Mesh-terms: Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Gene Expression Regulation, Developmental :: drug effects; Keywords: ;
Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species.
Department of Microbiology, University of Massachusetts Amherst, North, Amherst, MA 01003-9298, USA. email@example.com
Geobacter species play important roles in bioremediation of contaminated environments and in electricity production from waste organic matter in microbial fuel cells. To better understand physiology of Geobacter species, expression and function of citrate synthase, a key enzyme in the TCA cycle that is important for organic acid oxidation in Geobacter species, was investigated. Geobacter sulfurreducens did not require citrate synthase for growth with hydrogen as the electron donor and fumarate as the electron acceptor. Expression of the citrate synthase gene, gltA, was repressed by a transcription factor under this growth condition. Functional and comparative genomics approaches, coupled with genetic and biochemical assays, identified a novel transcription factor termed HgtR that acts as a repressor for gltA. Further analysis revealed that HgtR is a global regulator for genes involved in biosynthesis and energy generation in Geobacter species. The hgtR gene was essential for growth with hydrogen, during which hgtR expression was induced. These findings provide important new insights into the mechanisms by which Geobacter species regulate their central metabolism under different environmental conditions.
Antibacterial and anti-atrophic effects of a highly soluble, acid stable UDCA formula in Helicobacter pylori-induced gastritis.
College of Pharmacy, Sungkyunkwan University, Su-won 440-746, South Korea.
Helicobacter pylori is one of the main causes of atrophic gastritis and gastric carcinogenesis. Gastritis can also occur in the absence of H. pylori as a result of bile reflux suggesting the eradication of H. pylori by bile acids. However, the bile salts are unable to eradicate H. pylori due to their low solubility and instability at acidic pH. This study examined the effect of a highly soluble and acid stable ursodeoxycholic acid (UDCA) formula on H. pylori-induced atrophic gastritis. The H. pylori infection decreased the body weight, mitochondrial membrane potential and ATP level in vivo. Surprisingly, H. pylori-induced expression of malate dehydrogenase (MDH), a key enzyme in the tricarboxylic acid cycle, at both the protein and mRNA levels. However, the UDCA formula repressed MDH expression and increased the membrane potential thereby increasing the ATP level and body weight in vivo. Moreover, UDCA scavenged the reactive oxygen species (ROS), increased the membrane potential, and inhibited apoptosis in AGS cells exposed to H(2)O(2) in vitro through the mitochondria-mediated pathway. Taken together, UDCA decreases the MDH and ROS levels, which can prevent apoptosis in H. pylori-induced gastritis.
Department of Biological Sciences, Rutgers University, Piscataway, New Jersey 08855-1059.
Mitochondrial citrate synthase was purified from leaves of Pisum sativum L. cv Progress 9. A three step purification was employed using ATP-Sepharose affinity chromatography which resulted in a 600-fold enrichment. Enzyme activity was assayed spectrophotometrically during greening of etiolated leaves under constant white light illumination. An increase (1.4 fold) in citrate synthase activity was observed in response to light. Immunoblot analysis of the same samples indicated a constant steady state level of citrate synthase on a per milligram protein basis. These investigations provide supportive evidence for the ability of this trichloroacetic acid cycle enzyme to be active in photosynthesizing tissue.
Characterization of citrate synthase from Geobacter sulfurreducens and evidence for a family of citrate synthases similar to those of eukaryotes throughout the Geobacteraceae.
Daniel R Bond, Tünde Mester, Camilla L Nesbø, Andrea V Izquierdo-Lopez, Frank L Collart, Derek R Lovley
BioTechnology Institute, University of Minnesota, 140 Gortner, 1479 Gortner Ave., St. Paul, MN 55108. firstname.lastname@example.org.
Members of the family Geobacteraceae are commonly the predominant Fe(III)-reducing microorganisms in sedimentary environments, as well as on the surface of energy-harvesting electrodes, and are able to effectively couple the oxidation of acetate to the reduction of external electron acceptors. Citrate synthase activity of these organisms is of interest due to its key role in acetate metabolism. Prior sequencing of the genome of Geobacter sulfurreducens revealed a putative citrate synthase sequence related to the citrate synthases of eukaryotes. All citrate synthase activity in G. sulfurreducens could be resolved to a single 49-kDa protein via affinity chromatography. The enzyme was successfully expressed at high levels in Escherichia coli with similar properties as the native enzyme, and kinetic parameters were comparable to related citrate synthases (kcat= 8.3 s(-1); Km= 14.1 and 4.3 microM for acetyl coenzyme A and oxaloacetate, respectively). The enzyme was dimeric and was slightly inhibited by ATP (Ki= 1.9 mM for acetyl coenzyme A), which is a known inhibitor for many eukaryotic, dimeric citrate synthases. NADH, an allosteric inhibitor of prokaryotic hexameric citrate synthases, did not affect enzyme activity. Unlike most prokaryotic dimeric citrate synthases, the enzyme did not have any methylcitrate synthase activity. A unique feature of the enzyme, in contrast to citrate synthases from both eukaryotes and prokaryotes, was a lack of stimulation by K+ ions. Similar citrate synthase sequences were detected in a diversity of other Geobacteraceae members. This first characterization of a eukaryotic-like citrate synthase from a prokaryote provides new insight into acetate metabolism in Geobacteraceae members and suggests a molecular target for tracking the presence and activity of these organisms in the environment.
Citrate synthase mutants of Agrobacterium are attenuated in virulence and display reduced vir gene induction.
Department of Microbiology, University of Washington, Seattle, 98195-7242, USA.
A citrate synthase (CS) deletion mutant of Agrobacterium tumefaciens C58 is highly attenuated in virulence. The identity of the mutant was initially determined from its amino acid sequence, which is 68% identical to Escherichia coli and 77% identical to Brucella melitensis. The mutant lost all CS enzymatic activity, and a cloned CS gene complemented a CS mutation in Sinorhizobium. The CS mutation resulted in a 10-fold reduction in vir gene expression, which likely accounts for the attenuated virulence. When a plasmid containing a constitutive virG [virG(Con)] locus was introduced into this mutant, the level of vir gene induction was restored to nearly wild-type level. Further, the virG(Con)-complemented CS mutant strain induced tumors that were similar in size and number to those induced by the parental strain. The CS mutation resulted in only a minor reduction in growth rate in a glucose-salts medium. Both the CS mutant and the virG(Con)-complemented CS strain displayed similar growth deficiencies in a glucose-salts medium, indicating that the reduced growth rate of the CS mutant could not be responsible for the attenuated virulence. A search of the genome of A. tumefaciens C58 revealed four proteins, encoded on different replicons, with conserved CS motifs. However, only the locus that when mutated resulted in an attenuated phenotype has CS activity. Mutations in the other three loci did not result in attenuated virulence and any loss of CS activity, and none were able to complement the CS mutation in Sinorhizobium. The function of these loci remains unknown.
Probing the roles of key residues in the unique regulatory NADH binding site of type II citrate synthase of Escherichia coli.
David J Stokell, Lynda J Donald, Robert Maurus, Nham T Nguyen, Gillian Sadler, Kajal Choudhary, Philip G Hultin, Gary D Brayer, Harry W Duckworth
Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada.
The citrate synthase of Escherichia coli is an example of a Type II citrate synthase, a hexamer that is subject to allosteric inhibition by NADH. In previous crystallographic work, we defined the NADH binding sites, identifying nine amino acids whose side chains were proposed to make hydrogen bonds with the NADH molecule. Here, we describe the functional properties of nine sequence variants, in which these have been replaced by nonbonding residues. All of the variants show some changes in NADH binding and inhibition and small but significant changes in kinetic parameters for catalysis. In three cases, Y145A, R163L, and K167A, NADH inhibition has become extremely weak. We have used nanospray/time-of-flight mass spectrometry, under non-denaturing conditions, to show that two of these, R163L and K167A, do not form hexamers in response to NADH binding, unlike the wild type enzyme. One variant, R109L, shows tighter NADH binding. We have crystallized this variant and determined its structure, with and without bound NADH. Unexpectedly, the greatest structural changes in the R109L variant are in two regions outside the NADH binding site, both of which, in wild type citrate synthase, have unusually high mobilities as measured by crystallographic thermal factors. In the R109L variant, both regions (residues 260 -311 and 316-342) are much less mobile and have rearranged significantly. We argue that these two regions are elements in the path of communication between the NADH binding sites and the active sites and are centrally involved in the regulatory conformational change in E. coli citrate synthase.
Department of Agricultural Chemistry and Soil Science, University of Sydney, NSW, Australia.
Bacteroids formed by Mesorhizobium ciceri CC 1192 in symbiosis with chickpea plants (Cicer arietinum L.) contained a single form of citrate synthase [citrate oxaloacetate-lyase (CoA-acetylating) enzyme; EC 18.104.22.168], which had the same electrophoretic mobility as the enzyme from the free-living cells. The citrate synthase from CC 1192 bacteroids had a native molecular mass of 228 +/- 32 kDa and was activated by KCl, which also enhanced stability. Double reciprocal plots of initial velocity against acetyl-CoA concentration were linear, whereas the corresponding plots with oxaloacetate were nonlinear. The Km value for acetyl-CoA was 174 microM in the absence of added KCl, and 88 microM when the concentration of KCl in reaction mixtures was 100 mM. The concentrations of oxaloacetate for 50% of maximal activity were 27 microM without added KCl and 14 microM in the presence of 100 mM KCl. Activity of citrate synthase was inhibited 50% by 80 microM NADH and more than 90% by 200 microM NADH. Inhibition by NADH was linear competitive with respect to acetyl-CoA (Kis = 23.1 +/- 3 microM) and linear noncompetitive with respect to oxaloacetate (Kis = 56 +/- 3.8 microM and Kii = 115 +/- 15.4 microM). NADH inhibition was relieved by NAD+ and by micromolar concentrations of 5'-AMP. In the presence of 50 or 100 mM KCl, inhibition by NADH was apparent only when the proportion of NADH in the nicotinamide adenine dinucleotide pool was greater than 0.6. In the microaerobic environment of bacteroids, NADH may be at concentrations that are inhibitory for citrate synthase. However, this inhibition is likely to be relieved by NAD+ and 5'-AMP, allowing carbon to enter the tricarboxylic acid cycle.
Department of Molecular Biology, Uppsala University, Uppsala, Sweden. Siv.Andersson@molbio.uu.se
Mitochondria are thought to be derived from an ancestor of the alpha-proteobacteria and more specifically from the Rickettsiaceae. The bioenergetic repertoire of the obligate intracellular parasite Rickettsia prowazekii is consistent with its postulated role as the ancestor of the mitochondria. For example, the R. prowazekii genome contains genes encoding components of the tricarboxylic acid cycle as well as of the electron transport system, but lacks genes to support glycolysis. In addition, the R. prowazekii genome contains multiple genes coding for adenine nucleotide translocators which enables this intracellular parasite to exploit the cytoplasmic ATP of its host cell as a source of energy. The aim of this review is to describe the different aspects of the bioenergetic system in R. prowazekii and to discuss the results of phylogenetic reconstructions based on a variety of bioenergetic molecules which shed light on the origin and evolution of the mitochondrial genomes.
Characterization of the intron-containing citrate synthase gene from the alkanotrophic yeast Candida tropicalis: cloning and expression in Saccharomyces cerevisiae.
Laboratory of Applied Biological Chemistry, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-01, Japan.
Citrate synthase, an essential enzyme of the tricarboxylic acid cycle in mitochondria, was purified from acetate-grown Candida tropicalis. Results from SDS-PAGE and gel filtration showed that this enzyme was a dimer composed of 45-kDa subunits. A citrate synthase cDNA fragment was amplified by the 5'-RACE method. Nucleotide sequence analysis of this cDNA fragment revealed that the deduced amino acid sequence contained an extended leader sequence which is suggested to be a mitochondrial targeting signal, as judged from helical wheel analysis. Using this cDNA probe, one genomic citrate synthase clone was isolated from a yeast lambdaEMBL3 library. The nucleotide sequence of the gene encoding C. tropicalis citrate synthase, CtCIT, revealed the presence of a 79-bp intron in the N-terminal region. Sequences essential as yeast splicing motifs were present in this intron. When the CtCIT gene including its intron was introduced into Saccharomyces cerevisiae using the promoter UPR-ICL, citrate synthase activity was highly induced, which strongly indicated that this intron was correctly spliced in S. cerevisiae.
Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile 36688, USA.
Transcriptional regulation was demonstrated in Rickettsia prowazekii, an obligate intracytoplasmic bacterium. The level of citrate synthase (gltA) mRNA II, from promoter P2, was greater in the total RNA isolated from heavily infected L929 cells than in moderately infected L929 cells; conversely, the level of ATP/ADP translocase (tlc) mRNA was greater in moderately infected cells. The level of gltA mRNA I, from promoter P1, did not change under these conditions. The chemical half-lives of gltA mRNA II and tlc mRNA under these conditions were very similar.
Other papers by authors:
Citrate synthase from a Gram-positive bacterium. Purification and characterization of the Bacillus megaterium enzyme.
Citrate synthase was purified to homogeneity from a Gram-positive bacterium (Bacillus megaterium) for the first time. The Mr of the native enzyme was determined to be 84 000 (S.E.M.+/- 5000). Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis and gel filtration in guanidinium chloride revealed a single protein species of Mr 40 300 (S.E.M.+/- 4400), indicating a dimeric enzyme. This dimeric structure was confirmed by cross-linking the native enzyme with dimethyl suberimidate and with glutaraldehyde, followed by electrophoretic analysis. The enzyme follows Michaelis-Menten kinetics with respect to both substrates, acetyl-CoA and oxaloacetate, and is sensitive to non-specific inhibition by a range of adenine nucleotides. In both molecular and catalytic properties the citrate synthase closely resembles the enzyme from eukaryotic sources and contrasts markedly with the larger, hexameric, enzyme from Gram-negative bacteria.
Citrate synthase of Escherichia coli. Characterisation of the enzyme from a plasmid-cloned gene and amplification of the intracellular levels.
1. Citrate synthase has been purified from Escherichia coli and shown to exist at an equilibrium between three forms: monomer (mol.wt. 57000), tetramer (mol.wt. 230000) and, possibly, octamer. Modification of the enzyme by photo-oxidation and by treatment with specific chemical reagents has been carried out to gain information on the amino acid residues involved in enzymic activity and in the inhibition of activity by NADH and alpha-oxoglutarate. 2. Several photo-oxidizable amino acids appear to be involved in activity. The nature of the pH-dependence of their rates of photo-oxidation with Methylene Blue suggests that these are histidines, a conclusion supported by the greater rate of photo-inactivation with Rose Bengal and the destruction of activity by diethyl pyrocarbonate. 3. The participation of histidine at the alpha-oxoglutarate effector site is indicated by photo-oxidation and the participation of cysteine at the NADH effector site suggested by photo-oxidation is confirmed by the desensitization to NADH produced by treatment with 5,5'-dithiobis-(2-nitrobenzoate). Inactivation of the enzyme after modification with this reagent suggests the additional involvement of cysteine in catalytic activity. 4. Amino acid analyses of native and photo-oxidized enzyme are consistent with these conclusions. 5. Modification with 2-hydroxy-5-nitrobenzyl bromide indicates the participation of tryptophan in the activity of the enzyme.
Models of proteolysis of oligomeric enzymes and their applications to the trypsinolysis of citrate synthases.
Department of Biochemistry, University of Bath, Claverton Down, U.K.
A simple statistical approach was used to generate predictive models of the proteolysis of multisubunit enzymes in order to correlate the loss of enzyme activity with the loss of native subunit. The models were applied to the trypsinolysis of the citrate synthases of pig heart, Bacillus megaterium and Escherichia coli. With the dimeric citrate synthases (pig heart and B. megaterium) trypsinolysis of one of the subunits appears to destroy the activity of the whole enzymic molecule. The hexameric E. coli citrate synthase behaves like a trimer of dimeric units, each of the dimers behaving similarly to the B. megaterium and pig heart enzymes. Palmitoyl-CoA is required for the trypsinolysis of pig heart citrate synthase, and at relatively high concentrations of this compound trypsinolysis of one subunit leaves the other subunit fully active. Palmitoyl-CoA is not required for the trypsinolysis of the other citrate synthases, and high concentrations of this metabolite do not affect the correlation of proteolysis with inactivation of these enzymes.
A new spectrophotometric assay for citrate synthase and its use to assess the inhibitory effects of palmitoyl thioesters.
Department of Biochemistry, University of Bath, U.K.
We have demonstrated that citrate synthase may be assayed by a simple, discontinuous, spectrophotometric procedure based on the measurement of oxaloacetate utilization with 2,4-dinitrophenylhydrazine. The assay is applicable both to the purified enzyme and to cell extracts, and has the advantage that it can be used in the presence of high concentrations of thiols and thioesters. We have used this new assay in part of our investigations into the inhibitory effects of palmitoyl thioesters on diverse citrate synthases. Both palmitoyl-CoA and palmitoyl thioglycollate inhibit citrate synthases from pig heart, Bacillus megaterium and Escherichia coli, the E. coli enzyme showing the greatest sensitivity to these effectors. With palmitoyl-CoA the extent of inhibition is time-dependent, but the enzymes can be protected from the effect by the substrates oxaloacetate and acetyl-CoA. Using the dinitrophenylhydrazine assay, we have shown that the thioester bond is essential for inhibition; that is, if the palmitoyl thioesters are cleaved to give a mixture of palmitate and a thiol compound, the inhibitions of pig heart and B. megaterium citrate synthases are eliminated and that of the E. coli enzyme is markedly decreased.
Naturally occurring citrate synthases fall into distinct molecular and catalytic types. Gram-negative bacteria produce a 'large' enzyme, allosterically inhibited by NADH and, in the facultative anaerobes such as Escherichia coli, also by 2-oxoglutarate. On the other hand, Gram-positive bacteria and all eukaryotes produce a 'small' citrate synthase which is insensitive to these metabolites. As a complement to structure-function studies we have explored the possibility of genetically altering one type of citrate synthase to the other. By mutagenesis and suitable selection we have succeeded in isolating a mutant of E. coli whose citrate synthase is both 'small' and insensitive to NADH and 2-oxoglutarate. Some characteristics of the enzyme are described. Such mutant enzymes offer a novel approach to the study of citrate synthase, its regulation and its natural diversity.
The modification of Escherichia coli citrate synthase (citrate oxaloacetatelyase(pro-3S-CH2.COO- leads to acetyl-CoA, EC 22.214.171.124) with 5,5'-dithiobis-(2-nitrobenzoic acid) has been investigated.(1) In low ionic strength (20 mM Tris.HCl, pH 8.0):(A) Eight thiol groups per tetramer of the native enzyme reacted with Nbs2.(b) Two of the eight accessible thiols were modified rapidly with the loss of 26% enzyme activity but with no change in the NADH inhibition. The remaining six were modified more slowly, resulting in a further 60% loss of activity and complete densensitization to NADH.(c) The 2nd-order rate constant for the modification of the rapidly reacting thiols is 2.5.10(4) M-1.min-1. At the reagent concentrations used (0.1 to 0.2 mM) the modification of the six thiols in the slow kinetic set appeared to be 1st-order; at 0.1 mM dithionitrobenzoic acid their rate of modification was approximately 30 times slower than the thiols in the fast kinetic set.(2) In high ionic strength (20 mM Tris.HCl, pH 8.0, 0.1 M KCl):(a) Four thiol groups were modified in a single kinetic set and it appeared that these thiols are four of the six slowly modified in the absence of KCl.(b) The modification resulted in 70% loss of enzyme activity and complete loss of NADH inhibition.(3) From the kinetic analysis it is proposed that the four thiol groups accessible to dithionitrobenzoic acid in the absence and presence of 0.1 M KCl are those involved in the response of NADH. Modification of any one of these four groups produced no reduction in the inhibition; instead, loss of NADH sensitivity was coincident with the appearance of tetrameric protein possessing three substituted thiols, whereas enzyme with one or two modified groups was still fully inhibited by NADH.
Thermophile Research Unit, School of Science and Engineering, University of Waikato, Hamilton, New Zealand. email@example.com
Arising from careful measurements of the thermal behaviour of enzymes, a new model, the Equilibrium Model, has been developed to explain more fully the effects of temperature on enzymes. The model describes the effect of temperature on enzyme activity in terms of a rapidly reversible active-inactive (but not denatured) transition, revealing an additional and reversible mechanism for enzyme activity loss in addition to irreversible thermal inactivation at high temperatures. Two new thermal parameters, T(eq) and DeltaH(eq), describe the active-inactive transition, and enable a complete description of the effect of temperature on enzyme activity. We describe here the Model and its fit to experimental data, methods for the determination of the Equilibrium Model parameters, and the implications of the Model for the environmental adaptation and evolution of enzymes, and for biotechnology.
Reduced nicotinamide-adenine dinucleotide as an allosteric effector of citrate-synthase activity in Escherichia coli.
Department of Biochemistry, University of Leicester.