The effect of medium composition on the structure and physical state of sophorolipids produced by Candida bombicola ATCC 22214

Candida bombicola was grown using a variety of lipophilic carbon substrates. Most of the hydrocarbon and carboxylic acid substrates resulted in a mixture of sophorolipids consisting of free acids and the more desirable lactones. The ratio of diacylated lactone to free acid in these mixtures was a maximum when produced using hexadecane and heptadecane. All of the other lipophilic substrates resulted in significant amounts of free acids being produced. These lactone products were unique in that they precipitated as crystals, which were easily separated from the culture medium. All of the other products were isolated as oils as is usually reported in the literature. Finally, the amounts of these crystals recovered were significantly higher than those observed for any of the oily products. It was possible to determine the degree of direct incorporation of the lipophilic substrates into the sophorolipids for a homologous series of alkanes. The amount of direct incorporation increased with increasing chain length to a maximum for pentadecane, hexadecane and heptadecane. As the length of the alkane substrate increased further, the amount of direct incorporation then decreased until there was no apparent incorporation for eicosane.     

An approach to identifying novel substrates of bacterial arylamine N-acetyltransferases

Arylamine N-acetyltransferases (NATs) catalyse the acetylation of arylamine, arylhydrazine and arylhydroxylamine substrates by acetyl Coenzyme A. NAT has been discovered in a wide range of eukaryotic and prokaryotic species. Although prokaryotic NATs have been implicated in xenobiotic metabolism, to date no endogenous role has been identified for the arylamine N-acetyl transfer reaction in prokaryotes. Investigating the substrate specificity of these enzymes is one approach to determining a possible endogenous role for prokaryotic NATs. We describe an accurate and efficient assay for NAT activity that is suitable for high-throughput screening of potential NAT ligands. This assay has been utilised to identify novel substrates for pure NAT from Salmonella typhimurium and Mycobacterium smegmatis which show a relationship between the lipophilicity of the arylamine and its activity as a substrate. The lipophilic structure/activity relationship observed is proposed to depend on the topology of the active site using docking studies of the crystal structures of these NAT isoenzymes. The evidence suggests an endogenous role of NAT in the protection of bacteria from aromatic and lipophilic toxins.     

Subcellular distribution and membrane association of human neutrophil substrates for ADP-ribosylation by pertussis toxin and cholera toxin

Neutrophil guanine nucleotide-binding proteins are important components of receptor-mediated cellular responses such as degranulation, chemotaxis, and superoxide production. Because the cytoplasmic granules of neutrophils serve as an intracellular store of receptors and NADPH oxidase components, we investigated the subcellular distribution of substrates for ADP-ribosylation by both pertussis and cholera toxins. Cholera toxin substrates of Mr 43 and 52 kDa were present only in the plasma membrane fraction. A 39-kDa pertussis toxin substrate was present in the plasma membrane, cytosol, and a specific granule-enriched fraction. There were no substrates for either toxin in the primary granules. Quantitative GTP-gamma-5 binding was localized predominantly to the plasma membrane fraction (47%), but significant portions were found in the specific granule-enriched fractions (13%) and cytosol (34%) as well. Two-dimensional gel electrophoresis and chymotryptic digests of the pertussis toxin substrate from these three subcellular fractions suggested that they are highly homologous. Triton X-114 phase partitioning was used to investigate the hydrophobicity of the toxin substrates. The pertussis toxin substrates in the plasma membrane and granule fractions behaved like integral membrane proteins, whereas the cytosolic substrate partitioned into both lipophilic and aqueous fractions. ADP-ribosylation converted the substrates to a somewhat less lipophilic form. These data suggest that the specific granules or an organelle of similar density serve as an intracellular store of a G protein with a 39-kDa alpha-subunit and that the cytosolic fraction of neutrophils contains free alpha-subunits of the same size.     

Catalysis within the lipid bilayer-structure and mechanism of the MAPEG family of integral membrane proteins

Integral membrane enzymes of the MAPEG (membrane-associated proteins in eicosanoid and glutathione metabolism) family catalyze glutathione-dependent transformations of lipophilic substrates harvested from the lipid bilayer. Recent studies of members of this family have yielded extensive insights into the structural basis for their substrate binding and catalytic activity. Most informative are the structural studies of leukotriene C4 synthase, revealing a narrow hydrophobic substrate binding pocket allowing extensive recognition of the aliphatic chain of the LTA(4) substrate. A key feature of the pocket is a tryptophan residue that pins down the omega-end of the aliphatic chain into the active site. Since MAPEG members cannot utilize a hydrophobic effect for substrate binding, this novel mode of substrate recognition appears well suited for harvesting lipophilic substrates from the membrane. The binding mode also allows for the specific alignment of the substrate in the active site, positioning the C6 of the substrate for conjugation with glutathione. The glutathione is in turn bound in a polar pocket submerged into the protein core. Structure-based sequence alignments of human MAPEG members support the notion that the glutathione binding site is highly conserved among MAPEG enzymes and that they use a similar mechanism for glutathione activation.     

The substrate requirements of phospholipase D

The hydrolysis rates of different diphosphates, compared with the one observed with natural phosphatidylcholine, are used to identify the molecular basis for phospholipase D (PLD) catalysis. Experimental data strongly support the idea that PLD is a rather generic phosphodiesterase with very wide substrate specificity and a net preference for lipophilic substrates. The presence of choline in the polar head is not required for activity although it improves hydrolysis efficiency. Choline esters are found to be substrates for PLD hydrolysis, but only with long chain fatty acids.     

The regulation of xylanolytic enzyme formation by Butyrivibrio fibrisolvens NCFB 2249

Butyrivibrio fibrisolvens NCFB 2249 formed xylan-degrading enzymes on a wide range of carbohydrate growth substrates. The specific activities of α-L-arabinofuranosidase and β-D-xylosidase were increased (up 20-fold) after growth on xylan or xylose-containing saccharides. Xylose was not an effective substrate for xylanase production although its formation was induced on xylobiose and higher DP xylose-containing saccharides. Acetyl esterase activity was also highest after growth on xylan. The synthesis of xylanase and β-xylosidase was repressed by glucose and hemicellulosic pentoses and although α-L-arabinofuranosidase formation was also subject to catabolite regulation, xylose did not repress its synthesis.     

Kinetics of glycogen phosphorylase a with a series of semisynthetic, branched saccharides. A model for binding of polysaccharide substrates.

The requirement of muscle phosphorylase for branched polysaccharide substrates was investigated by kinetic studies on semisynthetic branched saccharides. One series of saccharides was prepared from maltoheptose by oxidizing the reducing group to a carboxyl group and coupling this with an amino group of ethylenediamine. The resulting aminooligosaccharide was coupled with p-nitrophenyl esters of mono-, di-, tetra-, and polycarboxylic aicds to produce saccharides containing one, two, four, and approximately 52 maltodextrin chains per molecule. A similar series of saccharides was prepared from a heterogeneous maltodextrin of average chain length 11.7. Kinetic constants were determined for the reaction with phoshorylase a in the direction of chain elongation. Michaelis constants are equilibrium constants for dissociation of saccharide from the enzyme-AMP-glucose-1P-saccharide complex. The Michaelis constants, expressed in terms of the concentration of nonreducing end groups, are independent of maltodextrin chain length but decrease considerably as the number of chains per molecule increases. Maximum velocities do not differ greatly from that for glycogen. Among the synthetic saccharides, only the polymer behaves similarly to glycogen in exhiiting a decreasing reaction rate as the chains are elongated. The kinetic constants are quantitatively consistent with a model in which two chain termini from the same saccharide molecule bind to the phosphorylase molecule simultaniously, Differences in binding between saccharides having different numbers of equally accessible chains are caused solely by statistical factors in the equilibrium. Highly branched substrates bind better because of their greater multiplicity of two end-group pairs.     

Effect of the lipophilic spin-labeled inhibitor of cytochrome P-450 on the activity of the microsomal system

It was shown that the lipophilic nitroxyl radical--2-hexyl-2,3,5,5-tetramethyl-4-(3-iodo-2-oxopropyliden)-im idazolidine- 1-oxyl, an affinity modified of rat liver microsomal cytochrome P-450, interacts with various forms of cytochrome P-450 as substrate type I, and it inhibits the oxidation of substrates specific for these forms. During its intravenous injection with egg phosphatidylcholine liposomes the radical is partly bound to liver microsomes, which is accompanied by a decrease of the oxygenase activity of microsomal preparations (by 30-50%) as well as by prolongation of the soporific effect of hexabarbital (2-3-fold).     

Interaction of flexible analogs of N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine and of N-methyl-4-phenylpyridinium with highly purified monoamine oxidase A and B.

Sixteen analogs of N-methyl-1,2,3,6-tetrahydropyridine (MPTP) of varying degrees of flexibility have been studied as substrates of highly purified monoamine oxidases (MAO) A and B. The relative effectiveness of the various tetrahydropyridines as substrates of MAO A and B were evaluated in terms of the function turnover number/Km, as determined by initial rate measurements. The insertion of a methylene bridge between the phenyl and tetrahydropyridine moieties of MPTP to yield N-methyl-4-benzyl-1,2,3,6-tetrahydropyridine, rendering the molecule more flexible, greatly enhances reactivity with MAO B, but not with MAO A, as compared with MPTP itself, in accord with data in the literature (Youngster et al., 1989a). The ethylene-bridged MPTP analog, on the other hand, is a far better substrate of both forms of MAO than is MPTP itself. The effect of molecular flexibility on the rate of oxidation of these compounds is obscured by substituents on the aromatic ring. Branching and rigidity were detrimental to the activity as substrates of both forms of MAO. Those analogs of 1 which contain small electron-withdrawing substituents in the phenyl ring were found to be more selective for MAO B, while those substituted with bulky groups were selectively oxidized by MAO A. The substrate binding site of MAO A probably contains a lipophilic pocket larger than that found in a similar site in MAO B.     

Vestibules are part of the substrate path in the multidrug efflux transporter AcrB of Escherichia coli

The path of substrates in the multidrug efflux pump AcrB of Escherichia coli was examined by using labeling with a lipophilic substrate mimic, Bodipy FL maleimide. Four (out of eight) residues in the vestibule bound the dye, suggesting its role in substrate transport, whereas only one (out of nine) residue in the central cavity tested positive.     

Cellobiose-oxidizing enzyme from a newly isolated cellulolytic bacterium Cytophaga sp. LX-7

Summary The cellobiose oxidizing enzyme of the newly isolated cellulolytic bacterium Cytophaga sp. LX-7 was produced extracellularly when grown on cellulose or other saccharides, which was previously noted only in fungi. The enzyme could use not only cellobiose, maltose, glucose and other saccharides but also cellulose as substrates, and use dichlorophenol indophenol and oxygen as electron acceptors.     

Substrate specificity of the RND-type multidrug efflux pumps AcrB and AcrD of Escherichia coli is determined predominantly by two large periplasmic loops

AcrAB-TolC is a constitutively expressed, tripartite efflux transporter complex that functions as the primary resistance mechanism to lipophilic drugs, dyes, detergents, and bile acids in Escherichia coli. TolC is an outer membrane channel, and AcrA is an elongated lipoprotein that is hypothesized to span the periplasm and coordinate efflux of such substrates by AcrB and TolC. AcrD is an efflux transporter of E. coli that provides resistance to aminoglycosides as well as to a limited range of amphiphilic agents, such as bile acids, novobiocin, and fusidic acid. AcrB and AcrD belong to the resistance nodulation division superfamily and share a similar topology, which includes a pair of large periplasmic loops containing more than 300 amino acid residues each. We used this knowledge to test several plasmid-encoded chimeric constructs of acrD and acrB for substrate specificity in a marR1 DeltaacrB DeltaacrD host. AcrD chimeras were constructed in which the large, periplasmic loops between transmembrane domains 1 and 2 and 7 and 8 were replaced with the corresponding loops of AcrB. Such constructs provided resistance to AcrB substrates at levels similar to native AcrB. Conversely, AcrB chimeras containing both loops of AcrD conferred resistance only to the typical substrates of AcrD. These results cannot be explained by simply assuming that AcrD, not hitherto known to interact with AcrA, acquired this ability by the introduction of the loop regions of AcrB, because (i) both AcrD and AcrA were found, in this study, to be required for the efflux of amphiphilic substrates, and (ii) chemical cross-linking in intact cells efficiently produced complexes between AcrD and AcrA. Since AcrD can already interact with AcrA, the alterations in substrate range accompanying the exchange of loop regions can only mean that substrate recognition (and presumably binding) is determined largely by the two periplasmic loops.     

Catalytic properties of an expressed and purified higher plant type zeta-carotene desaturase from Capsicum annuum.

The zeta-carotene desaturase from Capsicum annuum (EC 1.14.99.-) was expressed in Escherichia coli, purified and characterized biochemically. The enzyme acts as a monomer with lipophilic quinones as cofactors. Km values for the substrate zeta-carotene or the intermediate neurosporene in the two-step desaturation reaction are almost identical. Product analysis showed that different lycopene isomers are formed, including substantial amounts of the all-trans form, together with 7,7',9,9'-tetracis prolycopene via the corresponding neurosporene isomers. The application of different geometric isomers as substrates revealed that the zeta-carotene desaturase has no preference for certain isomers and that the nature of the isomers formed during catalysis depends strictly on the isomeric composition of the substrate.     

Structure of a human carcinogen-converting enzyme,SULT1A1. Structural and kinetic implications of substrate inhibition

Sulfonation catalyzed by sulfotransferase enzymes plays an important role in chemical defense mechanisms against various xenobiotics but also bioactivates carcinogens. A major human sulfotransferase, SULT1A1, metabolizes and/or bioactivates many endogenous compounds and is implicated in a range of cancers because of its ability to modify diverse promutagen and procarcinogen xenobiotics. The crystal structure of human SULT1A1 reported here is the first sulfotransferase structure complexed with a xenobiotic substrate. An unexpected finding is that the enzyme accommodates not one but two molecules of the xenobiotic model substrate p-nitrophenol in the active site. This result is supported by kinetic data for SULT1A1 that show substrate inhibition for this small xenobiotic. The extended active site of SULT1A1 is consistent with binding of diiodothyronine but cannot easily accommodate beta-estradiol, although both are known substrates. This observation, together with evidence for a disorder-order transition in SULT1A1, suggests that the active site is flexible and can adapt its architecture to accept diverse hydrophobic substrates with varying sizes, shapes and flexibility. Thus the crystal structure of SULT1A1 provides the molecular basis for substrate inhibition and reveals the first clues as to how the enzyme sulfonates a wide variety of lipophilic compounds.     

Interaction of substrate with cytochrome P-450 in microsomal and solubilized form]

In order to characterize the substrate binding sites, difference spectroscopic titrations in microsomal and solubilized cytochrome P-450 from induced and non-induced rat liver microsomes were performed. The binding constants determined show differences depending on the physicochemical nature of the substrate and the degree of integration of the enzyme system. In hydrophilic substrates the differences of the binding to the microsomal or solubilized form are less pronounced than in lipophilic ones. From the comparison of the parameters obtained at various levels of integration it is concluded that the micromilieu of the binding site is of great importance for the binding of the substrate of cytochrome P-450.     

The screening of selected microorganisms for use as models of mammalian drug metabolism

Summary Fifty fungi and two Streptomyces species were screened for their ability to metabolise the probe substrates aminopyrine, diazepam, testosterone, theophylline and warfarin. The metabolism of the ¹⁴C-labelled substrates by whole growing cells was compared with that by rat liver microsomes using TLC-autoradiography. Testosterone, warfarin and diazepam were readily metabolised by most microorganisms, and aminopyrine and theophylline were only metabolised by a few. A relationship between substrate lipophilicity and number of microorganisms able to biotransform the substrate was observed, lipophilic substrates being favoured for metabolism, analogous to mammalian cytochrome P-450. A wide variety of metabolites were produced by the screened cultures, with a significant number co-chromatographing with mammalian metabolites. Most microorganisms appeared to exhibit cytochrome P-450-type oxidative reactions such as hydroxylation and N-demethylation, similar to mammalian hepatic microsomal cytochrome P-450 systems. Offprint requests to: D. A. Griffiths     

Detergent-dependent kinetics of truncated Plasmodium falciparum dihydroorotate dehydrogenase

The survival of the malaria parasite Plasmodium falciparum is dependent upon the de novo biosynthesis of pyrimidines. P. falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the fourth step in this pathway in an FMN-dependent reaction. The full-length enzyme is associated with the inner mitochondrial membrane, where ubiquinone (CoQ) serves as the terminal electron acceptor. The lipophilic nature of the co-substrate suggests that electron transfer to CoQ occurs at the two-dimensional lipid-solution interface. Here we show that PfDHODH associates with liposomes even in the absence of the N-terminal transmembrane-spanning domain. The association of a series of ubiquinone substrates with detergent micelles was studied by isothermal titration calorimetry, and the data reveal that CoQ analogs with long decyl (CoQ(D)) or geranyl (CoQ(2)) tails partition into detergent micelles, whereas that with a short prenyl tail (CoQ(1)) remains in solution. PfDHODH-catalyzed reduction of CoQ(D) and CoQ(2), but not CoQ(1), is stimulated as detergent concentrations (Tween 80 or Triton X-100) are increased up to their critical micelle concentrations, beyond which activity declines. Steady-state kinetic data acquired for the reaction with CoQ(D) and CoQ(2) in substrate-detergent mixed micelles fit well to a surface dilution kinetic model. In contrast, the data for CoQ(1) as a substrate were well described by solution steady-state kinetics. Our results suggest that the partitioning of lipophilic ubiquinone analogues into detergent micelles needs to be an important consideration in the kinetic analysis of enzymes that utilize these substrates.     

Polysaccharide-degrading enzymes formed by three species of anaerobic rumen fungi grown on a range of carbohydrate substrates

The range of polysaccharide-degrading enzymes formed by three anaerobic rumen fungi (Neocallimastix patriciarum, Piromonas communis, and an unidentified isolate (F] was monitored following growth on seven mono-, di-, and poly-saccharide carbohydrate substrates. Enzymes capable of degrading a variety of alpha- and beta-glucans, beta-galactans, galactomannan, and hemicellulosic arabinoxylans were present in all three isolates. Although reducing saccharides were released from pectin, polygalacturonic acid was not degraded by the preparations. Enzyme activity was present in both the zoospore and vegetative stages of the life cycle and was also detected extracellularly in culture supernatants after vegetative growth. The specific activities of the polysaccharidases were affected by the growth substrate, being lowest in preparations grown on mono- and di-saccharides, whereas polysaccharidic growth substrates resulted in increased activity of the corresponding polysaccharidases. The enzymes were, however, formed after growth on all substrates. Oligomers and monosaccharides were produced as a result of polysaccharide breakdown by the unfractionated enzyme preparations. Studies on hemicellulose (arabinoxylan) breakdown by unfractionated vegetative preparations of the three isolates indicated that their modes of action, pH optima, substrate affinities, and response to potential inhibitors were similar.     

ATP-binding cassette (ABC) transporters in human metabolism and diseases

The ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of substrates including amino acids, lipids, inorganic ions, peptides, saccharides, metals, drugs, and proteins. The ABC transporters not only move a variety of substrates into and out of the cell, but also are also involved in intracellular compartmental transport. Energy derived from the hydrolysis of ATP is used to transport the substrate across the membrane against a concentration gradient. The typical ABC transporter consists of two transmembrane domains and two nucleotide-binding domains. Defects in 14 of these transporters cause 13 genetic diseases (cystic fibrosis, Stargardt disease, adrenoleukodystrophy, Tangier disease, etc.). Mutations in three genes affect lipid levels expressively. Mutations in ABCA1 cause severe HDL deficiency syndromes called Tangier disease and familial high-density lipoprotein deficiency, which are characterized by a severe deficiency or absence of high-density lipoprotein in the plasma. Two other ABCG transporters, ABCG5 and ABCG8, mutations of which cause sitosterolemia, have been identified. The affected individuals absorb and retain plant sterols, as well as shellfish sterols.     

Novel fluorescent ceramide derivatives for probing ceramidase substrate specificity

Ceramidases are key regulators of cell fate. The biochemistry of different ceramidases and of their substrate ceramide appears to be complex, mainly due to specific biophysical characteristics at the water-membrane interface. In the present study, we describe the design and synthesis of a set of fluorescently labeled ceramides as substrates for acid and neutral ceramidases. For the first time we have replaced the commonly used polar NBD-dye with the lipophilic Nile Red (NR) dye. Analysis of kinetic data reveal that although both the dyes do not have any noticeable preference for the substitution at acyl or sphingosine (Sph) part in ceramide towards hydrolysis by acid ceramidase, the ceramides with acyl-substituted NBD and Sph-substituted NR dyes have been found to be a better substrate for neutral ceramidase.