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PubMed2002

Cloning and characterization of a novel human pantothenate kinase gene.

Pantothenate kinase (PanK) is a key regulatory enzyme in the CoA biosynthetic pathway in bacteria and mammalian cells. It catalyzes the first committed step in the universal biosynthetic pathway leading to CoA. Here we report the molecular cloning and characterization of a new human PanK gene. The gene encoded a protein of 314 amino acid residues, which share high homology to mouse pantothenate kinase (mPanK) 1 beta. Northern blot analysis revealed a transcript of the gene of 2.6 kb in human liver and kidney. The human PanK gene was located to human chromosome between 10q22.3 and 10q23.2 by bioinformatics analysis.

Amino Acid Sequence↗

PubMed1973

Stimulation of ornithine decarboxylase activity and inhibition of S-adenosyl-L-methionine decarboxylase activity in leukaemic mice by methylglyoxal bis(guanylhydrazone).

Administration of methylglyoxal bis(guanylhydrazone) to leukaemic mice results in an early depression followed by a marked elevation of S-adenosyl-l-methionine decarboxylase activity. Further, there is an early prolonged increase in the activity of ornithine decarboxylase, the initial enzyme in the polyamine biosynthetic pathway. Because of the profound effects of methylglyoxal bis(guanylhydrazone) in vivo on the polyamine biosynthetic pathway, the drug can no longer be considered a specific inhibitor of spermidine synthesis.

Adenosine↗

PubMed2004

Identification of delphinidin 3-O-(6''-O-malonyl)-beta-glucoside-3'-O-beta-glucoside, a postulated intermediate in the biosynthesis of ternatin C5 in the blue petals of Clitoria ternatea (butterfly pea).

Ternatins are blue anthocyanins found in the petals of Clitoria ternata (butterfly pea). Among them, ternatin C5 (delphinidin 3-O-(6''-O-malonyl)-beta-glucoside-3',5'-di-O-beta-glucoside; 2) has the structure common to all the ternatins, which is characterized by its glucosylation pattern: a 3,3',5'-triglucosylated anthocyanidin. In the course of studying biosynthetic pathways of ternatins, the key enzymatic activities to produce ternatin C5 were discovered in a crude enzyme preparation from the petals of a blue petal line of C. ternatea. When this preparation was tested for activity against several delphinidin glycosides, delphinidin 3-O-(6''-O-malonyl)-beta-glucoside-3'-O-beta-glucoside (6), a postulated intermediate, was found in the reaction mixture, together with three known anthocyanins, which were spectroscopically structurally identified. As a result of structural identification, the following enzymatic activities were identified: UDP-glucose :delphinidin 3-O-(6''-O-malonyl)-beta-glucoside-3'-O-beta-glucoside 5'-O-glucosyltransferase (5'GT), UDP-glucose :delphinidin 3-O-(6''-O-malonyl)-beta-glucoside 3'-O-glucosyltransferase (3'GT), UDP-glucose :delphinidin 3-O-glucosyltransferase, and malonyl-CoA :delphinidin 3-O-beta-glucoside 6''-malonyltransferase. In a mauve petal line, which did not accumulate ternatins but delphinidin 3-O-(6''-O-malonyl)-beta-glucoside in its petal, there were neither 5'GT nor 3'GT activities. Thus, the early biosynthetic pathway of ternatins may be characterized by the stepwise transfer of two glucose residues to 3'- and 5'-position of delphinidin 3-O-(6''-O-malonyl)-beta-glucoside (1; Scheme) from UDP-glucose.

Anthocyanins↗

PubMed2006

High-level production of amorpha-4,11-diene in a two-phase partitioning bioreactor of metabolically engineered Escherichia coli.

Reconstructing synthetic metabolic pathways in microbes holds great promise for the production of pharmaceuticals in large-scale fermentations. By recreating biosynthetic pathways in bacteria, complex molecules traditionally harvested from scarce natural resources can be produced in microbial cultures. Here we report on a strain of Escherichia coli containing a heterologous, nine-gene biosynthetic pathway for the production of the terpene amorpha-4,11-diene, a precursor to the anti-malarial drug artemisinin. Previous reports have underestimated the productivity of this strain due to the volatility of amorphadiene. Here we show that amorphadiene evaporates from a fermentor with a half-life of about 50 min. Using a condenser, we take advantage of this volatility by trapping the amorphadiene in the off-gas. Amorphadiene was positively identified using nuclear magnetic resonance spectroscopy and determined to be 89% pure as collected. We captured amorphadiene as it was produced in situ by employing a two-phase partitioning bioreactor with a dodecane organic phase. Using a previously characterized caryophyllene standard to calibrate amorphadiene production and capture, the concentration of amorphadiene produced was determined to be 0.5 g/L of culture medium. A standard of amorphadiene collected from the off-gas showed that the caryophyllene standard overestimated amorphadiene production by approximately 30%.

Antimalarials↗

PubMed1999

Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis.

Prosthetic groups such as heme, chlorophyll, and cobalamin (vitamin B(12)) are characterized by their branched biosynthetic pathway and unique metal insertion steps. The metal ion chelatases can be broadly classed either as single-subunit ATP-independent enzymes, such as the anaerobic cobalt chelatase and the protoporphyrin IX (PPIX) ferrochelatase, or as heterotrimeric, ATP-dependent enzymes, such as the Mg chelatase involved in chlorophyll biosynthesis. The X-ray structure of the anaerobic cobalt chelatase from Salmonella typhimurium, CbiK, has been solved to 2.4 A resolution. Despite a lack of significant amino acid sequence similarity, the protein structure is homologous to that of Bacillus subtilis PPIX ferrochelatase. Both enzymes contain a histidine residue previously identified as the metal ion ligand, but CbiK contains a second histidine in place of the glutamic acid residue identified as a general base in PPIX ferrochelatase. Site-directed mutagenesis has confirmed a role for this histidine and a nearby glutamic acid in cobalt binding, modulating metal ion specificity as well as catalytic efficiency. Contrary to the predicted protoporphyrin binding site in PPIX ferrochelatase, the precorrin-2 binding site in CbiK is clearly defined within a large horizontal cleft between the N- and C-terminal domains. The structural similarity has implications for the understanding of the evolution of this branched biosynthetic pathway.

Amino Acid Sequence↗

PubMed1991

Sequential activation of genes for heme pathway enzymes during erythroid differentiation of mouse Friend virus-transformed erythroleukemia cells.

Changes in the level of transcripts encoding enzymes of the heme biosynthetic pathway as well as those encoding ubiquitous proteins were examined in murine Friend virus-transformed erythroleukemia cells during erythroid cell differentiation induced by chemicals including dimethyl sulfoxide (DMSO). Early changes following DMSO treatment were marked decreases in mRNAs for three ubiquitous proteins, i.e., a 70 kDa heat shock protein (less than 6 h), heme oxygenase and nonspecific delta-aminolevulinate synthase (ALAS) (less than 12 h). These changes were followed by sequential increases in mRNAs for enzymes in the heme biosynthetic pathway. Namely, mRNAs for the erythroid-specific ALAS, delta-aminolevulinate dehydratase, porphobilinogen deaminase and uroporphyrinogen decarboxylase started to increase at 12, 18, 18-24 and 24 h, respectively. Nuclear runoff studies revealed that these changes are largely transcriptional. Treatments with other inducers of erythroid differentiation, e.g., hexamethylene bisacetamide, n-butyric acid and N'-methylnicotinamide, also showed similar effects on mRNAs as those following DMSO. These findings suggest that both suppression of ubiquitous genes and activation of heme pathway enzyme genes are associated with erythroid differentiation, and the former occurs preceding changes in the latter.

Animals↗

PubMed2005

Slow-onset feedback inhibition: inhibition of Mycobacterium tuberculosis alpha-isopropylmalate synthase by L-leucine.

This report describes the first demonstration of slow-onset feedback inhibition of an enzyme that catalyzes the first committed step in a biosynthetic pathway. alpha-Isopropylmalate synthase (IPMS) catalyzes the first committed step of the l-leucine biosynthetic pathway and is feedback-inhibited by l-leucine. Initial velocity experiments on the Mycobacterium tuberculosis IPMS indicate that inhibition by l-leucine is linearly noncompetitive versus alpha-ketoisovalerate. Time-courses displayed a burst of product formation followed by a linear steady-state rate when reactions were initiated by the addition of enzyme. The burst rate showed a hyperbolic dependence on the concentration of l-leucine indicating that inhibition proceeds in two steps, an initial rapid binding step followed by slow isomerization to a more tightly bound complex.

2-Isopropylmalate Synthase↗

PubMed1988

Mouse protoporphyrinogen oxidase. Kinetic parameters and demonstration of inhibition by bilirubin.

The penultimate step of haem biosynthesis, the oxidation of protoporphyrinogen to protoporphyrin, was examined with purified murine hepatic protoporphyrinogen oxidase (EC 1.3.3.4) in detergent solution. The kinetic parameters for the two-substrate (protoporphyrinogen and oxygen) reaction were determined. The limiting Km for protoporphyrinogen when oxygen is saturating is 6.6 microM, whereas the Km for oxygen with saturating concentrations of protoporphyrinogen is 125 microM. The kcat. for the overall reaction is 447 h-1. The ratio of kcat. to the Km for protoporphyrinogen is approx. 20-fold greater than the kcat./Km,O2 ratio. The ratio of protoporphyrin formed to dioxygen consumed is 1:3. Ubiquinone-6, ubiquinone-10 and dicoumarol stimulate protoporphyrinogen oxidase activity at low concentrations (less than 15 microM), whereas coenzyme Q0 and menadione show no activation at these concentrations. Above 30 microM, all five quinones inhibit the enzyme activity. FAD does not significantly affect the activity of the enzyme. Bilirubin, a product of haem catabolism, is shown to be a competitive inhibitor of the penultimate enzyme of the haem-biosynthetic pathway, protoporphyrinogen oxidase, with a calculated Ki of 25 microM. The terminal enzyme of haem-biosynthetic pathway, namely ferrochelatase, is not inhibited by bilirubin at concentrations over double the Ki value for the oxidase. In contrast with other enzymic systems, the toxicity of bilirubin is not reversed by binding to albumin.

Animals↗

PubMed1976

Regulation of arginine and pyrimidine biosynthesis in Pseudomonas putida.

Repression of biosynthetic enzyme synthesis in Pseudomonas putida is incomplete even when the bacteria are growing in a nutritionally complex environment. The synthesis of four of the enzymes of the arginine biosynthetic pathway (N-acetyl-alpha-glutamokinase/N-acetylglutamate-gamma-semialdehyde dehydrogenase, ornithine carbamoyltransferase and acetylornithine-delta-transaminase) could be repressed and derepressed, but the maximum difference observed between repressed and derepressed levels for any enzyme of the pathway was only 5-fold (for ornithine carbamoyltransferase). No repression of five enzymes of the pyrimidine biosynthetic pathway (aspartate carbamoyltransferase, dihydro-orotase, dihydro-orotate dehydrogenase, orotidine-5'-phosphate pyrophosphorylase and orotidine-5'-phosphate decarboxylase) could be detected on addition of pyrimidines to minimal asparagine cultures of P. putida A90, but a 1-5- to 2-fold degree of derepression was found following pyrimidine starvation of pyrimidine auxotrophic mutants of P. putida A90. Aspartate carbamoyltransferase in crude extracts of P. putida A90 was inhibited in vitro by (in order of efficiency) pyrophosphate, CTP, UTP and ATP, at limiting but not at saturating concentrations of carbamoyl phosphate.

Aldehyde Oxidoreductases↗

PubMed1977

Role of transport systems in amino acid metabolism: leucine toxicity and the branched-chain amino acid transport systems.

The livR locus, which leads to a trans-recessive derepression of branched-chain amino acid transport and periplasmic branched-chain amino acid-binding proteins, is responsible for greatly increased sensitivity toward growth inhibition by leucine, valine, and serine and, as shown previously, for increased sensitivity toward toxicity by branched-chain amino acid analogues, such as 4-azaleucine or 5',5',5'-trifluoroleucine. These phenotypes are similar to those of relA mutants; however, the livR mutants retain the stringent response of ribonucleic acid synthesis. However, an increase in the rate of transport or in the steady-state intracellular level of amino acids in the livR strain cannot completely account for this sensitivity. The ability of the LIV-I transport system to carry out exchange of pool amino acids for extracellular leucine is a major factor in leucine sensitivity. The previous finding that inhibition of threonine deaminase by leucine contributes to growth inhibition is confirmed by simulating the in vivo conditions using a toluene-treated cell preparation with added amino acids at levels corresponding to the internal pool. The relationship between transport systems and corresponding biosynthetic pathways is discussed and the general principle of a coordination in the regulation of transport and biosynthetic pathways is forwarded. The finding that the LIV-I transport system functions well for amino acid exchange in contrast to the LIV-II system provides another feature that distinguishes these systems in addition to previously described differences in regulation and energetics.

Biological Transport, Active↗

PubMed1977

Examination of the structure of an unknown green fluorescent compound, compound G2, accumulated in non-growing cells of Eremothecium ashbyii by the addition of dimeric diacetyl.

The addition of dimeric diacetyl to Eremothecium ashbyii caused simultaneous accumulation of two green fluorescent compounds with the inhibition of riboflavin formation in non-growing cells. One compound, referred to as Compound G1, was identified as 6, 7-dimethyl-8-ribityllumazine as reported previously and the other is referred to as Compound G2. The latter compound was considered to be 6-methyl-7-(2-hydroxy-2-methyl-3-oxobutyl)-8-ribityllumazine because a violet fluorescent compound, 6-methyl-7-hydroxy-8-ribityllumazine was derived from Compound G2 in the presence of p-quinone and because the known action mechanism of dimeric diacetyl as a trapping agent of possible intermediates in the biosynthetic pathway. The results indicate that an immediate intermediate to 6, 7-dimethyl-8-ribityllumazine in the biosynthetic pathway of riboflavin is 4-ribitylamino-5-amino-2, 6-dihydroxypyrimidine, whose pyrimidine portion is derived by the elimination of a dimeric diacetyl fragment from the molecule of the isolated lumazine.

Ascomycota↗

PubMed1986

Uracil nucleotide synthesis in a human breast cancer cell line (MCF-7) and in two drug-resistant sublines that contain increased levels of enzymes of the de novo pyrimidine pathway.

Cultured wild-type MCF-7 human breast cancer cells and two MCF-7 sublines that overproduce enzymes of the de novo pyrimidine biosynthetic pathway were compared with regard to: rate of de novo biosynthesis of uracil nucleotides, sensitivity of the de novo and salvage pathways to the concentration of intracellular uracil nucleotides, and potential of exogenous uridine at concentrations equivalent to plasma levels to affect de novo pyrimidine biosynthesis. The PALAR MCF-7 subline, which is resistant to N-(phosphonacetyl)-L-aspartate and has 5.2 times the activity of the first de novo enzyme as the wild-type MCF-7 cells, synthesizes uracil nucleotides via the de novo pathway at a rate that is 5.8 times that of the wild type MCF-7 cells. The PYRR MCF-7 subline, which is resistant to pyrazofurin and has 15.1 times the activity of orotate phosphoribosyltransferase as the wild-type MCF-7 cells, synthesizes uracil nucleotides via the de novo pathway at a rate that is 1.4 times that of wild-type MCF-7 cells. These results are consistent with carbamyl phosphate synthetase being the rate-controlling step of de novo pyrimidine biosynthesis. In the presence of exogenous uridine at concentrations equivalent to that found in plasma (4.4-8.6 microM), the uracil nucleotide pool of wild-type MCF-7 cells was expanded by 20% and de novo synthesis was inhibited by 55%. Incubation of PALAR MCF-7 cells with uridine at concentrations between 7.3 and 16.8 microM caused a 40% increase in the uracil nucleotide pool and a 30% inhibition of de novo synthesis. De novo synthesis of uracil nucleotides in PYRR MCF-7 cells was not affected by a greater than 10-fold increase in the uracil nucleotide pool. Salvage of [14C] uridine was inhibited by an expanded uracil nucleotide pool in the wild-type and PYRR MCF-7 cells but was not inhibited in the PALAR MCF-7 cell line. These results demonstrate that, although the overproduced enzymes exhibit substrate affinities and specificities in cell-free preparations similar to those of the wild-type enzymes, in intact cells the resistant cell lines exhibit marked differences in the control of de novo and salvage pyrimidine biosynthetic pathways by intracellular uracil nucleotides.

Amides↗

PubMed1983

Identification of AAS genes and their regulatory role in general control of amino acid biosynthesis in yeast.

In yeast, most amino acid biosynthetic pathways are coregulated: starvation for a single amino acid results in derepression of enzyme activities for many different biosynthetic pathways. This phenomenon is referred to as "general control of amino acid biosynthesis." In this paper we describe the isolation and characterization of 43 amino acid analog-sensitive (aas-) mutants that are perturbed in this general regulatory system. These 43 mutations define four unlinked complementation groups, AAS101, AAS102, AAS103, and AAS104, two of which identify previously unreported genes involved in general control. These aas mutants are unable to derepress a number of amino acid biosynthetic genes, resulting in increased sensitivity to amino acid analogs, reduced growth rates, and reduced enzyme activity levels under amino acid starvation conditions. Thus, the AAS+ gene products function as positive regulatory elements for this system. We show that the AAS genes mediate these effects by regulating the mRNA levels of genes under their control.

Alcohol Oxidoreductases↗

PubMed2002

Regulation of pyrimidine synthesis in Pseudomonas mendocina.

Regulation of the de novo pyrimidine biosynthetic enzymes in the bacterium Pseudomonas mendocina was examined when its cells were grown on succinate as a carbon source. When P. mendocina was grown in the presence of orotic acid or uracil, the de novo enzyme activities were depressed with dihydroorotase activity being significantly depressed after uracil addition. Following pyrimidine limitation of a uracil auxotroph of P. mendocina deficient for orotate phosphoribosyltransferase activity, the pyrimidine biosynthetic pathway enzyme activities were affected indicating possible regulation at the level of enzyme synthesis. Of the de novo pathway enzymes assayed, dihydroorotate dehydrogenase exhibited the highest increase in its activity. The regulation of the pyrimidine biosynthetic pathway by pyrimidines in P. mendocina appeared similar to what was previously observed for the taxonomically-related species P. stutzeri.

Bacterial Proteins↗

PubMed2003

Metabolic engineering of glutamate production.

Since the discovery of Corynebacterium glutamicum as an efficient glutamate-overproducing microorganism in 1957, the production of L-amino acids by the fermentative method has become one of the most important research-target of industrial microbiology. Several research groups have developed metabolic engineering principles for L-amino acid-producing C. glutamicum strains over the last four decades. The mechanism of L-glutamate-overproduction by the microorganism is very unique and interesting. L-Glutamate overproduction by this bacterium, a biotin auxotroph, is induced by a biotin limitation and suppressed by an excess of biotin. Addition of a surfactant or penicillin is known to induce L-glutamate overproduction under excess biotin. After the development of the general molecular biology tools such as cloning vectors and DNA transfer technique, genes encoding biosynthetic enzymes were isolated. With those genes and tools, recombinant DNA technology can be applied in analysis of biosynthetic pathways and strain construction of C. glutamicum. In this review, key points of the L-glutamate biosynthetic pathways are summarized and the recent studies about triggering mechanism of L-glutamate overproduction by C. glutamicum are introduced. Then the metabolic flux analysis of L-glutamate overproduction is explored.

Cloning, Molecular↗

PubMed2003

Avermectin: biochemical and molecular basis of its biosynthesis and regulation.

Avermectin and its analogues, produced by Streptomyces avermitilis, are major commercial antiparasitic agents in the field of animal health, agriculture, and human infections. They are 16-membered pentacyclic lactone compounds derived from polyketide and linked to a disaccharide of the methylated deoxysugar l-oleandrose. Labeling studies, analyses of the biosynthetically blocked mutants, and the identification of the avermectin gene cluster allows characterization of most of the biosynthetic pathway. Recent completion of S. avermitilis genome sequencing is also expected to help in revealing the precise biosynthetic sequence and the complicated regulatory mechanism for avermectin biosynthesis, which has been long-awaited to be elucidated. The well characterized avermectin biosynthetic pathway and availability of S. avermitilis genome information in combination with the recent development of combinatorial biosynthesis should allow us to redesign more potent avermectin analogues and to engineer S. avermitilis as a more efficient host for the production of important commercial analogues.

Antiparasitic Agents↗

PubMed2006

Caterpillar herbivory and salivary enzymes decrease transcript levels of Medicago truncatula genes encoding early enzymes in terpenoid biosynthesis.

In response to caterpillar herbivory, alfalfa and related plant species defend themselves through the induction of saponin and volatile terpenoid biosynthesis. Both these types of defensive compounds are derived from the metabolic intermediate, isopentenyl diphosphate (IPP). In plants, two distinct biosynthetic pathways can generate IPP; the cytosolic mevalonate pathway and the plastid-associated 2C-methyl erythritol 4-phosphate (MEP) pathway. In Medicago truncatula, transcript levels of key regulatory genes active in the early steps of these biosynthetic pathways were measured in response to larval herbivory by the beet army worm, Spodoptera exigua. Transcripts encoding enzymes at early steps of both terpenoid pathways were lower in caterpillar-damaged leaves. Higher degrees of herbivore damage accentuated the decrease in transcript levels; however, transcript amounts were not affected by insect larval stage. Insect larvae, manipulated to reduce labial gland salivary secretions, were used to examine the role of the salivary elicitors in modulating gene expression. Results suggest that an insect salivary factor, possibly glucose oxidase (GOX), may be involved in reduction of transcript levels following herbivory. Addition of GOX or hydrogen peroxide to mechanically wounded leaves confirm these findings. In comparison, transcript levels of a gene encoding a putative terpene synthase are induced in mechanically- or insect-damaged leaves. These data show that insect salivary factors can act to suppress transcript levels of genes involved in plant defense pathways. Findings also suggest that in response to stress such as insect herbivory, regulation occurs at the early steps of the MEP pathway.

Animals↗

PubMed2003

Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein.

During polyketide biosynthesis, acyl carrier proteins (ACPs) perform the central role of transferring polyketide intermediates between active sites of polyketide synthase. The 4'-phosphopantetheine prosthetic group of a holo-ACP is a long and flexible arm that can reach into different active sites and provide a terminal sulfhydryl group for the attachment of acyl groups through a thioester linkage. We have determined the solution structure and characterized backbone dynamics of the holo form of the frenolicin acyl carrier protein (fren holo-ACP) by nuclear magnetic resonance (NMR). Unambiguous assignments were made for 433 hydrogen atoms, 333 carbon atoms, and 84 nitrogen atoms, representing a total of 94.6% of the assignable atoms in this protein. From 879 meaningful NOEs and 45 angle constraints, a family of 24 structures has been calculated. The solution structure is composed of three major alpha-helices packed in a bundle with three additional short helices in intervening loops; one of the short helices slowly exchanges between two conformations. Superposition of the major helical regions on the mean structure yields average atomic rmsd values of 0.49 +/- 0.09 and 0.91 +/- 0.08 A for backbone and non-hydrogen atoms, respectively. Although the three-helix bundle fold is conserved among acyl carrier proteins involved in fatty acid synthases and polyketide synthases, a detailed comparison revealed that ACPs from polyketide biosynthetic pathways are more related to each other in tertiary fold than to their homologues from fatty acid biosynthetic pathways. Comparison of the free form of ACPs (NMR structures of fren ACP and the Bacillus subtilis ACP) with the substrate-bound form of ACP (crystal structure of butyryl-ACP from Escherichia coli) suggests that conformational exchange plays a role in substrate binding.

Acyl Carrier Protein↗