Selection and biochemical studies of pyrimidine-requiring mutants of Lactobacillus plantarum

Mutagenesis and mutant enrichment in Lactobacillus plantarum, a lactic acid bacterium used in silage, sauerkraut and sausage fabrication, were studied. In optimal conditions, auxotrophic mutants were obtained that permitted investigation of the de novo pyrimidine biosynthesis. Uracil-requiring mutants were characterized for their enzymatic defect, in aspartate transcarbamylase (ATCase), dihydro-orotase (DHOase), dihydro-orotate dehydrogenase (DHOdehase), orotidine monophosphate pyrophosphorylase (OMPppase) or in orotidine monophosphate decarboxylase (OMPdecase). The five enzymatic activities are totally repressed by uracil in the growth medium.     

The mechanism of orotidine 5'-monophosphate decarboxylase: catalysis by destabilization of the substrate

The mechanism of orotidine 5'-monophosphate decarboxylase (OMP decarboxylase, ODCase) was studied using the decarboxylation of orotic acid analogues as a model system. The rate of decarboxylation of 1,3-dimethylorotic acid and its analogues as well as the stability of their corresponding carbanion intermediates was determined. The results have shown that the stability of the carbanion intermediate is not a critical factor in the rate of decarboxylation. On the other hand, the reaction rate is largely dependent on the equilibrium constant for the formation of a zwitterion. Based on these results, we have proposed a new mechanism in which ODCase catalyzes the decarboxylation of OMP by binding the substrate in a zwitterionic form and providing a destabilizing environment for the carboxylate group of OMP.     

Carbon isotope effect study on orotidine 5'-monophosphate decarboxylase: support for an anionic intermediate

Orotidine 5'-monophosphate decarboxylase has been heavily examined in recent years due to its enzymatic proficiency, which provides a catalytic enhancement to a reaction rate approximately 1017 times greater than that of the nonenzymatic reaction. Several mechanisms proposed to explain this catalytic enhancement have included covalent addition, ylide or carbene formation, and most recently concerted protonation. All of these mechanisms have circumvented the formation of a high-energy vinyl anionic intermediate. To investigate the presence of an anionic intermediate, 13C isotope effect studies have been performed using the alternate substrate 5-fluoro-OMP (OMP = orotidine 5'-monophosphate). Isotope effects obtained for the wild-type enzyme with OMP and 5-fluoro-OMP are 1.0255 and 1.0106, respectively, corresponding to a decrease of approximately 1.5% for 5-fluoro-OMP. With the K59A enzyme, the intrinisic isotope effects show a similar decrease of approximately 1.9% from 1.0543 with OMP to 1.0356 with 5-fluoro-OMP. This decrease results from the inductive effect of the fluorine, which stabilizes the carbanion intermediate by electron withdrawal and produces a reaction with an earlier transition state. The isotope effect for the decarboxylation of the slow substrate 2'-deoxy-OMP produced a intrinsic isotope effect of nearly 1.0461.     

Determination of the mechanism of orotidine 5'-monophosphate decarboxylase by isotope effects

Orotidine 5'-monophosphate shows a (15)N isotope effect of 1.0036 at N-1 for decarboxylation catalyzed by orotidine 5'-monophosphate decarboxylase. Picolinic acid shows a (15)N isotope effect of 0.9955 for decarboxylation in ethylene glycol at 190 degrees C, while N-methyl picolinic acid shows a (15)N isotope effect of 1.0053 at 120 degrees C. The transition state for enzymatic decarboxylation of orotidine 5'-monophosphate resembles the transition state for N-methyl picolinic acid in that no bond order changes take place at N-1. This rules out enolization to give a quaternary nitrogen at N-1 in the enzymatic mechanism and suggests a carbanion intermediate stabilized by simple electrostatic interaction with Lys-93. The driving force for the reaction appears to be ground-state destabilization resulting from charge repulsion between the carboxyl of the substrate and Asp-91.     

SYNTHESIS OF CARBOCYCLIC OROTIDINE ANALOGS AS POTENTIAL OROTIDINE DECARBOXYLASE INHIBITORS

An asymmetric synthesis of carbocyclic orotidine 15 and its monophosphate 16 were accomplished via the key intermediate cyclopentanone 4, which was prepared from D-γ-ribonolactone in steps. None of synthesized the compounds inhibited orotidine 5′-monophosphate decarboxylase (EC 4.1.1.23) or orotate phosphoribosyltransferase (EC 2.4.2.10)     

Control of Pyrimidine Biosynthesis in Pseudomonas aeruginosa

The pathway of pyrimidine biosynthesis in Pseudomonas aeruginosa has been shown to be the same as in other bacteria. Twenty-seven mutants requiring uracil for growth were isolated and the mutant lesions were identified. Mutants lacking either dihydroorotic acid dehydrogenase, orotidine monophosphate pyrophosphorylase, orotidine monophosphate decarboxylase, or aspartic transcarbamylase were isolated; none lacking dihydroorotase were found. By using transduction and conjugation, four genes affecting pyrimidine biosynthetic enzymes have been identified and shown to be unlinked to each other. The linkage of pyrB to met-28 and ilv-2 was shown by contransduction. Repression by uracil alone or by broth could not be demonstrated for any enzymes of this pathway, in contrast to the situation in Escherichia coli and Serratia marcescens. In addition, derepression of these enzymes could not be demonstrated. A low level of feedback inhibition of aspartic transcarbamylase was found to occur. It is suggested that the control of such constitutive biosynthetic enzymes in P. aeruginosa may be related to the comprehensive metabolic activities of this organism.     

Isolation of Candida tropicalis auxotrophic mutants

An enrichment scheme using nystatin was designed for the isolation of auxotrophic mutants from the diploid-alkane-utilizing yeast Candida tropicalis. A collection of 194 auxotrophs representing 7 phenotypes was isolated. One class of mutants was identified as having a defect in histidinol dehydrogenase activity and a second class of mutants was identified as having a defect in orotidine monophosphate decarboxylase activity. These strains are good candidates to be carrying mutations corresponding to the HIS4 and URA3 genes of Saccharomyces cerevisiae.     

酿酒酵母中过表达URA5及URA3基因催化合成UMP的初步研究

为提高乳清酸到尿嘧啶核苷酸(UMP)的转化效率,利用PCR方法扩增酿酒酵母乳清酸磷酸核糖转移酶基因URA5, 并将其连接到携带乳清苷酸脱羧酶基因URA3的表达载体pYX212中,构建了重组质粒pYX212-URA5,然后转化到酿酒酵母BJX12中进行表达,并进行转化乳清酸到UMP的初步研究。试验结果表明: pYX212-URA5/ BJX12发酵培养40h后以32 mM乳清酸为底物催化产生UMP的量约为7 mM。明显高于同等条件下pYX212/ BJX12的UMP产量2.7 mM和对照组野生型BJX12的UMP产量2.4 mM。     

Heat sensitivity of mercuric ion and organomercurial degrading enzymes of aquatic,mercury-resistant bacteria

Activities of both Hg²⁺-reductase and organomercurial lyase of Hg-resistant aquatic bacteria were stable at 20°C for several days within whole cells. Organomercurial lyase activity degrading specifically thimersol, an organomercurial, was more stable than the corresponding enzyme activity degrading other organomercurials like phenylmercuric acetate (PMA) and methoxyethyl mercuric chloride (MEMC). Hg²⁺-reductases of Gram-negative bacteria in cell-free extract were more heat resistant than those of Gram-positive bacteria, except for those of two species of Bacillus, which were as heat resistant as those of the Gram-negative bacteria. Differences in the heat resistances of organomercurial lyases of two different broad-spectrum Hg-resistant bacteria indicate the presence of two enzyme systems for degrading thimersol, PMA and MEMC.     

Isolation and transformation of uracil auxotrophs of the edible basidiomycete Pleurotus ostreatus

Uracil auxotrophs of Pleurotus ostreatus were isolated using the selectable marker, resistance to 5'-fluoro-orotic acid (5'-FOA). Two of the nine uracil auxotrophs obtained were transformed to prototrophy using plasmid pTRura 3-2 that contains the orotidine monophosphate decarboxylase (ura3) gene from Trichoderma reesei. Southern blot analyses of the transformants showed that the transforming DNA had integrated into the genome of the protoplasts. Using 2 x 10(7) protoplasts, this system gave a transformation efficiency of about 30 transformants per microg of DNA. Normal fruiting bodies were induced in the transformants by crossing them with wild-type monokaryons, and the basidiospores collected from these fruiting bodies showed a biased segregation rate to prototrophy. These results indicate the integrated DNA was stably inherited.     

Induction of oxalate decarboxylase by oxalate in a newly isolated Pandoraea sp. OXJ-11 and its ability to protect against Sclerotinia sclerotiorum infection

Pandoraea sp. OXJ-11 has been shown to produce an oxalate decarboxylase. The enzyme could be induced by increasing the oxalate in the medium. An increasing concentration of yeast extract was able to stimulate the cell growth but could not increase the specific oxalate decarboxylase activity. The oxalate decarboxylase was produced maximally at 25-35 degrees C and pH 4.0-9.0, favoring its potential application in protection of host plants from oxalate-producing phytopathogens. The influence of glucose on the induction of oxalate decarboxylase by oxalate was examined, and it was found that glucose inhibited the production of the oxalate decarboxylase. Resistance results showed that Pandoraea sp. OXJ-11 was capable of suppressing Sclerotinia sclerotiorum infection on detached leaflets of Brassica napus plants.     

Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily

Pseudomonas aeruginosa PA4872 was identified by sequence analysis as a structurally and functionally novel member of the PEP mutase/isocitrate lyase superfamily and therefore targeted for investigation. Substrate screens ruled out overlap with known catalytic functions of superfamily members. The crystal structure of PA4872 in complex with oxalate (a stable analogue of the shared family alpha-oxyanion carboxylate intermediate/transition state) and Mg2+ was determined at 1.9 A resolution. As with other PEP mutase/isocitrate lyase superfamily members, the protein assembles into a dimer of dimers with each subunit adopting an alpha/beta barrel fold and two subunits swapping their barrel's C-terminal alpha-helices. Mg2+ and oxalate bind in the same manner as observed with other superfamily members. The active site gating loop, known to play a catalytic role in the PEP mutase and lyase branches of the superfamily, adopts an open conformation. The Nepsilon of His235, an invariant residue in the PA4872 sequence family, is oriented toward a C(2) oxygen of oxalate analogous to the C(3) of a pyruvyl moiety. Deuterium exchange into alpha-oxocarboxylate-containing compounds was confirmed by 1H NMR spectroscopy. Having ruled out known activities, the involvement of a pyruvate enolate intermediate suggested a decarboxylase activity of an alpha-oxocarboxylate substrate. Enzymatic assays led to the discovery that PA4872 decarboxylates oxaloacetate (kcat = 7500 s(-1) and Km = 2.2 mM) and 3-methyloxaloacetate (kcat = 250 s(-1) and Km = 0.63 mM). Genome context of the fourteen sequence family members indicates that the enzyme is used by select group of Gram-negative bacteria to maintain cellular concentrations of bicarbonate and pyruvate; however the decarboxylation activity cannot be attributed to a pathway common to the various bacterial species.     

Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution

Oxalate decarboxylase is a manganese-dependent enzyme that catalyzes the conversion of oxalate to formate and carbon dioxide. We have determined the structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution in the presence of formate. The structure reveals a hexamer with 32-point symmetry in which each monomer belongs to the cupin family of proteins. Oxalate decarboxylase is further classified as a bicupin because it contains two cupin folds, possibly resulting from gene duplication. Each oxalate decarboxylase cupin domain contains one manganese binding site. Each of the oxalate decarboxylase domains is structurally similar to oxalate oxidase, which catalyzes the manganese-dependent oxidative decarboxylation of oxalate to carbon dioxide and hydrogen peroxide. Amino acid side chains in the two metal binding sites of oxalate decarboxylase and the metal binding site of oxalate oxidase are very similar. Four manganese binding residues (three histidines and one glutamate) are conserved as well as a number of hydrophobic residues. The most notable difference is the presence of Glu333 in the metal binding site of the second cupin domain of oxalate decarboxylase. We postulate that this domain is responsible for the decarboxylase activity and that Glu333 serves as a proton donor in the production of formate. Mutation of Glu333 to alanine reduces the catalytic activity by a factor of 25. The function of the other domain in oxalate decarboxylase is not yet known.     

The Sites of Action of Allopurinol in Crithidia fasciculata*

Reversal of the growth inhibition of Crithidia fasciculata by allopurinol requires both a purine and a pyrimidine. Hypoxanthine is the most effective purine in the reversal. Cell-free extracts were prepared which were capable of the decarboxylation of orotidine 5′-phosphate. Other enzyme preparations carried out the phosphoribosylation of allopurinol. By the use of [4-¹⁴C] orotidine 5′-phosphate (enzymatically prepared), it was shown that allopurinol ribotide (enzymatically prepared), but not the free base, inhibits orotidine 5′-phosphate decarboxylase.     

The purification and preliminary characterization of UMP synthase from human placenta

Orotate phosphoribosyltransferase (EC 2.4.2.10) and orotidine 5'-monophosphate decarboxylase (EC 4.1.1.23) are the final two of six enzymatic steps required in the de novo biosynthesis of uridine 5'-monophosphate (UMP). Earlier work of this laboratory showed that, in the mouse Ehrlich ascites carcinoma, both of these enzymatic activities were contained on the single multifunctional polypeptide chain, UMP synthase. We report here that the placenta provided an available human source for UMP synthase with 40-fold higher orotate phosphoribosyltransferase and orotidine 5'-monophosphate decarboxylase specific activities than erythrocytes, a human source previously used by others. By using the placenta as a source of UMP synthase and by developing a novel purification procedure different from that used in the purification of UMP synthase from the Ehrlich ascites carcinoma (the only other homogeneous preparation of a mammalian UMP synthase), we achieved the purification of human UMP synthase to apparent homogeneity. This represents the first publication to homogeneity of UMP synthase from a human source as well as from a source other than malignant cell lines. Contrary to earlier reports human placental UMP synthase was found to be a multifunctional protein containing both enzymatic activities on a single polypeptide of 51,000 molecular weight. Preliminary characterization of the human placental UMP synthase showed it to be similar to UMP synthase from the Ehrlich ascites carcinoma in subunit molecular weight, native molecular weight, isozyme pattern (although not absolute pI values), pH optima of enzymatic activities, and kinetic constants for orotidine 5'-monophosphate (Km) and 6-azauridine 5'-monophosphate (Ki) at the decarboxylase site.     

Development of an integrative DNA transformation system for the yeast Candida tropicalis.

We developed the alkane and fatty-acid utilizing yeast Candida tropicalis as a host for DNA transformations. The system is based on an auxotrophic mutant host of C. tropicalis which is defective in orotidine monophosphate decarboxylase (ura3). The ura3 host was isolated by mutagenesis and a double-selection procedure that combined nystatin enrichment selection and 5-fluoro-orotic acid resistance selection. As a selectable marker, we isolated and characterized the C. tropicalis URA3 gene. Plasmid vectors that contained the C. tropicalis URA3 gene transformed the C. tropicalis mutant host at a frequency of 10(3) to 10(4) transformants per micrograms of plasmid DNA. Vectors that contained the Saccharomyces cerevisiae URA3 gene could not transform C. tropicalis. DNA transfer was accomplished by modified versions of either spheroplast generation (CaCl2-polyethylene glycol)-fusion or cation (LiCl) procedures developed for S. cerevisiae. Plasmid vectors that had been cut within the C. tropicalis URA3 fragment integrated by homologous recombination at the URA3 locus.     

Phosphopantothenoylcysteine synthetase from Escherichia coli. Identification and characterization of the last unidentified coenzyme A biosynthetic enzyme in bacteria

Phosphopantothenoylcysteine synthase catalyzes the formation of (R)-4'-phospho-N-pantothenoylcysteine from 4'-phosphopantothenate and l-cysteine: this enzyme, involved in the biosynthesis of coenzyme A (CoA), has not previously been identified. Recently it was shown that the NH(2)-terminal domain of the Dfp protein from bacteria catalyzes the next step in CoA biosynthesis, the decarboxylation of (R)-4'-phospho-N-pantothenoylcysteine to form 4'-phosphopantetheine (Kupke, T., Uebele, M., Schmid, D., Jung, G., Blaesse, M., and Steinbacher, S. (2000) J. Biol. Chem. 275, 31838-31846). We have partially purified phosphopantothenoylcysteine decarboxylase from Escherichia coli and demonstrated that the protein encoded by the dfp gene, here renamed coaBC, also has phosphopantothenoylcysteine synthetase activity, using CTP rather than ATP as the activating nucleoside 5'-triphosphate. This discovery completes the identification of all the enzymes involved in the biosynthesis of coenzyme A in bacteria.     

Orotidine 5'-monophosphate decarboxylase: transition state stabilization from remote protein-phosphodianion interactions

Mutants of orotidine 5'-monophosphate decarboxylase containing all possible single (Q215A, Y217F, and R235A), double, and triple substitutions of the side chains that interact with the phosphodianion group of the substrate orotidine 5'-monophosphate have been prepared. Essentially the entire effect of these mutations on the decarboxylation of the truncated neutral substrate 1-(β-d-erythrofuranosyl)orotic acid that lacks a phosphodianion group is expressed as a decrease in the third-order rate constant for activation by phosphite dianion. The results are consistent with a model in which phosphodianion binding interactions are utilized to stabilize a rare closed enzyme form that exhibits a high catalytic activity for decarboxylation.