Metabolism aliphatics

The metabolic processes underpinning the catabolism of aliphatic and aromatic compounds are described in the BIOTOL text "Energy Sources for Cell". 

The metabolism of foreign compounds (xenobiotics) often takes place in two consecutive reactions, classically referred to as phases one and two. Phase I is a functionalization of the lipophilic compound that can be used to attach a conjugate in Phase II. The conjugated product is usually sufficiently water-soluble to be excretable into the urine. The most important biotransformations of Phase I are aromatic and aliphatic hydroxylations catalyzed by cytochromes P450. Other Phase I enzymes are for example epoxide hydrolases or carboxylesterases. Typical Phase II enzymes are UDP-glucuronosyltrans-ferases, sulfotransferases, N-acetyltransferases and methyltransferases e.g. thiopurin S-methyltransferase. 

The NHase responsible for aldoxime metabolism from the i -pyridine-3-aldoxime-degrading bacterium, Rhodococcus sp. strain YH3-3, was purified and characterized. Addition of cobalt ion was necessary for the formation of enzyme. The native enzyme had a Mr of 130000 and consisted of two subunits (a-subunit, 27 100 (3-subunit, 34500). The enzyme contained approximately 2 mol cobalt per mol enzyme. The enzyme had a wide substrate specificity it acted on aliphatic saturated and unsaturated as well as aromatic nitriles. The N-terminus of the (3-subunit showed good sequence similarities with those of other NHases. Thus, this NHase is part of the metabolic pathway for aldoximes in microorganisms. 

Some green algae are able to use aromatic sulfonic acids (Figure 2.4a) (Soeder et al. 1987) and aliphatic sulfonic acids (Figure 2.4b) (Biedlingmeier and Schmidt 1983) as sources of sulfur. Cultures of Scenedesmus obliquus under conditions of sulfate limitation metabolized naphthalene-l-sulfonate to l-hydroxy-naphthalene-2-sulfonate and the gluco-side of naphth-l-ol (Kneifel et al. 1997). These results are consistent with formation of a 1,2-epoxide followed by an NIH shift. 

Ensign SA, FJ Smakk, JR Allen, MK Sluis (1998) New roles for COj in the microbial metabolism of aliphatic epoxides and ketones. Arch Microbiol 169 179-187. 

Stable metabolic associations generally between pairs of anaerobic bacteria have been termed syntrophs, and these are effective in degrading a number of aliphatic carboxylic acids or benzoate under anaerobic conditions. These reactions have been discussed in reviews (Schink 1991, 1997 Lowe et al. 1993) that provide lucid accounts of the role of syntrophs in the degradation of complex organic matter. Two examples are given here to illustrate the experimental intricacy of the problems besetting the study of syntrophic metabolism under anaerobic conditions ... 

Boyd JM, A Ellsworth, SA Ensign (2006) Characterization of 2-bromoethanesulfonate as a selective inhibitor of the coenzyme M-dependent pathway and enzymes of bacterial aliphatic epoxide metabolism. J Bacteriol 188 8062-8069. 

Krum JG, SA Ensign (2001) Evidence that a linear megaplasmid encodes enzymes of aliphatic alkene and epoxide metabolism and coenzyme M (2-mercaptoethanesulfonate) biosynthesis in Xanthobacter strain Py2. J Bacterial 183 2172-2177. 

Small FJ, SA Ensign (1997) Alkene monooxygenase from Xanthobacter strain Py2. Purification and characterization of a four-component system central to the bacterial metabolism of aliphatic alkenes. J Biol Chem 272 24913-24920. 

FIGURE 11.9 Elimination reactions during metabolism of aliphatic sulfur compounds (a) cysteine, (b) methionine, and (c) 2-dimethylsulfoniopropionate. 

Fournier D, S Trott, J Hawari, J Spain (2005) Metabolism of the aliphatic nitramine 4-nitro-2,4-diazabutranal by Methylobacterium sp. strain JS 178. Appl Environ Microbiol 71 4199-4202. 

Aliphatic compounds Several water-soluble simple organic acids and alcohols are cannon plant and soil constituents. They include methanol, ethanol, n-propanol and butanol (40), and crotonic, oxalic, formic, butyric, lactic, acetic and succinic acids (41, 42), all of which inhibit seed germination or plant growth. Under aerobic conditions, however, aliphalic acids are metabolized in the soil and therefore, should not be considered a major source of allelopathic activity (40). 

Aliphatic acids such as butyric acid have been previously implicated as being allelopathic compounds (46, 47, 23). Chou and Patrick (23) isolated butyric acid from soil amended with rye and showed that it was phytotoxic. Hydroxy acids have also been shown to possess phytotoxic properties (48) but have not been implicated in any allelopathic associations. Since SHBA is a stereo isomer, and the enantiomer was not identified because of impurity, all bioassays were run using a racemic mixture. The D-(-) stereo isomer of SHBA has been isolated from both microorganisms and root nodules of legumes and is suspected to be a metabolic intermediate in these systems (49). It is likely that only one enantiomer was present in the extract therefore, the true phytotoxic potential of this compound awaits clarification of the phytotoxicity of the individual enantiomers. 

In some cases, microorganisms can transform a contaminant, but they are not able to use this compound as a source of energy or carbon. This biotransformation is often called co-metabolism. In co-metabolism, the transformation of the compound is an incidental reaction catalyzed by enzymes, which are involved in the normal microbial metabolism.33 A well-known example of co-metabolism is the degradation of (TCE) by methanotrophic bacteria, a group of bacteria that use methane as their source of carbon and energy. When metabolizing methane, methanotrophs produce the enzyme methane monooxygenase, which catalyzes the oxidation of TCE and other chlorinated aliphatics under aerobic conditions.34 In addition to methane, toluene and phenol have been used as primary substrates to stimulate the aerobic co-metabolism of chlorinated solvents. 

Rinkus SJ, Legator MS. 1985. Fluorometric assay using high-pressure liquid chromatography for the microsomal metabolism of certain substituted aliphatics to 1, Ne-ethenoadenine-forming metabolites. Anal Biochem 150 379-393. 

The authors have also synthesized134 fatty acids labelled with deuterium and carbon-11 in order to investigate if kinetic isotope effects related to fatty acid metabolism can be observed in vivo by pet133,135-137. In vitro, the large kinetic deuterium isotope effects are observed in the oxidation of deuteriated aliphatic carboxylic acids with alkaline permanganate and manganate135-139. 

Acetyltransferases catalyze the acetylation of amino, hydroxyl, and thiol functional groups. Acetylation of hydroxy and thiol groups is comparatively rare and of much less importance in alkaloid metabolism than reactions with amino functional groups. The types of amines that are acetylated include arylamines (the major route of metabolism in many species), aliphatic amines, hydrazines, sulfonamides, and the a-amino group of cysteine conjugates. The purification, physical properties, and specificity of the N-acetyltransfereases have been reviewed (116-118). 

The theory predicting the stability of the radical formed assumes that the rate-limiting step is the extraction of the hydrogen atom to form a radical, and this hypothesis is in principle valid for aliphatic hydroxylation, but it might not be the case for other reactions. Several examples in the literature show that this method is useful for the prediction of the site of metabolism for compounds undergoing metabolism by CYP3A4 [8]. Nevertheless, there is a lack of a theory that could explain all the different metabolism reactions and mechanisms that may or may not involve radical formation. 

Vesey et al. 1976) and a series of commercially important, simple, aliphatic nitriles (e.g., acetonitrile, propionitrile, acrylonitrile, n-butyronitrile, maleonitrile, succinonitrile) (Willhite and Smith 1981) release cyanide upon metabolism. These drugs and industrial chemicals have been associated with human exposure to cyanide and have caused serious poisoning and, in some cases, death. 

Thus a distinction was provided between simple esterases, such as fiver esterase, which catalysed the hydrolysis of simple aliphatic esters but were ineffective towards choline esters. The term 1 cholinesterase was extended to other enzymes, present in blood sera and erythrocytes of other animals, including man, and in nervous tissue, which catalysed the hydrolysis of acetylcholine. It was assumed that only one enzyme was involved until Alles and Hawes2 found that the enzyme present in human erythrocytes readily catalysed the hydrolysis of acetylcholine, but was inactive towards butyrylcholine. Human-serum enzyme, on the other hand, hydrolyses butyrylcholine more rapidly than acetylcholine. The erythrocyte enzyme is sometimes called true cholinesterase, whereas the serum enzyme is sometimes called pseudo-cholinesterase. Stedman,3 however, prefers the names a-cholinesterase for the enzyme more active towards acetylcholine, and / -cholinesterase for the one preferentially hydrolysing butyrylcholine. Enzymes of the first type play a fundamental part in acetylcholine metabolism in vivo. The function of the second type in vivo is obscure. Not everyone agrees with the designation suggested by Stedman. It must also be stressed that enzymes of one type from different species are not always identical in every respect.4 Furthermore,... 

Halogenated aliphatics can be partially or completely degraded under anaerobic conditions through a transformation reaction called reductive de-halogenation. Often a co-metabolic degradation step, reductive dehalogenation... 

The first systematic study of the metabolic hydrolysis of primary aliphatic amides was carried out by Bray et al. in 1950 [1]. The substrates were incubated in rabbit liver preparations for 5 h at 37°. In Fig. 4.2, the effect of chain length on the degree of hydrolysis of amides containing 1 to 18 C-atoms (4.1) is shown. The extent of hydrolysis was very small for the first three homo-... 

Like the simple aliphatic secondary amides discussed above, structurally more-complex compounds may also be expected to undergo hydrolysis. However, very few such results are available, implying either that xenobio-tics are relatively stable, or that they have been insufficiently studied. It seems that the former reason is the more likely, since the amide bond, in general, is chemically stable and is metabolized over only a narrow range of structures (see, e.g., the /V-alkyl-substituted amides discussed above). Some of the few reported examples of structurally complex xenobiotics that undergo amide hydrolysis are discussed below. 

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