Nucleotide second messenger-mediated regulation of a muralytic enzyme in Streptomyces.

Peptidoglycan degradative enzymes have important roles at many stages during the bacterial life cycle, and it is critical that these enzymes be stringently regulated to avoid compromising the integrity of the cell wall. How this regulation is exerted is of considerable interest: promoter-based control and protein-protein interactions are known to be employed; however, other regulatory mechanisms are almost certainly involved. In the actinobacteria, a class of muralytic enzymes - the 'resuscitation-promoting factors' (Rpfs) - orchestrates the resuscitation of dormant cells. In this study, we have taken a holistic approach to exploring the mechanisms governing RpfA function using the model bacterium Streptomyces coelicolor and have uncovered unprecedented multilevel regulation that is coordinated by three second messengers. Our studies show that RpfA is subject to transcriptional control by the cyclic AMP receptor protein, riboswitch-mediated transcription attenuation in response to cyclic di-AMP, and growth stage-dependent proteolysis in response to ppGpp accumulation. Furthermore, our results suggest that these control mechanisms are likely applicable to cell wall lytic enzymes in other bacteria.

Simultaneous Fitting of Absorption Spectra and Their Second Derivatives for an Improved Analysis of Protein Infrared Spectra.

Infrared spectroscopy is a powerful tool in protein science due to its sensitivity to changes in secondary structure or conformation. In order to take advantage of the full power of infrared spectroscopy in structural studies of proteins, complex band contours, such as the amide I band, have to be decomposed into their main component bands, a process referred to as curve fitting. In this paper, we report on an improved curve fitting approach in which absorption spectra and second derivative spectra are fitted simultaneously. Our approach, which we name co-fitting, leads to a more reliable modelling of the experimental data because it uses more spectral information than the standard approach of fitting only the absorption spectrum. It also avoids that the fitting routine becomes trapped in local minima. We have tested the proposed approach using infrared absorption spectra of three mixed α/ß proteins with different degrees of spectral overlap in the amide I region: ribonuclease A, pyruvate kinase, and aconitase.

Studies on aconitase species from Saccharomyces cerevisiae, porcine and bovine heart, obtained by a modified isolation method.

Aconitase (citrate (isocitrate) hydro-lyase, EC 4.2.1.3) was isolated from Saccharomyces cerevisiae, porcine and bovine heart by a simplified method including affinity chromatography on Blue Dextran-Sepharose. Partial characterisation reveals that the aconitase species are all similar due to molecule size, amino acid composition, isoelectric point and enzymatic activity. Aconitase appears as a single polypeptide chain with a small carbohydrate content. A molecular weight of 79000 +/- 2000 and a Svedberg constant of s20,w = 4.75 +/- 0.2 S indicate a compact structure of aconitase. Due to different properties among the yeast aconitase species concerning isoelectric point and enzymatic activity a coherence between net charge of the protein and redox state of the Fe-S cluster can be expected.

Electrophoretic variation of aconitase and phosphoglucomutase detected in Microtus californicus.

Four electrophoretic variants of cytoplasmic aconitase (citrate (isocitrate) hydro-lyase, EC 4.2.1.3) were detected in a population of Microtus californicus when samples were screened by starch gel electrophoresis using Tris/citrate buffers at pH 7.0 and pH 8.7. Variation at what is presumed to be the phosphoglucomutase-3 locus (alpha-D-glucose-1,6-diphosphate:alpha-D-glucose-1-phosphate phosphotransferase, EC 2.7.5.1) was also detected with liver samples but was not detected in kidney samples or red blood cells lysates. This nongenetic variation is due to oxidation of free sulfhydryl groups.

Expression and properties of the mitochondrial and cytosolic forms of aconitase in maize scutellum.

Aconitase (EC 4.2.1.3) catalyzes the reversible interconversion of citrate, cis-aconitate, and D-isocitrate. It operates in mitochondria and cytosol. We investigated the expression of two aconitase genes (Aco1 and Aco4) and activities of the mitochondrial and cytosolic forms in maize (Zea mays L.) scutellum during germination. Both forms were isolated and purified. The cytosolic form had a higher pH optimum (8.0), twice higher affinity to citrate (K(m) 9.5 mM), and slightly lower affinity to D,L-isocitrate (K(m) 1.7 mM) as compared to the mitochondrial form (optimum pH 7.5, K(m) with citrate 21 mM, and K(m) with isocitrate 1.5 mM). The highest activity of both forms of aconitase was observed on the 4th day of germination; then the activity and expression of the cytosolic form sharply decreased, while the mitochondrial form decreased more slowly. The mitochondrial aconitase was more strongly inhibited by H2O2 (half-inhibition at 35 µM) than the cytosolic form (60 µM). Aconitase activity was not detected in the glyoxysomal fraction beyond the cross-contamination level. It is suggested that the mitochondrial form operates in the tricarboxylic acid cycle, whereas the cytosolic form participates in the reactions of the glyoxylate cycle taking place outside the glyoxysome.

The aconitase of yeast. II. Crystallization and general properties of yeast aconitase.

Yeast aconitase [citrate (isocitrate) hydro-lyase, ED 4.2.1.3], inductively formed by Candida iipolytica in the presence of fluoroacetate, was purified approximately 100-fold by Sephadex G-100 gel filtration and DEAE-Sephadex column chromatography, yielding dark-brown needle crystals. The crystalline aconitase was homogenious as judged by polyacrylamide gel electrophoresis and sedimentation by ultracentrifugation. The enzyme showed maximal activity at pH 8.0 and at 55 degrees. It has an S20, W of 5.03 S, a molecular weight of 68,500 and an isolectric point of pH 4.2. The presence of 2.10 moles of iron per mole of the enzyme was demonstrated by atomic absorption spectroscopy.

Kinetic studies of cytoplasmic and mitochondrial aconitate hydratases from rat liver.

The kinetic properties of the cytoplasmic and mitochondrial aconitate hydratases of rat liver have been studied by measuring the formation of the two products from each of the three tricarboxylic acids used as substrate. The kinetic properties of the two enzymes are very similar; the similarity of the Km values for each of the three substrates is particularly remarkable. The results are discussed with particular reference to a possible role of the cytoplasmic aconitate hydratase in the process of gluconeogenesis. With both aconitate hydratases, substrate activation by citrate and D-isocitrate has been observed.

[Catalytic properties of cytoplasmic and mitochondrial aconitate hydratase from rat cardiomyocytes]. / Kataliticheskie svoistva tsitoplazmaticheskoi i mitokhondrial'noi akonitatgidratazy iz kardiomiotsitov krysy.

Enzymatic activity of aconitate hydratase (aconitase, EC 4.2.1.3) from the rat heart is localized in the cytoplasm (65%) and mitochondria (35%). Cytoplasmic and mitochondrial forms of aconitate hydratase were separated by ion-exchange chromatography on CM-Cellulose and CM-Sephadex. The two forms have similar molecular weight, optimal pH range, and spectral properties; however, they have different chromatography properties, Km for citrate and isocitrate, as well as sensitivity to Fe2+ ions.

Enhancement of over expression and chaperone assisted yield of folded recombinant aconitase in Escherichia coli in bioreactor cultures.

A major portion of the over expressed yeast mitochondrial aconitase, a large 82 kDa monomeric TCA cycle enzyme, in Escherichia coli led to the formation of inclusion bodies. Bacterial chaperonin GroEL mediated the correct folding of aconitase with the assistance of its co-chaperonin GroES in an ATP dependent manner. Till date the chaperonin assisted folding of aconitase was limited to the shake flask studies with relatively low yields of folded aconitase. No attempt had yet been made to enhance the yield of chaperone mediated folding of aconitase using a bioreactor. The current report deals with the effect of co-expression of GroEL/GroES in the production of soluble, biologically active recombinant aconitase in E. coli by cultivation in a bioreactor at different temperatures under optimized conditions. It revealed that the yield of functional aconitase was enhanced, either in presence of co-expressed GroEL/ES or at low temperature cultivation. However, the outcome from the chaperone assisted folding of aconitase was more pronounced at lower temperature. A 3-fold enhancement in the yield of functional aconitase from the bioreactor based chaperone assisted folding was obtained as compared to the shake flask study. Hence, the present study provides optimized conditions for increasing the yield of functional aconitase by batch cultivation in a bioreactor.

Iron-dependent RNA-binding activity of Mycobacterium tuberculosis aconitase.

Cellular iron levels are closely monitored by iron regulatory and sensor proteins of Mycobacterium tuberculosis for survival inside macrophages. One such class of proteins systematically studied in eukaryotes and reported in a few prokaryotes are the iron-responsive proteins (IRPs). These IRPs bind to iron-responsive elements (IREs) present at untranslated regions (UTRs) of mRNAs and are responsible for posttranscriptional regulation of the expression of proteins involved in iron homeostasis. Amino acid sequence analysis of M. tuberculosis aconitase (Acn), a tricarboxylic acid (TCA) cycle enzyme, showed the presence of the conserved residues of the IRP class of proteins. We demonstrate that M. tuberculosis Acn is bifunctional. It is a monomeric protein that is enzymatically active in converting isocitrate to cis-aconitate at a broad pH range of 7 to 10 (optimum, pH 8). As evident from gel retardation assays, M. tuberculosis Acn also behaves like an IRP by binding to known mammalian IRE-like sequences and to predicted IRE-like sequences present at the 3' UTR of thioredoxin (trxC) and the 5' UTR of the iron-dependent repressor and activator (ideR) of M. tuberculosis. M. tuberculosis Acn when reactivated with Fe(2+) functions as a TCA cycle enzyme, but upon iron depletion by a specific iron chelator, it behaves like an IRP, binding to the selected IREs in vitro. Since iron is required for the Acn activity and inhibits the RNA-binding activity of Acn, the two activities of M. tuberculosis Acn are mutually exclusive. Our results demonstrate the bifunctional nature of M. tuberculosis Acn, pointing to its likely role in iron homeostasis.

Purification and partial amino acid sequence of human aconitase.

Aconitase has been purified from membranes prepared from both the human gastric carcinoma cell line Okajima and from porcine gastric mucosa by chromatography on concanavalin A-Sepharose and carboxymethyl-Sepharose, and preparative polyacrylamide gel electrophoresis. Automated Edman degradation of the intact proteins yielded no N-terminal amino acid sequence due, presumably, to N-terminal blockage. Sequence analysis of tryptic peptides derived from S-carboxymethyl porcine and human aconitases established the positions of 95 and 64 amino acid residues, respectively. The amino acid sequence data for porcine aconitase was in perfect agreement with the previously reported cDNA-deduced amino acid sequence [Zheng et al. (1990) J Biol Chem 265:2814-2821]. Comparison of the human amino acid sequence data with the cDNA-deduced amino acid sequence of porcine aconitase indicated that these two proteins have 95% amino acid sequence identity within the sequenced region.

Lack of aconitase in glyoxysomes and peroxisomes.

The aim of this work was to find out whether aconitase [citrate (isocitrate) hydro-lyase, EC 4.2.1.3] which is rapidly inactivated by H2O2, is present in the microbodies from plant cells. The separation of intact organelles from castor-bean (Ricinus communis) endosperm and potato (Solanum tuberosum) tuber indicated that aconitase activity is essentially limited to the mitochondria and cytosol fraction, but was not detected in highly purified castor-bean endosperm and potato tuber peroxisomes. An isotropic e.p.r. signal of the type expected for the 3Fe cluster of oxidized aconitase was not detected in microbodies. In immunoblot analyses, antibodies raised against potato tuber mitochondrial aconitase did not cross-react with any glyoxysomal or peroxisomal protein. Positive reactions were found for cytosol fraction and mitochondria of castor-bean endosperm. The operation of the full glyoxylate cycle in isolated glyoxysomes requires the presence of aconitase in the incubation medium. It is concluded that glyoxysomes are probably devoid of aconitase and that the glyoxylate cycle requires a detour via the cytosol, which contains a powerful aconitase activity.

The soluble "high potential" type iron-sulfur protein from mitochondria is aconitase.

Properties of soluble high potential type iron-sulfur protein (HiPIP) from beef heart mitochondria were compared to those of aconitase from pig heart. The two proteins when purified to homogeneity by the criteria of sodium dodecyl sulfate (SDS)-polyacrylamide electrophoresis show identical light absorption characteristics. EPR signals of the HiPIP type centered at g = 2.01 when oxidized, isoelectric points at pH 8.5 to 8.6, are inseparable by SDS-polyacrylamide electrophoresis, and exhibit aconitase activity when activated by reducing agents in the presence of ferrous iron. The requirement for activation goes parallel to the intensity of the signal from the oxidized iron-sulfur cluster, i.e. the cluster is reduced in the active enzyme. We conclude that the soluble mitochondrial HiPIP is identical with aconitase. The relationships of iron to labile sulfide, molecular weight and unpaired spins in the EPR signal, and implications of our findings for the role of iron in aconitase are discussed.

The aconitase of Escherichia coli: purification of the enzyme and molecular cloning and map location of the gene (acn).

The aconitase of Escherichia coli was purified to homogeneity, albeit in low yield (0.6%). It was shown to be a monomeric protein of Mr 95,000 or 97,500 by gel filtration and SDS-PAGE analysis, respectively. The N-terminal amino acid sequence resembled that of the Bacillus subtilis enzyme (citB product), but the similarity at the DNA level was insufficient to allow detection of the E. coli acn gene using a 456 bp citB probe. Phages containing the acn gene were isolated from a lambda-E. coli gene bank by immunoscreening with an antiserum raised against purified bacterial enzyme. The acn gene was located at 28 min (1350 kb) in the physical map of the E. coli chromosome by probing Southern blots with a fragment of the gene. Attempts to locate the gene using the same procedure with oligonucleotide probes encoding segments of the N-terminal amino acid sequence were complicated by the lack of probe specificity and an inaccuracy in the physical map of Kohara et al. (Cell 50, 495-508, 1987). Aconitase specific activity was amplified some 20-200-fold in cultures transformed with pGS447, a derivative of pUC119 containing the acn gene, and an apparent four-fold activation-deactivation of the phagemid-encoded enzyme was observed in late exponential phase. The aconitase antiserum cross-reacted with both the porcine and Salmonella typhimurium (Mr 120,000) enzymes.

Synthesis and evaluation of (+) and (-)-2,2-difluorocitrate as inhibitors of rat-liver ATP-citrate lyase and porcine-heart aconitase.

The enantiomers (+) and (-)-2,2-difluorocitrate have been synthesized. Both are good inhibitors of ATP-citrate lyase, showing competitive inhibition against citrate, with Kis = 0.7 microM for (+)-2,2-difluorocitrate and 3.2 microM for (-)-2,2-difluorocitrate. The inhibition patterns with either ATP or CoA as the varied substrate were uncompetitive and mixed, respectively, but with much weaker inhibition constants. Neither isomer undergoes carbon-carbon bond cleavage as a substrate and there is no evidence of irreversible time-dependent inactivation. When ATP-citrate lyase is incubated with CoA and difluorocitrate, the maximal intrinsic ATPase rate is 10% of the citrate-induced rate for the (+)-enantiomer and 2% for the (-)-enantiomer. 19F-NMR studies confirm that only the (+)-enantiomer is chemically processed. The effects of the difluorocitrate enantiomers on the reaction catalysed by aconitase were examined. (-)-2,2-Difluorocitrate is a competitive inhibitor against citrate (Kis = 1.5 microM), whereas the (+)-enantiomer is a relatively poor mixed inhibitor (Ki greater than 300 microM). The (-)-enantiomer irreversibly inactivates aconitase at 1.1 min-1.mM-1 at 25 degrees C and pH 7.4, whereas no irreversible inhibition is seen with the (+)-enantiomer. Therefore, it would be expected that the (+)-enantiomer would slow the rate of acetyl-CoA synthesis in vivo, without inhibiting the citric acid cycle.

Isozyme electrophoresis patterns of the liver fluke, Clonorchis sinensis from Kimhae, Korea and from Shenyang, China.

An enzyme analysis of the liver fluke, Clonorchis sinensis from Kimhae, Korea and from Shenyang, China was conducted using a horizontal starch gel electrophoresis in order to elucidate their genetic relationships. A total of eight enzymes was employed from two different kinds of buffer systems. Two loci from each enzyme of aconitase and esterase (alpha-Na and beta-Na); and only one locus each from six enzymes, glucose-6-phosphate dehydrogenase (G6PD), alpha-glycerophosphate dehydrogenase (GPD), 3-hydroxybutyrate dehydrogenase (HBDH), malate dehydrogenase (MDH), phosphoglucose isomerase (PGI), and phosphoglucomutase (PGM) were detected. Most of loci in two populations of C. sinensis showed homozygous monomorphic banding patterns and one of them, GPD was specific as genetic markers between two different populations. However, esterase (alpha-Na), GPD, HBDH and PGI loci showed polymorphic banding patterns. Two populations of C. sinensis were more closely clustered within the range of genetic identity value of 0.998-1.0. In summarizing the above results, two populations of C. sinensis employed in this study showed mostly monomorphic enzyme protein banding patterns, and genetic differences specific between two populations.

Induction of aconitate hydratase in hepatocytes of starving rats.

Induction of the activity of aconitate hydratase (AH) was observed in rat hepatocytes under the conditions of food deprivation. The increase in AH activity after 4 days of starvation in the studied tissues was from 0.57 to 2.05 U/g crude liver weight. The induction of aconitase was associated both with the cytoplasmic and mitochondrial AH isoforms. The activities of cytosolic and mitochondrial AH isoforms in starving animals consisted of 83 and 17% of the total activity, respectively. The cytoplasmic and mitochondrial isoforms of the enzyme with specific activities 11.1 and 6.13 U/mg protein, respectively, were obtained by a five-step purification procedure that included fractionation with ammonium sulfate, ion-exchanging chromatography on DEAE-Toyopearl and gel filtration. The purified preparations of these AH isoforms were electrophoretically homogenous. The molecular weights of these isoforms were estimated and several kinetic and regulatory properties were studied.

Sulfolobus aconitase, a regulator of iron metabolism?

The aconitase of Sulfolobus solfataricus, a hyperthermophilic crenarchaeon, was cloned and heterologously expressed in Escherichia coli. Enzymic analyses and EPR measurements indicated clearly that the iron-sulphur cluster of the thermophilic aconitase was already inserted in the mesophilic host. The enzyme was purified to a specific activity of approx. 44 units/mg and to 90% homogeneity. The enzymic parameters of the recombinant aconitase turned out to be in the same range as the respective values for the previously characterized native enzyme from the closely related S. acidocaldarius. Based on its primary sequence, the recombinant aconitase is closely related to bacterial A-like and to eukaryotic iron regulatory protein-like proteins. Specific aconitase activities in cytosolic extracts of S. acidocaldarius were found to be decreased markedly in iron-starved compared with iron-repleted cells. However, no differences in aconitase levels between iron-starved and iron-supplemented cells could be detected by immunostaining.