 x 10(-3)m; for succinyl-CoA to propionate it was 6.8 x 10(-5)m, and for propionate, in the same reaction, 6.2 x 10(-4)m. Methods are described for the enzymatic production of methyl-malonyl-CoA, malonyl-CoA, propionyl-CoA, acetyl-CoA, and succinyl-CoA. The role of these enzymes in the propionic acid fermentation as well as the possible mechanism responsible for the high yields of adenosine triphosphate from glucose are considered.

METABOLISM OF DICARBOXYLIC ACIDS IN ACETOBACTER XYLINUM

Benziman, Moshe (The Hebrew University of Jerusalem, Jerusalem, Israel), and A. Abeliovitz. Metabolism of dicarboxylic acids in Acetobacter xylinum. J. Bacteriol. 87:270-277. 1964.-During the oxidation of fumarate or l-malate by whole cells or extracts of Acetobacter xylinum grown on succinate, a keto acid accumulated in the medium in considerable amounts. This acid was identified as oxaloacetic acid (OAA). No accumulation of OAA was observed when succinate served as substrate. These phenomena could be explained by the kinetics of malate, succinate, and OAA oxidation. OAA did not inhibit malate oxidation, even when present at high concentrations. When cells were incubated with OAA or fumarate in the presence of C(14)O(2), only the beta-carboxyl of residual OAA was found to be labeled. Evidence was obtained indicating that nicotinamide adenine dinucleotide (NAD) or nicotinamide adenine dinucleotide phosphate (NADP) are not directly involved in malate oxidation by cell-free extracts. The results suggest that malate oxidation in A. xylinum is irreversible, and is catalyzed by an enzyme which is not NAD- or NADP-linked.

Biotin-dependent carboxylation catalyzed by transcarboxylase is a stepwise process

To investigate the mechanism of the carboxylation of pyruvate to oxalacetate catalyzed by the enzyme transcarboxylase, we have measured the D(V/K) and 13(V/K) isotope effects. Comparison of the double-reciprocal plots of the initial velocities with [1H3]pyruvate and with [2H3]pyruvate as substrate yields a deuterium isotope effect on Vmax/Km of 1.39 +/- 0.04. The 13C kinetic isotope effect on the carboxylation of pyruvate to oxalacetate has been measured by the competitive method and is 1.0227 +/- 0.0008. To determine whether the removal of the proton from pyruvate and the addition of the carboxyl group occur in the same or in different steps, the double-isotope fractionation test has been used. When [2H3]pyruvate replaces [1H3]pyruvate as the substrate, the observed 13(V/K) isotope effect falls from 1.0227 to 1.0141 +/- 0.001. The latter value is in excellent agreement with the value of 1.0136, predicted for a stepwise pathway. We may conclude, therefore, that the carboxylation of pyruvate catalyzed by transcarboxylase proceeds by a stepwise mechanism involving the intermediate formation of the substrate carbanion.

Propionate formation in Rhodospirillum rubrum under anaerobic dark conditions

Experiments with 14C labelled propionyl-CoA, methylmalonyl-CoA and succinyl-CoA showed that these compounds are intermediates of propionate synthesis in fermentative metabolism of Rhodospirillum rubrum. The rate of propionate and succinate production is dependent on the CO2 concentration of the medium. There is, however, no evidence for a transcarboxylation, and high concentrations of propionate in the medium did not inhibit propionate synthesis as in the case in propionibacteria. PEP-carboxykinase (EC 4.1.1.32) and propionyl-CoA-carboxylase (EC 6.4.1.3) showed high activities, whereas the other two PEP-carboxylases (EC 4.1.1.31, EC 4.1.1.38), and the pyruvate-carboxylase (EC 4.1.1.1.) showed only very low activity. It is probable that in pyruvate fermentation metabolism of R. rubrum no specific enzymes are activated for propionate formation and all enzymes are still present from aerobic or phototrophic preculture.

The anatomy of transcarboxylase and the role of its subunits

Biotin enzymes in general catalyze the fixation of CO2 and in a few instances decarboxylations yielding CO2. Transcarboxylase is an exception; it catalyzes the transfer of a carboxyl group from one compound to another and CO2 is not involved. This enzyme plays an essential role in the formation of propionic acid by propionibacteria and its structure and catalytic mechanism have been extensively investigated including studies of the quaternary structure by electron microscopy. The structure is complex, consisting of three types of subunits: (1) a central hexameric subunit, (2) six dimeric outside subunits, and (3) twelve biotinyl subunits which bind the outside subunits to the central subunit. There are 12 substrate sites on the central subunit (2 per polypeptide) and 2 substrate sites on each of the dimeric outside subunits. The carboxyl is transferred between these sites via the biotin of the biotinyl subunit. The biotinyl subunit (approximately 123 residues) has been completely sequenced and it has been shown that the first 42 residues serve in binding the outside subunits to the central subunit and the remainder of the sequence is involved in placing the biotin between the subunits so that it may serve as the carboxyl carrier between the substrate sites on the central and outside subunits. It is proposed that the dual sites on the polypeptides of the central subunit have arisen as a consequence of gene duplication and fusion. An intriguing question is why such a complicated structure is required for catalysis of a rather simple reaction.

Nutritional Requirements of Selenomonas ruminantium for Growth on Lactate, Glycerol, or Glucose

The nutritional requirements of Selenomonas ruminantium HD4 for growth on glucose, glycerol, or lactate were investigated to clarify the results of previous studies and to relate the nutrition of the organism to its physiology. The organism required l -aspartate, CO 2 , p -aminobenzoic acid, and biotin for growth on a lactate-salts medium that contained small amounts of dithiothreitol. Aspartate could be replaced by l -malate or fumarate but not by succinate or l -asparagine. Requirements for growth with glycerol as an energy source were similar, except that aspartate was not required. With glucose as the energy source, neither aspartate nor p -aminobenzoic acid was required, but a requirement for volatile fatty acids, which could be met by n -valerate, was observed. CO 2 was required for growth on lactate or glycerol but not on glucose on complex media containing Trypticase and yeast extract. Sulfide could be used as the sole source of sulfur.

Kinetics and catalytic properties of coenzyme A transferase from Peptostreptococcus elsdenii

Coenzyme A (CoA) transferase from Peptostreptococcus elsdenii was purified to homogeneity, and some of its physical and catalytic properties were determined. The native enzyme has a molecular weight of 181,000 and is composed of two alpha subunits (molecular weight, 65,000) and one beta subunit (molecular weight 50,000). Heat treatment of the crude cell extract to 58 degrees C causes proteolysis of the native enzyme and yields a catalytically active enzyme with an approximate molecular weight of 120,000. The native CoA transferase is specific for CoA esters of short-chain alkyl monocarboxylic acids. With acetate as CoA acceptor the enzyme is active with propionyl-, butyryl-, isobutyryl-, valeryl-, isovaleryl,- and hexanoyl-CoA but not with heptanoyl or longer-chain CoA esters. There is no activity with acetoacetyl-CoA or the CoA esters of dicarboxylic acids. Steady-state kinetics indicated that the reaction proceeds via a classical bi-, bi-ping-pong mechanism. Maximal activity is obtained with propionyl- or butyryl-CoA, and both the Vmax and Km decrease as the alkyl chain length of the CoA ester increases. All CoA esters apompetitive inhibitor although it is not active as a substrate. Evidence for an enzyme CoA intermediate was provided by demonstration of an exchange between 14C-free acids (acetate and butyrate) and their corresponding CoA esters and by isolation of a 3H-labeled CoA enzyme after incubation of the enzyme with 3H-labeled acetyl-CoA. Approximately 2 mol of CoA was bound per mol of enzyme.

Factors influencing rumen fermentation: effect of hydrogen on formation of propionate

The effect of hydrogen on fermentation of lactate, pyruvate, fumarate, and succinate by resting rumen microorganisms has been investigated. Under an atmosphere of nitrogen, lactate was fermented to yield acetate as the major product (85 to 100 mole %) and propionate (0 to 17 mole %) and butyrate (0 to 3%) as secondary products. Under hydrogen, there was increased formation of both propionate and total volatile fatty acids. The amount of propionate increased 4 to 8 times and total volatile fatty acids 2.5 to 3.2 times. Propionate formation was proportional to the hydrogen concentration and reached a maximum at a partial pressure of hydrogen of .2 N/m2. With [2-carbon-14] lactate, propionate was formed via the dicarboxylic acid pathway under both nitrogen or hydrogen. Hydrogen did not affect significantly the fermentation of pyruvate or succinate. With fumarate under hydrogen, propionate and total volatile fatty acids increased 6.8 and 2 times while acetate was unchanged. The mechanism by which hydrogen exerts these effects is discussed in relation to the role of methanogenesis in the rumen.

Lactate metabolism by Veillonella parvula

A strain of Veillonella parvula M4, which grows readily in lactate broth without a requirement for carbon dioxide, has been isolated from the oral cavity. Anaerobic, washed cells of this organism fermented sodium lactate to the following products (moles/100 moles of lactate): propionate, 66; acetate, 40; carbon dioxide, 40; and hydrogen, 14. Cells grew readily in tryptone-yeast extract broth with pyruvate, oxaloacetate, malate, and fumarate, but poorly with succinate. The fermentation of pyruvate, oxaloacetate, or lactate plus oxaloacetate by washed cells resulted in the formation of propionate and acetate in ratios significantly lower than those observed with lactate as the sole carbon source. This was primarily due to increased acetate production. Cell-free extracts were unable to degrade lactate but metabolized lactate in the presence of oxaloacetate, indicating the presence of malic-lactic transhydrogenase in this organism. Lactic dehydrogenase activity was not observed. Evidence is presented for oxaloacetate decarboxylase and malic dehydrogenase activities in extracts.

Alternate pathways of metabolism of short-chain fatty acids

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Biotin-deficient growth of Bacillus polymyxa

When Bacillus polymyxa, a wild-type biotin auxotroph, is grown in biotin-deficient medium, a retardation of cell division and consequential cell elongation are the initial detectable consequences of limited biotin. Subsequent events in biotin-deficient cells include, in chronological order: inhibition of net ribonucleic acid (RNA) synthesis and a simultaneous arithmetical accumulation of protein; loss of net RNA, deoxyribonucleic acid, and protein synthesis; morphological aberration, death, and lysis. Incorporation studies employing (32)P-phosphate and (14)CO(2) demonstrate an initial selective inhibition of net ribosomal RNA synthesis over that of ribosomal protein or total protein. Biotin could not be replaced by various extracts from which biotin had been removed, nor could osmotic stabilizers be found which could prevent lysis of the culture.

Aminoimidazole ribonucleotide carboxylase. Partial purification and properties

The enzyme aminoimidazole ribonucleotide carboxylase has been partially purified from chicken livers. A somewhat higher degree of purification was achieved with pigeon liver acetone powder as the starting material. This enzyme carboxylates the ribonucleotide but cannot use the free base, aminoimidazole, as its substrate. An investigation of the requirements for optimal activity reveals that magnesium ions are essential. Inhibition by a variety of reagents which react with sulfhydryl groups indicates their importance in the fixation of carbon dioxide to aminoimidazole ribonucleotide. An exhaustive search revealed that none of the B-vitamin cofactors play a role in this reaction. The lack of an energy requirement, e.g. ATP, for activity and the nucleophilic nature of the amino-substituted ring suggest that the carboxylation of aminoimidazole ribonucleotide proceeds via a direct enzyme-mediated reaction involving Mg++ions and active sulfhydryl groups.