How do anaerobic organisms obtain energy

This 3-methylaspartate pathway is initiated by the coenzyme B 12 -dependent carbon skeleton rearrangement of S -glutamate to 2 S ,3 S methylaspartate Barker et al. Addition of water yields S -citramalate 2-methylmalate Blair and Barker, , which is cleaved to acetate and pyruvate Buckel and Bobi, The remaining 2 Fd — are used to produce 1 H 2.

The fermentations of glutamate via methylaspartate or 2-hydroxyglutarate lead to identical products and to identical amounts of conserved ATP. Therefore, the question arises why bacteria exclusively use one of these pathways.

These cofactors are not pathway specific, because they are also necessary for anabolism. Hence, F. Therefore, the reason for the existence of this pathway must be found somewhere else. The organisms using the 2-hydroxyglutarate pathway, A.

In contrast, the members of the 3-methylaspartate pathway C. The employment of the 2-hydroxyglutarate pathway in the human gut could be due to the much lower oxygen concentration as compared to soil which encounters often exposures to air through plant roots, earthworms, moles, etc. Probably, the oxygen sensitivity of enzymes of an important pathway might be responsible for the ecology of the organism. Both glutamate fermenting pathways contain oxygen sensitive radical enzymes.

Whereas coenzyme B 12 -dependent glutamate mutase in the 3-methylaspartate pathway is only moderately oxygen sensitive, 2-hydroxyglutaryl-CoA dehydratase in the 2-hydroxyglutarate pathway immediately becomes inactive after exposure to air. Coenzyme B 12 -dependent mutases catalyze the reversible radical rearrangement of a methine radical to a methylene radical.

The process is initiated by homolysis of the carbon-cobalt bond of coenzyme B After each turnover, the radical disappears by reformation of the carbon-cobalt bond of the coenzyme, for a review see Buckel and Golding Thus, in the presence of air, the radicals are only transiently exposed to oxygen as the coenzyme B 12 -dependent methylmalonyl-CoA mutase in human mitochondria. In contrast, 2-hydroxyglutaryl-CoA dehydratase acts with a completely different radical mechanism Buckel and Keese, , for a review see Buckel The enzyme system is composed of two proteins.

The homodimeric activator contains one ADP in each subunit and one [4Fe-4S] cluster coordinated by four cysteines, two from each subunit, similar to the iron protein NifH of nitrogenase Locher et al. The heterodimeric dehydratase holds one [4Fe-4S] cluster in each subunit. Each cluster is coordinated by three cysteines; the fourth coordination is occupied in subunit A by a sulfur atom and in subunit B by water, which can be replaced by the thioester carbonyl of the substrate.

The electron in cluster B reduces the thioester carbonyl to a ketyl radical, which due to its lower basicity is replaced from the iron by the hydroxyl group at C-2, a process called ligand swapping.

Aided by the iron of cluster B, the nucleophilic ketyl eliminates the hydroxyl group to form an enoxy radical. The resulting allylic ketyl replaces the formed water by a second ligand swapping and returns the electron via cluster B to cluster A. The formed product glutaconyl-CoA is released and cluster B is able to accept the next substrate together with the electron form cluster A.

The dehydratase is able to catalyze at least turnovers before another ATP molecule has to be hydrolyzed to continue catalysis Kim et al. Proof of this mechanism was obtained by detection of the corresponding allylic ketyl radical of R hydroxyisocaproyl-CoA dehydratase from C. It has been shown experimentally that R hydroxyacyl-CoA dehydratases are indeed much more oxygen sensitive than coenzyme B 12 -dependent carbon skeleton mutases. Whereas 2-hydroxyglutarate dehydratases had to be purified and assayed under strict exclusion of oxygen Kim et al.

During catalysis, however, after about 1 min a significant effect of air on the rate of 3-methylaspartate formation from glutamate was observed Leutbecher et al. In the dehydratases, the electron never disappears during the catalytic cycle and the iron-sulfur cluster of the activator is solvent accessible, which makes it extremely oxygen sensitive. Thus, only during catalysis the radical is exposed to oxygen. In contrast, in R hydroxyglutaryl-CoA dehydratase of the alternative glutamate fermenting pathway, the radical is always present and exposed to the medium.

In addition, the iron-sulfur clusters of the dehydratase and its activator are very oxygen-sensitive. Most likely, this is the reason, why organisms of the 2-hydroxyglutarate pathway are only found in the gut or in strictly anaerobic marine sediments. Furthermore, B 12 -dependent carbon skeleton mutases and eliminases as well as thiamin diphosphate dependent enzymes are substituted in the gut by glycyl radical enzymes Table 2. Similar to R hydroxyacyl-CoA dehydratases, glycyl radical enzymes also require specific activating enzymes.

This radical irreversibly abstracts one hydrogen from a conserved glycine residue of the enzyme to give a stable protein-bound radical. Upon binding of substrate, the glycyl radical abstracts the sulfhydryl hydrogen form a nearby cysteine residue, which in turn removes the hydrogen atom from the substrate.

After the rearrangement, the radical returns to the glycine residue and remains stable until the next turnover, unless it is attacked by oxygen Knappe and Sawers, ; Shisler and Broderick, Table 2. Pairs of oxygen-tolerant and intolerant enzymes which catalyze the same reaction or are key enzymes of alternative pathways leading to the same products.

Many organisms including humans are able to degrade propionate via carboxylation of propionyl-CoA to S -methylmalonyl-CoA and racemization to R -methylmalonyl-CoA, which is rearranged to succinyl-CoA mediated by coenzyme B The Krebs cycle converts succinyl-CoA to oxaloacetate, which enters gluconeogenesis or is degraded via pyruvate to acetyl-CoA.

Propionibacteria use the reverse pathway to produce propionate from succinate. Veillonella alcalescens and P. In contrast, Clostridium propionicum , isolated from marine mud Cardon and Barker, , converts alanine, cysteine and serine via pyruvate Hofmeister et al. Like 2-hydroxyglutaryl-CoA dehydratase, lactyl-CoA dehydratase is an extremely oxygen sensitive radical enzyme Parthasarathy et al. The rumen micro-organism Megasphaera elsdenii reduces about half of the consumed lactate in the same way as C.

Homocysteine, derived from methionine, suffers a similar elimination to 2-oxobutyrate, ammonia and sulfide. Some anaerobic bacteria oxidize 2-oxobutyrate with ferredoxin to propionyl-CoA catalyzed by a thiamin diphosphate TDP -dependent enzyme and excrete propionate. Three eliminations of water from 1,2-diols are known, each of which is catalyzed by two different enzymes, either coenzyme B 12 -dependent or by the much more oxygen-sensitive glycyl radical enzymes Table 2.

The coenzyme B 12 -dependent glycerol dehydratase catalyzes the removal of the central hydroxyl group of glycerol yielding 3-hydroxypropanal Forage and Foster, , which can be reduced to 1,3-propanediol, a building block for polyesters. Abeles Zagalak et al. In the human gut, degradation of L-fucose 6-deoxygalactose and L-rhamnose 6-deoxymannose affords propane-1,2-diol, which is dehydrated to propanal, catalyzed by the glycyl radical enzyme propane-1,2-diol dehydratase Levin and Balskus, The third pair of coenzyme B 12 and glycyl radical enzymes catalyzing the same reaction are classes II and III of ribonucleotide reductase Greene et al.

The reduction of the formed enoxy radical differs between the classes. In class II the reductants are two cysteine residues which form a disulfide, whereas class III uses formate for this purpose. In the eliminations of ammonia from ethanolamine or trimethylamine from choline, carbon nitrogen bonds are broken. Interestingly, for the deamination of ethanolamine only a coenzyme B 12 -dependent enzyme is known Shibata et al.

Perhaps the different elimination mechanisms, but not the oxygen sensitivity, are responsible for the kind of radical enzyme applied. It has been proposed theoretically Buckel, ; Feliks and Ullmann, ; Kovacevic et al.

Coenzyme B 12 -dependent propane-1,2-diol dehydratase and glycerol dehydratase, however, shift the hydroxyl group at C2 to C1, forming propane-1,1-diol or 3-hydroxypropane-1,1-diol which dehydrate to the aldehydes. Because trimethylamine is a better leaving group than ammonia, chemistry might compel choline lyase to use the glycyl radical mechanism.

The oxidation of pyruvate to acetyl-CoA is a complex reaction for which nature has developed thiamin diphosphate, which causes Umpolung of the carbonyl group of the 2-oxo acid to enable decarboxylation. Most likely a concealed radical is involved in the reaction Chen et al. Thus this reaction is an example of anaerobes being more efficient energy converters than aerobes.

Under strict anaerobic conditions, pyruvate dehydrogenase of E. The enzyme is also present in other enterobacteria and several clostridia. The degradation of taurine 2-aminoethylsulfonate in aerobes and facultative anaerobes affords sulfoacetaldehyde by amino transfer to pyruvate.

The aldehyde is converted by the TDP-dependent sulfoacetaldehyde acetyltransferase Xsc to acetyl phosphate and sulfite Ruff et al. Under the strict anaerobic conditions in the gut, the Bacillus Bilophila wadsworthia bypasses Xcs with an aldehyde reductase and the glycyl radical enzyme isethionate lyase. This enzyme catalyzes the radical diol dehydratase-like elimination of isethionate 2-sulfoethanol yielding acetaldehyde and sulfite which is reduced to H 2 S Peck et al.

The genes iseG and iseH coding for isethionate lyase and its activating enzyme were also detected in several well-known sulfate reducing organisms Dawson et al. The genes from Desulfovibrio vulgaris str. Hildenborough were expressed in E.

In this review it has become apparent that radical reactions play an important part in the metabolism of anaerobes and most likely already in prebiotic chemistry Dragicevic et al. Table 2 summarizes the pairs of oxygen-tolerant and intolerant enzymes which catalyze radical reactions leading to the same product or are key enzymes of alternative pathways. Whereas the oxygen-intolerant 2-hydroxyacyl-CoA dehydratases and glycyl radical enzymes have simple cofactors, the oxygen-tolerant coenzyme B 12 and TDP-dependent enzymes use the most complex cofactors known in biochemistry Jurgenson et al.

Apparently, the oxygen-intolerant radical enzymes evolved first and prevailed under the primeval atmosphere until the oxygen concentration raised, which forced nature to develop the oxygen tolerant and much more complex cofactors coenzyme B 12 and TDP.

The oxygen-intolerant radical enzymes survived only in strictly anaerobic places such as the human gut and marine sediments. Probably, these coenzyme B 12 and TDP dependent fermentations were not present at the origin of life, but emerged just before or during the Great Oxidation event at 2. Many obligate anaerobic bacteria in the human gut produce butyrate. The most common pathway is the condensation of two acetyl-CoA to acetoacetyl-CoA, followed by the first reduction to S hydroxybutyryl-CoA, dehydration to crotonyl-CoA and the second reduction to butyryl-CoA as shown in the fermentation of glutamate via 3-methylaspartate.

The second reduction by NADH is coupled to the reduction of ferredoxin via electron bifurcation Buckel and Thauer, This pathway is used by most organisms fermenting carbohydrates, as are bacteria related to Roseburia intestinalis , Faecalibacterium prausnitzii , and Eubacterium hallii all belong to Firmicutes. The majority of the bacteria in the human gut belong to Bacteroidetes Gevers et al.

As mentioned above A. Probably no anaerobe wants to abandon the large energy released during butyrate synthesis by taking another route.

Actually the enzyme acts as crotonyl-CoA carboxylase yielding ethylmalonyl-CoA. Fermentations of amino acids, which give rise to butyrate, are degraded to acetyl-CoA or directly to crotonyl-CoA as shown by the fermentation of glutamate via 2-hydroxyglutarate. Clostridium propionicum oxidizes threonine and methionine to R hydroxybutyrate which is converted to crotonyl-CoA by a mechanism similar to that shown for R hydroxyglutarate Barker and Wiken, The complex anaerobic degradation of lysine in Clostridium subterminale SB4 Barker, and Fusobacterium nucleatum Barker et al.

The latter is deaminated to 3-oxoaminohexanoate and cleaved with acetyl-CoA to acetoacetate and 3-aminobutyryl-CoA followed by deamination to crotonyl-CoA Jeng and Barker, and reduction to butyryl-CoA, which forms butyrate and acetoacetyl-CoA with acetoacetate. Histidine is degraded to butyrate via glutamate either by C.

In a Stickland type fermentation, proline is reduced to 5-aminovalerate by Clostridium sporogenes Stickland, , which is deaminated to 5-hydroxyvalerate and further converted via homocrotonyl-CoA to valerate homobutyrate by Clostridium viride Eikmanns and Buckel, ; Buckel et al. In the human gut, butyrate is the preferred nutrient of the mucosa cells, which form the inner wall of the large intestine, also called colonic epithelia cells.

NO is further oxidized to nitrate, an electron acceptor for potentially pathogenic enterobacteria. For example, E. However, in the presence of oxygen or nitrate the facultative anaerobe forms pyruvate dehydrogenase eq. In case, the quickly spreading E. To prevent such events, butyrate nourishes colonic epithelia cells, which provides an oxygen-free medium for the microbiome in the large intestine and protects the host from harmful bacteria Cani, For a constant butyrate production, the microbiome must be well fed with carbohydrates and amino acids.

However, glucose, lactose, starch, glycogen and most proteins are digested and resorbed already in the small intestine, and nothing is left for the microbiome in the gut. Therefore, the human diet must contain indigestible carbohydrate and protein fibers for the mircrobiome, which is able to hydrolyze almost every glycosidic and peptide bond. Hence, fibers for the human diet are necessary for a healthy gut. The author confirms being the sole contributor of this work and has approved it for publication.

The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers.

Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. Anbar, A. A whiff of oxygen before the great oxidation event?

Science , — Barker, H. Amino acid degradation by anaerobic bacteria. Pathway of lysine degradation in Fusobacterium nucleatum. The purification and properties of beta-methylaspartase. Glutamate mutase reaction. The origin of butyric acid in the fermentation of threonine by Clostridium propionicum. Google Scholar. Bergdoll, L. From low- to high-potential bioenergetic chains: thermodynamic constraints of Q-cycle function. Acta , — Biegel, E. Blair, A. Boiangiu, C. Sodium ion pumps and hydrogen production in glutamate fermenting anaerobic bacteria.

The genome sequence of Clostridium tetani , the causative agent of tetanus disease. Buckel, W. Colloquium - Mosbach , eds G. Hauska and R. Thauer Heidelberg: Springer Verlag , 21— Unusual dehydrations in anaerobic bacteria: considering ketyls radical anions as reactive intermediates in enzymatic reactions.

FEBS Lett. Sodium ion-translocating decarboxylases. Acta , 15— Unusual enzymes involved in five pathways of glutamate fermentation. The final product varies depending on the metabolic pathway involved. For example, in denitrification, the final product is N 2. In fumarate respiration, succinate is the final product. In methanogenesis, the final product is methane whereas, in acetogenesis, it is acetate. In dehalorespiration, the final products are halide ions and dehalogenation compound.

In fermentation, the final product may be lactic acid or ethanol. Apart from these substances, energy in the form of ATP molecules is also produced. Where does anaerobic respiration occur? In the fluid part of the cytoplasm, anaerobic respiration both glycolysis and fermentation takes place, while the majority of the energy production in aerobic respiration takes place in the mitochondria.

Aerobic respiration occurs in the presence of oxygen, hence the name. The aerobic respiration equation is as follows:.

During aerobic respiration, there is an exchange of gases where oxygen is absorbed and carbon dioxide is released. It can be found in the mitochondria of the eukaryotes and the cytoplasm of the prokaryotes. The end products of aerobic respiration are water, carbon dioxide, and energy. During aerobic respiration, a total of 38 ATPs are produced, some of which are lost during the process. Also, during aerobic respiration, complete oxidation of carbohydrates takes place.

Aerobic respiration is relatively slower than anaerobic respiration. Aerobic respiration occurs in most of the higher species including plants and animals. Cellular respiration in humans is an example. In anaerobic respiration, the process occurs in the absence of oxygen.

Examples of an anaerobic respiration equation are the following:. During anaerobic respiration exchange of gases does not take place. However, some organisms release some gases, such as sulfur and nitrogen gases.

Anaerobic respiration can be found only in the cytoplasm of a cell. The end products of anaerobic respiration vary, such as gases, alcohols, acids, and energy. In fermentation, only 2 ATPs are produced.

Also, there is incomplete oxidation of carbohydrates. It occurs in simple prokaryotes, yeasts, and the muscle cells of humans during intense exercise.

Anaerobic respiration is shorter than aerobic respiration. To summarize what has been described so far, here are the equations of various cellular respirations:.

All living organisms undergo cellular respiration. In certain types of bacteria and yeast, anaerobic respiration is preferred. It gives them the advantage of surviving or thriving in an anoxic environment that would be lethal to aerobic organisms. Anaerobic respiration also has a very high speed. It produces ATP very rapidly. Aerobic respiration, on the other hand, produces ATP rather slowly. One of the most significant functions of fermentation is that it protects the cells from dying in the small amount of time between each breath and during intense activity when the red blood cells fail to provide adequate oxygen to the body cells due to under-oxygenation.

Fermentation takes over as this happens and releases a substance called lactic acid which keeps the cells of the body intact during the above-mentioned cycles of under-oxygenation. Although this quite useful for the time being, yet unfortunately, a build-up of lactic acid may cause discomfort in the muscles later. Lactic acid production in muscles. During vigorous exercise, our muscles use oxygen to generate more ATP as compared to the supply.

When this happens, the muscle cells undergo glycolysis faster than they can supply oxygen to the mitochondrial electron transport chain. As a result, anaerobic respiration and lactic acid fermentation occur within the cells and during extended activity, the built-up lactic acid will keep our muscles painful.

Alcoholic fermentation by yeasts. Fermentation is another category of anaerobic respiration that occurs in anaerobic organisms such as yeast. When carbohydrate-rich substances are bottled with yeasts to ensure a minimal oxygen level in the container, yeasts undergo the process of anaerobic respiration. As a process, fermentation occurs where the yeast converts sugars into ethyl alcohol. Methanogens are prokaryotes that belong to the Archaea. These species are considered methanogens because they produce methane as a by-product by oxidizing carbohydrates in the absence of oxygen.

This process is called methanogenesis. Cookies deactivated. To use all functions of this page, please activate cookies in your browser. Login Register. Additional recommended knowledge. Topics A-Z. All topics. To top. About bionity. Your browser is not current. Microsoft Internet Explorer 6.

Your browser does not support JavaScript. To use all the functions on Chemie. DE please activate JavaScript. Obligate anaerobes will die when exposed to atmospheric levels of oxygen. Facultative anaerobes can use oxygen when it is present.