Conservation of structure in the human gene encoding argininosuccinate synthetase and the argG genes of the archaebacteria Methanosarcina barkeri MS and Methanococcus vannielii.

The DNA sequences of the argG genes of Methanosarcina barkeri MS and Methanococcus vannielii were determined. The polypeptide products of these methanogen genes have amino acid sequences which are 50% identical to each other and 38% identical to the amino acid sequence encoded by the exons of the human argininosuccinate synthetase gene. Introns in the human chromosomal gene separate regions which encode amino acids conserved in both the archaebacterial and human gene products. An open reading frame immediately upstream of argG in Methanosarcina barkeri MS codes for an amino acid sequence which is 45 and 31% identical to the sequences of the large subunits of carbamyl phosphate synthetase in Escherichia coli and Saccharomyces cerevisiae, respectively. If this gene encodes carbamyl phosphate synthetase in Methanosarcina barkeri, this is the first example, in an archaebacterium, of physical linkage of genes that encode enzymes which catalyze reactions in the same amino acid biosynthetic pathway.     

Gene dosage effect of L-proline biosynthetic enzymes on L-proline accumulation and freeze tolerance in Saccharomyces cerevisiae

We have previously reported that L-proline has cryoprotective activity in Saccharomyces cerevisiae. A freeze-tolerant mutant with L-proline accumulation was recently shown to carry an allele of the PRO1 gene encoding gamma-glutamyl kinase, which resulted in a single amino acid substitution (Asp154Asn). Interestingly, this mutation enhanced the activities of gamma-glutamyl kinase and gamma-glutamyl phosphate reductase, both of which catalyze the first two steps of L-proline synthesis and which together may form a complex in vivo. Here, we found that the Asp154Asn mutant gamma-glutamyl kinase was more thermostable than the wild-type enzyme, which suggests that this mutation elevated the apparent activities of two enzymes through a stabilization of the complex. We next examined the gene dosage effect of three L-proline biosynthetic enzymes, including Delta(1)-pyrroline-5-carboxylate reductase, which converts Delta(1)-pyrroline-5-carboxylate into L-proline, on L-proline accumulation and freeze tolerance in a non-L-proline-utilizing strain. Overexpression of the wild-type enzymes has no influence on L-proline accumulation, which suggests that the complex is very unstable in nature. However, co-overexpression of the mutant gamma-glutamyl kinase and the wild-type gamma-glutamyl phosphate reductase was effective for L-proline accumulation, probably due to a stabilization of the complex. These results indicate that both enzymes, not Delta(1)-pyrroline-5-carboxylate reductase, are rate-limiting enzymes in yeast cells. A high tolerance for freezing clearly correlated with higher levels of L-proline in yeast cells. Our findings also suggest that, in addition to its cryoprotective activity, intracellular L-proline could protect yeast cells from damage by oxidative stress. The approach described here provides a valuable method for breeding novel yeast strains that are tolerant of both freezing and oxidative stresses.     

Crystal structure of inositol phosphate multikinase 2 and implications for substrate specificity

Inositol polyphosphates perform essential functions as second messengers in eukaryotic cells, and their cellular levels are regulated by inositol phosphate kinases. Most of these enzymes belong to the inositol phosphate kinase superfamily, which consists of three subgroups, inositol 3-kinases, inositol phosphate multikinases, and inositol hexakisphosphate kinases. Family members share several strictly conserved signature motifs and are expected to have the same backbone fold, despite very limited overall amino acid sequence identity. Sequence differences are expected to play important roles in defining the different substrate selectivity of these enzymes. To investigate the structural basis for substrate specificity, we have determined the crystal structure of the yeast inositol phosphate multikinase Ipk2 in the apoform and in a complex with ADP and Mn(2+) at up to 2.0A resolution. The overall structure of Ipk2 is related to inositol trisphosphate 3-kinase. The ATP binding site is similar in both enzymes; however, the inositol binding domain is significantly smaller in Ipk2. Replacement of critical side chains in the inositolbinding site suggests how modification of substrate recognition motifs determines enzymatic substrate preference and catalysis.     

Molecular characterization of an Arabidopsis gene encoding a phospholipid-specific inositol polyphosphate 5-phosphatase

Phosphoinositides are important molecules that serve as second messengers and bind to a complex array of proteins modulating their subcellular location and activity. The enzymes that metabolize phosphoinositides can in some cases serve to terminate the signaling actions of phosphoinositides. The inositol polyphosphate 5-phosphatases (5PTases) comprise a large protein family that hydrolyzes 5-phosphates from a variety of inositol phosphate and phosphoinositide substrates. We previously reported the identification of 15 putative 5PTase genes in Arabidopsis and have shown that overexpression of the At5PTase1 gene can alter abscisic acid signaling. At5PTase1 and At5PTase2 have been shown to hydrolyze the 5-phosphate from inositol phosphate substrates. We have examined the substrate specificity of the At5PTase11 protein, which is one of the smallest predicted 5PTases found in any organism. We report here that the At5PTase11 gene encodes an active 5PTase enzyme that can only dephosphorylate phosphoinositide substrates containing a 5-phosphate. In addition to hydrolyzing known substrates of 5PTase enzymes, At5PTase11 also hydrolyzes the 5-phosphate from phosphatidylinositol (3,5) bisphosphate. We also show that the At5PTase11 gene is regulated by abscisic acid, jasmonic acid, and auxin, suggesting a role for phosphoinositide action in these signal transduction pathways.     

Multiple regulatory roles of a novel Saccharomyces cerevisiae protein, encoded by YOL002c, in lipid and phosphate metabolism

The yeast open reading frame YOL002c encodes a putative membrane protein. This protein is evolutionarily conserved across species, including humans, although the function of each of these proteins remains unknown. YOL002c is highly expressed in yeast cells that are grown in the presence of saturated fatty acids such as myristate. Furthermore, cells in which the YOL002c gene is disrupted grow poorly on this carbon source. These mutant cells are also resistant to the polyene antibiotic, nystatin. Gene chip analysis on yol002cDelta cells revealed that a variety of genes encoding proteins involved in fatty acid metabolism and in the phosphate signaling pathway are induced in this mutant strain. In addition, our studies demonstrated that in the disruption strain acid phosphatase activity is expressed constitutively, and the cells accumulate polyphosphate to much higher levels than wild-type cells. A homologous human protein is able to partially rescue these defects in phosphate metabolism. We propose that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism.     

G-protein-coupled receptor stimulation of the p42/p44 mitogen-activated protein kinase pathway is attenuated by lipid phosphate phosphatases 1, 1a, and 2 in human embryonic kidney 293 cells

Sphingosine 1-phosphate, lysophosphatidic acid, and phosphatidic acid bind to G-protein-coupled receptors to stimulate intracellular signaling in mammalian cells. Lipid phosphate phosphatases (1, 1a, 2, and 3) are a group of enzymes that catalyze de-phosphorylation of these lipid agonists. It has been proposed that the lipid phosphate phosphatases exhibit ecto activity that may function to limit bioavailability of these lipid agonists at their receptors. In this study, we show that the stimulation of the p42/p44 mitogen-activated protein kinase pathway by sphingosine 1-phosphate, lysophosphatidic acid, and phosphatidic acid, all of which bind to G(i/o)-coupled receptors, is substantially reduced in human embyronic kidney 293 cells transfected with lipid phosphate phosphatases 1, 1a, and 2 but not 3. This was correlated with reduced basal intracellular phosphatidic acid and not ecto lipid phosphate phosphatase activity. These findings were supported by results showing that lipid phosphate phosphatases 1, 1a, and 2 also abrogate the stimulation of p42/p44 mitogen-activated protein kinase by thrombin, a peptide G(i/o)-coupled receptor agonist whose bioavailability at its receptor is not subject to regulation by the phosphatases. Furthermore, the lipid phosphate phosphatases have no effect on the stimulation of p42/p44 mitogen-activated protein kinase by other agents that do not use G-proteins to signal, such as serum factors and phorbol ester. Therefore, these findings show that the lipid phosphate phosphatases 1, 1a, and 2 may function to perturb G-protein-coupled receptor signaling per se rather than limiting bioavailability of lipid agonists at their respective receptors.     

Properties of the enzymes catalyzing the biosynthesis of lysophosphatidate and its ether analog in cultured fibroblasts from Zellweger syndrome patients and normal controls

The activities, properties, and steady-state kinetics of the five enzymes catalyzing the synthesis of 1-acyl- and 1-alkyl-sn-glycerol 3-phosphate in the cultured skin fibroblasts from Zellweger syndrome patients and normal controls were studied in detail. Judging from their Km and Vmax values, glycerol phosphate acyltransferase (EC 2.3.1.15), acyl/alkyl dihydroxyacetone phosphate reductase (EC 1.1.1.101), and acyl coenzyme A reductase (long-chain alcohol forming), appear to be affected only slightly by the absence of peroxisomes characteristic of the Zellweger syndrome. Glycerophosphate acyltransferase also showed no differences in N-ethylmaleimide sensitivity nor in inhibition by dihydroxyacetone phosphate between these cell types. Dihydroxyacetone phosphate acyltransferase (EC 2.3.1.42) and alkyl dihydroxyacetone phosphate synthase (EC 2.5.1.26) have altered activity and kinetic constants in homogenates from Zellweger syndrome fibroblasts. Dihydroxyacetone phosphate acyltransferase has similar Km (DHAP) values in both control and Zellweger syndrome cells; however, the value for the Vmax in Zellweger syndrome cells is only 6% of that found in the controls. This is interpreted as indicating that this enzyme is not defective in this disease but is simply present at a depressed level. Also, this enzyme activity has a maximum rate at pH 7.0-7.5 in the mutant cells as opposed to pH 5.4 in the controls. Acylation of dihydroxyacetone phosphate by control cell homogenate was stimulated by N-ethylmaleimide at both pH 5.7 and 7.5 whereas this activity from Zellweger syndrome cells was slightly inhibited at pH 5.7 and strongly inhibited at pH 7.5. In the absence of detergent, dihydroxyacetone phosphate acyltransferase in the Zellweger syndrome cells was much more labile to trypsin than in the control cells. Alkyl dihydroxyacetone phosphate synthase had a slightly higher Km (33 vs 17 microM) for palmitoyl dihydroxyacetone phosphate and a lower Vmax (0.07 vs 0.24 mU/mg protein) in the Zellweger syndrome cells as compared to controls. Although this is a substantial decrease in activity, it probably contributes little to the decreased rate of ether lipid synthesis in these cells. The major problem in this respect is apparently the loss of dihydroxyacetone phosphate acyltransferase activity. All of these enzymes, in both control and Zellweger syndrome cell homogenates, are sedimentable by centrifugation at 100,000g. Also, with the exception of dihydroxyacetone phosphate acyltransferase they had similar patterns of inactivation by heat in both cell types.     

Enzymatic analysis of lipid phosphate phosphatases

Lipid phosphate monoesters including phosphatidic acid, lysophosphatidic acid, sphingosine 1-phosphate and ceramide 1-phosphate are intermediates in phosho- and sphingo-lipid biosynthesis and also play important roles in intra- and extra-cellular signaling. Dephosphorylation of these lipids terminates their signaling actions and, in some cases, generates products with additional biological activities or metabolic fates. The key enzymes responsible for dephosphorylation of these lipid phosphate substrates are collectively termed lipid phosphate phosphatases (LPPs). They are integral membrane enzymes with a core domain of six transmembrane spanning alpha-helices linked by extramembrane loops. LPPs are oriented in the membrane with their N- and C-termini facing the cytoplasm. LPPs exhibit isoform and cell specific localization patterns being variably distributed between endomembrane compartments (primarily the endoplasmic reticulum and Golgi apparatus) and the plasma membrane. The active site of these enzymes is formed from residues within two of the extramembrane loops and faces the lumen of endomembrane compartments or, when localized to the plasma membrane, towards, the extracellular space. Biochemical, pharmacological, cell biological and genetic studies identify roles for LPPs in both intracellular lipid metabolism and the regulation of both intra- and extra-cellular signaling pathways that control cell growth, survival and migration. This article describes procedures for the expression of LPPs in insect and mammalian cells and their analysis by SDS-PAGE and Western blotting. The most straightforward way to determine LPP activity is to measure release of the substrate phosphate group. We described methods for the synthesis and purification of [(32)P]-labeled LPP substrates. We describe the use of both radiolabeled and fluorescent lipid substrates for the detection, quantitation and analysis of the enzymatic activities of the LPPs measured using intact or broken cell preparations as the source of enzyme.     

Optimizing Electroporation Conditions in Primary and Other Difficult-to-Transfect Cells

Electroporation is a valuable tool for nucleic acid delivery because it can be used for a wide variety of cell types. Many scientists are shifting toward the use of cell types that are more relevant to in vivo applications, including primary cells, which are considered difficult to transfect. The ability to electroporate these cell types with nucleic acid molecules of interest at a relatively high efficiency while maintaining cell viability is essential for elucidating the pathway(s) in which a gene product is involved. We present data demonstrating that by optimizing electroporation parameters, nucleic acid molecules can be delivered in a highly efficient manner. We display transfection results for primary and difficult-to-transfect cell types including human primary fibroblasts, human umbilical vein endothelial cells, Jurkat cells, and two neuroblastoma cell lines [SK-N-SH (human) and Neuro-2A (mouse)] with plasmid DNAs and siRNAs. Our data demonstrate that by determining proper electroporation conditions, glyceraldehyde phosphate dehydrogenase mRNA was silenced in Jurkat cells when compared with negative control siRNA electroporations as early as 4 h post-transfection. Other experiments demonstrated that optimized electroporation conditions using a fluorescently labeled transfection control siRNA resulted in 75% transfection efficiency for Neuro-2A, 93% for human primary fibroblasts, and 94% for HUVEC cells, as analyzed by flow cytometry.     

Characterization of a prostate-specific tyrosine phosphatase by mutagenesis and expression in human prostate cancer cells

The cellular form of human prostatic acid phosphatase (PAcP) is a neutral protein-tyrosine phosphatase (PTP) and may play a key role in regulating the growth and androgen responsiveness of prostate cancer cells. The functional role of the enzyme is at least due in part to its dephosphorylation of c-ErbB-2, an in vivo substrate of the enzyme. In this study, we investigated the molecular mechanism of phosphotyrosine dephosphorylation by cellular PAcP. We mutated several amino acid residues including one cysteine residue that was proposed to be involved in the PTP activity of the enzyme by serving as the phosphate acceptor. The cDNA constructs of mutant enzymes were transiently transfected into C-81 LNCaP and PC-3 human prostate cancer cells that lack the endogenous PAcP expression. The phosphotyrosine level of ErbB-2 in these transfected cells was subsequently analyzed. Our results demonstrated that the phosphotyrosine level of ErbB-2 in cells expressing H12A or D258A mutant PAcP is similar to that in control cells without PAcP expression, suggesting that these mutants are incapable of dephosphorylating ErbB-2. In contrast, cells expressing C183A, C281A, or wild-type PAcP had a decreased phosphotyrosine level of ErbB-2, compared with the control cells. Similar results were obtained from in vitro dephosphorylation of immunoprecipitated ErbB-2 by these mutant enzymes. Furthermore, transient expression of C183A, C281A, or the wild-type enzyme, but not H12A or D258A, decreased the growth rate of C-81 LNCaP cells. The data collectively indicate that His-12 and Asp-258, but not Cys-183 or Cys-281, are required for the PTP activity of PAcP.     

METABOLIC INTERMEDIATES IN ADAPTIVE FERMENTATION OF GALACTOSE BY YEAST

Pyruvic acid, which is known to be an intermediate of glucose fermentation, was added to yeast during adaptation to galactose fermentation. It was found to neutralize the inhibition by sodium fluoride, and to decrease the apparent time of adaptation from 90 to about 45 or 60 minutes. In control experiments, it was shown that intact yeast is unable appreciably to ferment or decarboxylate alone, although it oxidizes the compound readily. Experiments in which galactose and pyruvate were added at various times and in different orders were used to eliminate the possible complications of the rates at which these compounds penetrate the cells. Under these conditions, it was not possible to reduce the time of adaptation below 45 minutes. It was concluded that the rôle of added pyruvate was to serve as a source of acetaldehyde, which in turn could accept hydrogen and be reduced to alcohol. Substances, such as triose phosphate, which could serve as hydrogen donors were not produced from galactose in appreciable quantities until 45 minutes had elapsed. This time was therefore inferred to be the true adaptation time, during which the first synthesis of adaptive enzymes occurred. Some determinations of the distribution of phosphorylated intermediates at various stages during the adaptive process were carried out. It was found that ATP, which usually serves to phosphorylate hexoses, accumulates during the preadaptive phase, diminishes rapidly after 60 minutes, and subsequently increases once more. The source of the ATP phosphate appeared to be PPA or triose phosphate initially present in the cells. It was inferred that the adaptive enzyme was concerned with the phosphorylation of galactose and the conversion of the phosphate ester to a glucose ester, which could then be fermented by the normal enzymes of the cell. Added ATP was found to stimulate adaptation to a considerable extent, but did not shorten the time of adaptation below 75 minutes. This seemed consistent with the rôle of ATP as a phosphate donor for galactose. Creatine was found to inhibit adaptation to some degree, in agreement with its known ability to act as a competitive phosphate acceptor. It was demonstrated that yeast produces, during and after adaptation, substances which shorten the apparent adaptation time of fresh samples of yeast. In agreement with our other findings, it appeared that such substances were not formed before about 45 minutes. They are probably not metabolic intermediates, and may be identical with the adaptive principle which can be extracted from adapted cells.     

Regulation of Pyrimidine Biosynthesis in Saccharomyces cerevisiae

Biochemical steps of the pyrimidine pathway have been found to be the same in yeast as in bacteria, and all except one step have been characterized. The activities of the first two enzymes, carbamoyl phosphate synthetase and aspartic transcarbamylase, are simultaneously controlled by feedback inhibition and repression. Moreover, these enzymes are coded by the same genetic region (ura-2) and seem to form a single enzymatic complex. The enzymes that follow later in the pathway are induced in a sequential way by the intermediary products and are insensitive to pyrimidine repression. The corresponding genes (ura-4, ura-1, ura-3) are not linked to each other or to ura-2, the gene for carbamoyl phosphate synthetase and aspartic transcarbamylase. Mutants that have simultaneously lost feedback inhibition by uridine triphosphate for carbamoyl phosphate synthetase and for aspartic transcarbamylase have been found and mapped in the gene ura-2.     

New insights into the biology of cytokinin degradation

A survey of recent results is presented concerning the role of cytokinin degradation in plants, which is catalyzed by cytokinin oxidase/dehydrogenase (CKX) enzymes. An overview of Arabidopsis CKX gene expression suggests that their differential regulation by biotic and abiotic factors contributes significantly to functional specification. Here, we show using reporter gene and semiquantitative RT-PCR analyses regulation of individual CKX genes by cytokinin, auxin, ABA, and phosphate starvation. Partially overlapping expression domains of CKX genes and cytokinin-synthesizing IPT genes in meristematic tissues and endo-reduplicating cells lend support for a locally restricted function of cytokinin. On the other hand, their expression in vascular tissue suggests a function in controlling transported cytokinin. Recent studies led to a model for the biochemical reaction mechanism of CKX-mediated catalysis, which was refined on the basis of the three-dimensional enzyme structure. Last but not least, the developmental functions of CKX enzymes are addressed. The recent identification of the rice OSCKX2 gene as an important novel breeding tool is highlighted. Together the results corroborate the relevance of metabolic control in determining cytokinin activity.     

Nucleic acid enzymes as a novel generation of anti-gene agents

Recent molecular and cellular studies have highlighted the important role of some gene products in the cause and/or perpetuation of human pathological conditions including cancer and autoimmune diseases. The identification of such gene products has led to the development of new candidate therapies. The discovery of catalytic nucleic acid enzymes has provided researchers with a potentially important tool to block the expression of abnormal genes, provided that their sequences are known. The cleavage specificity of these compounds is determined by their hybridizing antisense arms, which anneal with the target mRNA in a complementary fashion. Nucleic acid enzymes can be delivered to cells either endogenously as gene encoding RNA enzymes (ribozymes) or exogenously as in vitro made agents. Given the progress reported during the last years, a wide range of molecular designs and chemical modifications can be introduced into these compounds, in particular the hammerhead type ribozyme. Here, we review the design, stability and the therapeutic application of these agents with the goals of illustrating relevant gene targets and signal pathways for molecular medicine. Relevant in vivo problems of the technology, mRNA repair by group I intron ribozymes and gene regulation by endogenous RNA will also be discussed.     

Identity and activities of lysosomal enzymes in parenchymal and non-parenchymal cells from rat liver.

1. Intact parenchymal and non-parenchymal cells were isolated from rat liver. The parenchymal cells were purified by differential centrifugation, while non-parenchymal cells were obtained free of parenchymal cell contamination by preferentially destroying the parenchymal cells with the aid of pronase (0.25%). 2. The ability to isolate pure intact parenchymal and non-parenchymal cells permitted the characterization and measurement of specific activities of various lysosomal enzymes, representing the main functional hydrolytic activities of the lysosomes in these distinct cell types. 3. Lysosomal enzymes catalysing the hydrolysis of the terminal carbohydrate moiety of glycoproteins and glycolipids were not particularly enriched in the non-parenchymal cells as compared to parenchymal cells. The ratio of the specific activities of non-parenchymal cells over parenchymal cells varied between 0.7 for N-acetyl-beta-D-hexoseaminidase to 2.1 for alpha-glucosidase. This suggests no specific role of the non-parenchymal cells in the hydrolysis of terminal carbohydrate moieties of glycoproteins and glycolipids. 4. The enzymes acid phosphatase and aryl sulphatase, representing the phosphate and sulphate hydrolyzing activities, were enriched in the non-paranchymal cells as compared to the parenchymal cells by a factor of 2.5. 5. The most important peptidase cathepsin D, representing protein breakdown capacity, is enriched in the non-parenchymal cells as compared to parenchymal cells by a factor 6.0, suggesting a possible specific function of non-parenchymal cells in protein breakdown. 6. The most enriched lysosomal enzyme, representing lipid hydrolysis, is acid lipase, which is enriched in the non-parenchymal cells with a factor of 10. 7. The distribution of lysosomal enzymes between parenchymal and non-parenchymal cells suggests different functional roles of the lysosomes in these cell types. It can be concluded that the non-parenchymal cells possess a set of lysosomal enzymes which makes them extremely suitable for a phagocytic and antimicrobial function in the liver.     

Studies on the pigeon red blood cell metabolism

1. Pigeon erythrocyte was found to depend on the glycolytic and pentose phosphate pathway for most of its energy production in the form of adenosine triphosphate and reducing potential, since there was no detectable activity of any of the citric acid cycle (TCA) cycle enzymes measured. 2. The absence of detectable amounts of 2,3-diphosphoglyceric acid (2-3-DPG) indicated that there is no direct relationship between the active glycolytic system and the function of these cells. 3. A comparison of the mass action ratios with the equilibrium constants of the glycolytic reactions showed that hexokinase, phosphofructokinase and pyruvate kinase reactions are displaced from equilibrium, implying that these are the key regulatory enzymes of glycolysis in pigeon erythrocytes. 4. The changes in the concentrations of the glycolytic metabolites under hypoxic conditions that stimulate the flux through the glycolytic pathway were found to be consistent with the above hypothesis. 5. Flux measurements of the pentose phosphate pathway showed that it metabolizes only 3.4% of the total glucose consumed by the resting erythrocyte. 6. Hypoxic conditions resulted in a stimulation of the pentose phosphate pathway by as much as four-fold, whilst the glycolytic pathway was not stimulated by more than about twice.     

Is your ribozyme design really correct?: A proposal of simple single turnover competition assay to evaluate ribozymes

Today, many nucleic acid enzymes are used in gene therapy and gene regulations. However, no simple assay methods to evaluate enzymatic activities, with which we judge the enzyme design, have been reported. Here, we propose a new simple competition assay for nucleic acid enzymes of different types to evaluate the cleaving efficiency of a target RNA molecule, of which the recognition sites are different but overlapped. Two nucleic acid enzymes were added to one tube to make a competition of these two enzymes for one substrate. The assay was used on two ribozymes, hammerhead ribozyme and hairpin ribozyme, and a DNA-enzyme. We found that this assay method is capable of application to those enzymes, as a powerful tool for the selection and designing of RNA-cleaving enzymes.