High efficiency of a sequential recombinase-mediated cassette exchange reaction in Escherichia coli

A comparison between the efficiency of recombinase-mediated cassette exchange (RMCE) reactions catalyzed in Escherichia coli by the site-specific recombinases Flp of yeast and Int of coliphage HK022 has revealed that an Flp-catalyzed RMCE reaction is more efficient than an Int-HK022 catalyzed reaction. In contrast, an RMCE reaction with 1 pair of frt sites and 1 pair of att sites catalyzed in the presence of both recombinases is very inefficient. However, the same reaction catalyzed by each recombinase individually supplied in a sequential order is very efficient, regardless of the order. Atomic force microscopy images of Flp with its DNA substrates show that only 1 pair of recombination sites forms a synaptic complex with the recombinase. The results suggest that the RMCE reaction is sequential.     

The DNA unwinding reaction catalyzed by Rep protein is facilitated by an RHSP-DNA interaction.

The unwinding reaction catalyzed by the Escherichia coli Rep protein is stimulated by a small 15 kDa protein called Rep helicase stimulatory protein (RHSP)(1). The RHSP-stimulated unwinding reaction catalyzed by Rep protein proceeded at a rapid rate after a time lag of 1-2 min at 37 degrees C. This time lag was eliminated by preincubating RHSP with the DNA substrate, indicating that stimulation resulted from an interaction between RHSP and DNA. RHSP was shown to increase the rate as well as the extent of the unwinding reaction catalyzed by Rep protein. RHSP bound both single- and double-stranded DNA with apparent equal affinity, forming an unusually stable complex. Electron microscopy illustrated that the RHSP-DNA complex consisted of large protein aggregates bound to DNA forming a highly condensed, aggregated DNA-protein complex. The protein aggregates were not observed in the absence of DNA and appeared to form cooperatively in the presence of DNA. NH2-terminal amino acid sequence analysis suggested that RHSP was identical to E. coli ribosomal-protein L14. Binding assays showed that the interaction between RHSP and rRNA was similar to the RHSP-DNA interaction. Several models are put forth to explain the stimulation of the unwinding reaction catalyzed by Rep protein. In addition, the potential physiological significance of the RHSP-stimulated Rep protein unwinding reaction is discussed.     

The mechanism of dextransucrase action. Direction of dextran biosynthesis

Appropriate combinations of purified components of the reversible glycine cleavage system of rat liver catalyze three partial reactions: (1) decarboxylation of glycine or its reverse reaction catalyzed by P- and H-protein, (2) condensation of one carbon substrate and ammonia or its reverse reaction catalyzed by T- and H-protein, and (3) oxidation and reduction of active disulfide of H-protein catalyzed by L-protein. Reactions (1) and (2) give the same product which is bound to H-protein. The protein-bound product was isolated by gel filtration and converted to glycine by incubation with P-protein and CO₂ or degraded further to one carbon unit and ammonia by incubation with T-protein and tetrahydrofolate. The data are consistent with the conclusion that the enzyme-bound product is an intermediate in the reversible glycine cleavage reaction. A scheme is presented for the reactions catalyzed by the enzyme system.     

Regioselective bromohydroxylation of alkenes catalyzed by chloroperoxidase: Advantages of the immobilization of enzyme on talc

The bromohydroxylation of alkenes catalyzed by chloroperoxidase (CPO) from the mould Caldariomyces fumago adsorbed on different types of talc or in reverse micelles was compared to that of the same reaction catalyzed by the free enzyme in buffer. High reactivity was observed in all media, but the reaction was optimized with an enzyme-talc combination that produced the halohydrin with no oxidative by-products in a Markovnikov-type regioselective addition. The reaction was facilitated by the use of this solid and a recyclable biocatalyst, which gave rise to the halohydrin in a quantitative yield. The protective influence of the talc (hydrophilic or hydrophobic) with respect to hydrogen peroxide enabled use of large amounts of oxidizing agent and substrate, opening perspectives for CPO in the synthesis of fine chemicals.     

Reverse hydrolysis reaction of a recombinant alkaline ceramidase of Pseudomonas aeruginosa

Recently, we purified an alkaline ceramidase (CDase) of Pseudomonas aeruginosa and found that the enzyme catalyzed a reversible reaction in which the N-acyl linkage of ceramide was hydrolyzed or synthesized [J. Biol. Chem. 273 (1998) 14368-14373]. Here, we report the characterization of the reverse hydrolysis reaction of the CDase using a recombinant enzyme. The reverse hydrolysis reaction of the CDase was clearly distinguishable from the reaction of an acyl-coenzyme A (CoA) dependent N-acyltransferase, because the CDase catalyzed the condensation of a free fatty acid to sphingosine (Sph) without cofactors but did not catalyze the transfer of a fatty acid from acyl-CoA to Sph. The reverse hydrolysis reaction proceeded most efficiently in the presence of 0.05% Triton X-100 at neutral pH, while the hydrolysis reaction tended to be favored with an increase in the concentration of the detergent at alkaline pH. The specificity of the reverse reaction for fatty acids is quite broad; saturated and unsaturated fatty acids were efficiently condensed to Sph. In contrast, the stereo-specificity of the reverse reaction for the sphingoid bases is very strict; the D-erythro form of Sph, not the L-erythro or D/L-threo one, was only acceptable for the reverse reaction. Chemical modification of the enzyme protein affected or did not affect both the hydrolysis and reverse reactions to the same extent, suggesting that the two reactions are catalyzed at the same catalytic domain.     

Modification of the Microenvironment of Enzymes in Organic Solvents. Substitution of Water by Polar Solvents

Enzyme catalysis in water-immiscible organic solvents is strongly influenced by the amount of water present in the reaction mixture. Effects of substitution of part of the water by other polar solvents were studied. In an alcoholysis reaction catalyzed by chymotrypsin deposited on celite, it was possible to exchange half of the water by formamide, ethylene glycol or dimethyl sulfoxide with often increased initial reaction rate. Furthermore, these substitutions caused the suppression of the competing hydrolysis reaction. However, formamide caused enzyme inactivation, and ethylene glycol participated as a reactant in the alcoholysis to some extent, hence dimethyl sulfoxide was considered the best water substitute among the solvents tested. These effects were noted for chymotrypsin catalyzed alcoholysis in several water immiscible solvents and also for interesterification reactions catalyzed by Candida cylindracea lipase on celite. In the latter case a change in the stereoselectivity was observed. At a low water content a high stereoselectivity was observed; when the amount of polar solvent was increased, either by doubling the water content or adding an equal amount of DMSO, the stereoselectivity decreased.     

Microsome catalyzed conversion of N-hydroxy-N-acetyl-2-aminofluorene by cumene-hydroperoxide.

This report presents heretofore unreported data which demonstrate that the microsomal fraction of rat liver in the presence of cumene-hydroperoxide catalyzed the disappearance of the carcinogen N-hydroxy-N-acetyl-2-aminofluorene. Utilizing optical spectroscopy we have found that the carcinogen disappearance corresponds kinetically with an absorption increase at 340 nm. The compound (s) absorbing at 340 nm has not been identified. The microsomal catalyzed reaction was heat labile, manifested a reaction rate which was proportional to microsomal protein content, and had a k_m of 2.6 μM for the carcinogen in the presence of a large excess of cumene-hydroperoxide.     

Kinetic study on the reaction mechanism of pantothenase: existence of an acyl-enzyme intermediate and role of general acid catalysis.

A kinetic study was performed on the reaction mechanism of pantothenase (EC 3.5.1.22) catalyzed hydrolysis of the pantothenic acid. A nonlinear progress curve is derived if the reaction occurs at low buffer concentrations. The nonlinearity is due to partial reversibility of the reaction; an acylenzyme (pantoyl-enzyme) is formed during the reaction, and beta-alanine, the other end product, is able to react with the acyl-enzyme and return back to pantothenate. The dependence of the beta-alanine return reaction on buffer concentration and on pH suggests a general acid catalysis during the reaction. A reaction mechanism is suggested, in which the -NH3+ form of beta-alanine participates in the return reaction, and the deacylation of the acyl-enzyme is acid catalyzed.     

Direct evidence for anthocyanidin synthase as a 2-oxoglutarate-dependent oxygenase: molecular cloning and functional expression of cDNA from a red forma of Perilla frutescens

Anthocyanidin synthase (ANS), an enzyme of the biosynthetic pathway to anthocyanin, has been postulated to catalyze the reaction(s) from the colorless leucoanthocyanidins to the colored anthocyanidins. Although cDNAs have been isolated that encode putative ANS, which exhibits significant similarities in amino acid sequence with members of a family of 2-oxoglutarate-dependent oxygenases, no biochemical evidence has been presented which identifies the actual reaction that is catalyzed by ANS. Here we show that anthocyanidins are formed in vitro through 2-oxoglutarate-dependent oxidation of leucoanthocyanidins catalyzed by the recombinant ANS and subsequent acid treatment. A cDNA encoding ANS was isolated from red and green formas of Perilla frutescens by differential display of mRNA. Recombinant ANS tagged with maltose-binding-protein (MBP) was purified, and the formation of anthocyanidins from leucoanthocyanidins was detected by the ANS-catalyzed reaction in the presence of ferrous ion, 2-oxoglutarate and ascorbate, being followed by acidification with HCI. Equimolar stoichiometry was confirmed for anthocyanidin formation and liberation of CO2 from 2-oxoglutarate. The presumptive two-copy gene of ANS was expressed in leaves and stems of the red forma of P. frutescens but not in the green forma plant. This corresponds to the accumulation pattern of anthocyanin. The mechanism of the reaction catalyzed by ANS is discussed in relation to the molecular evolution of a family of 2-oxoglutarate-dependent oxygenases.     

Energetics of ribonuclease A catalysis. 2. Nonenzymatic hydrolysis of cytidine cyclic 2',3'-phosphate

Various kinetic aspects of the nonenzymatic hydrolysis of cytidine cyclic 2',3'-phosphate and uridine cyclic 2',3'-phosphate have been studied in order to provide a basis for comparison with the ribonuclease A catalyzed hydrolysis reaction. Studies of the pH dependence of the nonenzymatic reaction reveal mechanisms that are first order in hydroxide concentration and second order in hydrogen ion concentration, in addition to a "water" reaction. The rate constant for the water reaction was found to be very small, approximately equal to 2.5 X 10(-6) min-1. General base catalyzed hydrolysis reactions were also studied with imidazole as the catalyst. At pH values in which both the protonated and neutral forms of imidazole are present, a kinetic mechanism was observed that appears to be second order in total imidazole concentration, thus suggesting that bifunctional catalysis occurs. The activation enthalpy for the hydroxide, hydrogen ion, water, and imidazole catalyzed reactions was determined.     

Generalization of the Monod-Wyman-Changeux model for the case of multisubstrate reactions]

A general equation is derived for the rate of multisubstrate reaction catalyzed by oligomeric enzyme E(R, T) liable to concerted transitions Ro in equilibrium To or Ro in equilibrium 2To. It is shown that with some assumptions about the enzymes the rate equations can be constructed from the rates of corresponding reactions catalyzed by a single active site. These single active site rate equations are known for the majority of catalysis mechanisms, otherwise they can be easily deduced. As an example the rate equation is derived for the reaction S1 + S2 + S3 in equilibrium S4 + S5 catalyzed by an oligomeric enzyme according to the ordered ter-bi mechanism.     

The iron-sulfur-cluster-containing L-serine dehydratase from Peptostreptococcus asaccharolyticus. Stereochemistry of the deamination of L-threonine.

The stereochemistry of the deamination of L-threonine to 2-oxobutyrate, catalyzed by purified L-serine dehydratase of Peptostreptococcus asaccharolyticus, was elucidated. For this purpose the enzyme reaction was carried out with unlabelled L-threonine in 2H2O and in 3HOH, as well as with L-[3-3H]threonine in unlabelled water. Isotopically labelled 2-oxobutyrate thus formed was directly reduced in a coupled reaction with L- or D-lactate dehydrogenase and NADH. The (2R)- or (2S)-2-hydroxybutyrate species obtained were then subjected to configurational analyses of their labelled methylene group. The results from 1H-NMR spectroscopy and, after degradation of 2-hydroxybutyrate to propionate, the transcarboxylase assay consistently indicated that the deamination of L-threonine catalyzed by L-serine dehydratase of P. asaccharolyticus proceeds with inversion and retention in a 2:1 ratio. This partial racemization is the first ever to be observed for a reaction catalyzed by serine dehydratase, therefore confirming the distinction of the L-serine dehydratase of P. asaccharolyticus as an iron-sulfur protein from those dehydratases dependent on pyridoxal phosphate. For the latter enzymes exclusively, retention has been reported.     

Effect of aspartate on complexes between glutamate dehydrogenase and various aminotransferases.

In previous studies it was found that: (a) aspartate aminotransferase increases the aspartate dehydrogenase activity of glutamate dehydrogenase; (b) the pyridoxamine-P form of this aminotransferase can form an enzyme-enzyme complex with glutamate dehydrogenase; and (c) the pyridoxamine-P form can be dehydrogenated to the pyridoxal-P form by glutamate dehydrogenase. It was therefore concluded (Fahien, L.A., and Smith, S.E. (1974) J. Biol. Chem 249, 2696-2703) that in the aspartate dehydrogenase reaction, aspartate converts the aminotransferase into the pyridoxamine-P form which is then dehydrogenated by glutamate dehydrogenase. The present results support this mechanism and essentially exclude the possibility that aspartate actually reacts with glutamate dehydrogenase and the aminotransferase is an allosteric activator. Indeed, it was found that aspartate is actually an activator of the reaction between glutamate dehydrogenase and the pyridoxamine-P form of the aminotransferase. Aspartate also markedly activated the alanine dehydrogenase reaction catalyzed by glutamate dehydrogenase plus alanine aminotransferase and the ornithine dehydrogenase reaction catalyzed by ornithine aminotransferase plus glutamate dehydrogenase. In these latter two reactions, there is no significant conversion of aspartate to oxalecetate and other compounds tested (including oxalacetate) would not substitute for aspartate. Thus aspartate is apparently bound to glutamate dehydrogenase and this increases the reactivity of this enzyme with the pyridoxamine-P form of aminotransferases. This could be of physiological importance because aspartate enables the aspartate and ornithine dehydrogenase reactions to be catalyzed almost as rapidly by complexes between glutamate dehydrogenase and the appropriate mitochondrial aminotransferase in the absence of alpha-ketoglutarate as they are in the presence of this substrate. Furthermore, in the presence of aspartate, alpha-ketoglutarate can have little or no affect on these reactions. Consequently, in the mitochondria of some organs these reactions could be catalyzed exclusively by enzyme-enzyme complexes even in the presence of alpha-ketoglutarate. Rat liver glutamate dehydrogenase is essentially as active as thebovine liver enzyme with aminotransferases. Since the rat liver enzyme does not polymerize, this unambiguously demonstrates that monomeric forms of glutamate dehydrogenase can react with aminotransferases.     

有机相中脂肪酶L—1754促有机硅烷醇的酯化

在有机介质中脂肪酶Ｌ－１７５４催化非天然有机硅化合物三甲基硅烷醇酯化反应的速度高于Ｌｉｐｏｚｙｍｅ。Ｌ－１７５４对脂肪酸链长有很强的特异性且不同于Ｌｉｐｏｚｙｍｅ。     

Production of conjugated linoleic acids through KOH-catalyzed dehydration of ricinoleic acid

Production of conjugated linoleic acids (CLA) using castor oil as starting material involves conversion of ricinoleic acid to methyl 12-mesyloxy-octadec-9-enoate (MMOE) followed by dehydration. This process usually uses 1,8-diazabicyclo-(5.4.0)-undec-7-ene (DBU) as an expensive dehydrating reagent. The present study reports that potassium hydroxide (KOH) can serve as a dehydrating reagent in replacement of DBU. The results showed that conversion of MMOE to CLA catalyzed by KOH was an efficient reaction, with a 77% conversion efficiency at 80 degrees C. The CLA isomeric profile produced in KOH-catalyzed dehydration reaction was similar to that catalyzed by DBU. The CLA mixture produced in KOH-catalyzed dehydration of MMOE at 80 degrees C contained 72% 9c,11t-18:2 and 26% 9c,11c-18:2 while in that catalyzed by DBU, 9c,11t-18:2 and 9c,11c-18:2 accounted for 78 and 16%, respectively. It was found that the temperature of dehydration was an important factor in the determination of CLA isomer composition and yield of conversion. Elevating the temperature from 78 to 180 degrees C decreased not only the conversion efficiency but also production of total c,t-18:2 and c,c-18:2 isomers regardless of dehydration catalyzed by either DBU or KOH. It is concluded that KOH may replace DBU as a dehydrating reagent in conversion of MMOE to CLA when the reaction conditions are optimized.     

Biosynthesis of cholic acid in rat liver. 24-Hydroxylation of 3alpha, 7alpha, 12alpha-trihydroxy-5beta-cholestanoic acid.

Conversion of 3alpha, 7alpha, 12alpha-trihydroxy-5beta-[7beta-3H]cholestanoic acid into 3alpha, 7alpha, 12alpha, 24-tetrahydroxy-5beta-cholestanoic acid in rat liver was catalyzed either by the mitochondrial fraction fortified with the 100,000 times g supernatant fluid or the microsomal fraction fortified with 100,000 times g supernatant fluid and ATP. The microsomal system was more active than the mitochondrial system. With the microsomal system the rate of reaction was considerably faster with free 3alpha, 7alpha, 12alpha-trihydroxy-5beta-cholestanoic acid as substrate than with the corresponding coenzyme A ester. Addition of coenzyme A inhibited the activity. Addition of cofactors other than ATP and coenzyme A did not markedly influence the reaction. The 100,000 times g supernatant fluid could be substituted with a protein fraction obtained by ammonium sulfate precipitation and Sephadex chromatography of the 100,000 times g supernatant fluid. The reaction was not catalyzed by a mixed function oxidase since there was no incorporation of 18O into the product when the reaction was performed in an atmosphere containing 18O2. On the other hand, oxygen may be obligatory since there was almost complete inhibition when the reaction was performed in an atmosphere consisting of nitrogen. Carbon monoxide did not inhibit the reaction. One atom of deuterium was incorporated into the product when the reaction was performed in a medium containing deuterated water. It was concluded that microsomal 24-hydroxylation of 3alpha, 7alpha, 12alpha-trihydroxy-5beta-cholestanoic acid involves the combined action of a desaturase and a hydratase. The reaction catalyzed by the hydratase appears to be stereospecific since the 24alpha epimer of 3alpha, 7alpha,12alpha-trihydroxy-5beta-cholestanoic acid was the predominant product. In contrast to the microsomal system, the mitochondrial system was not stimulated by the addition of ATP and was not inhibited by coenzyme A. The coenzyme A ester of 3alpha, 7alpha, 12alpha-trihydroxy-5beta-cholestanoic acid was 24-hydroxylated more efficiently than the free acid.     

Historical review: Peptidyl transfer, the Monro era

The peptide bond-forming reaction of protein synthesis, the peptidyl transfer reaction, takes place in a region of the 50S ribosomal subunit that consists entirely of RNA, the peptidyl transferase centre. Basic to the present knowledge of peptidyl transfer was the discovery by Robin Monro and his colleagues in the 1960s that the reaction is catalyzed by the 50S ribosome. The Monro experiments, and the historical context in which they were conceived, are described in this personal recollection. Monro's 'fragment reaction', the ribosome catalyzed reaction of a fragment of formylmethionyl-tRNA with puromycin, remains in use in work on peptidyl transfer.