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PubMed2005

Structural and functional comparison of HemN to other radical SAM enzymes.

Radical SAM enzymes have only recently been recognized as an ancient family sharing an unusual radical-based reaction mechanism. This late appreciation is due to the extreme oxygen sensitivity of most radical SAM enzymes, making their characterization particularly arduous. Nevertheless, realization that the novel apposition of the established cofactors S-adenosylmethionine and [4Fe-4S] cluster creates an explosive source of catalytic radicals, the appreciation of the sheer size of this previously neglected family, and the rapid succession of three successfully solved crystal structures within a year have ensured that this family has belatedly been noted. In this review, we report the characterization of two enzymes: the established radical SAM enzyme, HemN or oxygen-independent coproporphyrinogen III oxidase from Escherichia coli, and littorine mutase, a presumed radical SAM enzyme, responsible for the conversion of littorine to hyoscyamine in plants. The enzymes are compared to other radical SAM enzymes and in particular the three reported crystal structures from this family, HemN, biotin synthase and MoaA, are discussed.

Atropine Derivatives↗
PubMed2005

Current progress in proteomic study of hepatitis C virus-related human hepatocellular carcinoma.

Chronic infection with hepatitis C virus (HCV) is known to be a risk factor for not only cirrhosis and steatosis but also hepatocellular carcinoma (HCC). A number of diagnostic and prognostic molecular markers are being identified by transcriptomic and proteomic analysis of HCC today. However, the analyses are performed on HCC in general, and the studied tissues are HCV infected, HBV infected, infected with both or neither, or the infection status may be unknown. The authors performed proteomic analysis of cancerous and noncancerous tissues from HCC patients with HCV infection, and determined that, in the cancerous tissues, HSP70 family proteins such as GRP78, HSC70, GRP75 and HSP70.1, glutaine synthetase isoforms, HSP60, alpha-enolase, phosphoglycerate mutase 1, ATP synthetase beta chain and triosephosphate isomerase were increased whereas albumin, ferritin light chain, smoothelin, tropomyosin beta chain, arginase 1, aldolase B and kietohexokinase were decreased. The aim of this study is to understand the pathogenesis of HCV-HCC using proteomic analysis of samples from HCV-HCC patients on which transcriptomics has already been performed.

Animals↗
PubMed2006

Changes in the muscle proteome after compensatory growth in pigs.

Sixteen female pigs (Duroc x Landrace x Large White) were divided into 2 groups, which had either free access to the diet (control group) or were feed-restricted from d 28 to 80 and then had free access to the diet (compensatory growth group). The sensory analysis showed that the pigs exhibiting compensatory growth produced meat with increased tenderness compared with control pigs (P < 0.05). To gain further knowledge of the influence of compensatory growth on meat tenderness, the sarcoplasmic protein fraction of muscle tissue was studied at the time of slaughter and 48 h postmortem using proteome analysis. At slaughter, 7 different proteins were found to be affected by compensatory growth: HSC70, HSP27, enolase 3, glycerol-3-phosphate dehydrogenase, aldehyde dehydrogenase E2, aldehyde dehydrogenase E3, and biphosphoglycerate mutase. The HSC70 and HSP27 both belong to the heat shock family and are known to play a role during muscle development. Hence, they may be affected by compensatory growth and increased protein turnover. Forty-eight hours after slaughter, 8 different proteins were found to be affected by compensatory growth: myosin light chain (MLC) II, MLC III, sulfite oxidase, chloride intracellular channel 1, 14-3-3 protein gamma, elongin B, and phosphohistidine phosphatase 14. The changes observed on MLC II and MLC III could be a consequence of enzymatic cleavage in the neck region of the globular myosin head domain that causes the release of MLC II and MLC III from the actomyosin complex. It has previously been hypothesized that compensatory growth results in an increased postmortem proteolysis; thus it was presumed that the intensity of some protein fragments would be affected by compensatory growth. However, the peptides that were found to be affected at 48 h postmortem were all full-length proteins. The 14-3-3 protein gamma has been proposed to play a role in the contraction of muscle during rigor and may thereby have an effect on meat tenderness. This study reveals some very interesting changes in the muscle proteome affected by compensatory growth, which may be useful in understanding the relationship among compensatory growth, protein turnover, and meat tenderness.

Animal Feed↗
PubMed1996

Cobalamin.

Cobalamin (vitamin B12) is an essential nutrient derived exclusively from bacterial sources. It is an essential cofactor for three known enzymatic reactions. Untreated deficiency, caused by either the autoimmune disease pernicious anemia or nutritional lack, results in a macrocytic anemia and/or subacute combined degeneration of the spinal cord and is eventually fatal. Cobalamin in serum is bound to two proteins, transcobalamin and haptocorrin. The former is responsible for the essential delivery of cobalamin to most tissues. Inadequate tissue availability of cobalamin results in increased concentration of methylmalonic acid and homocyst(e)ine due to inhibition of methylmalonyl-CoA mutase and methionine synthase, respectively. Strict vegetarians have long been known to be at risk of cobalamin deficiency, which develops insidiously over many years. It is now clear that a significant number of the elderly and HIV-positive individuals are also at increased risk of deficiency. Any individual with reduced ability to split cobalamin from food-protein may also become deficient even though intrinsic factor is present. Diagnosis of cobalamin deficiency has frequently relied on total serum cobalamin and the Schilling test. Newer approaches such as analysis of methylmalonic acid, homocyst(e)ine, holotranscobalamin, anti-intrinsic factor antibodies, and serum gastrin may provide more cost-effective testing, as well as identify those with a covert deficiency.

Aged↗
PubMed1997

Progress in myocardial damage detection: new biochemical markers for clinicians.

New clinical requirements for triaging chest pain patients challenge the abilities of the current cardiac markers. Serial measurements of myoglobin, creatine kinase (CK) isoenzyme MB (CKMB) mass, or CK isoforms in emergency rooms help to rapidly rule out acute myocardial infarction (AMI). However, within the first 3 to 4 h from chest pain onset, their sensitivities are too low to contribute significantly to AMI diagnosis during this period. CKMB and lactate dehydrogenase (LDH) isoenzyme 1 are not heart-specific, which hampers reliable diagnosis in patients with concomitant skeletal muscle damage. By contrast, the regulatory proteins troponin I and troponin T are expressed in three different isoforms: one for slow-twitch skeletal muscle fibers, one for fast-twitch skeletal muscle fibers, and one for cardiac muscle (cTnI, cTnT); cardiac-specific cTnI and cTnT assays are already available for routine use. cTnT and cTnI are the most promising markers for risk stratification in patients with unstable angina pectoris. Recent reports on increased cTnT in patients with renal failure or myopathy without evidence of myocardial injury and undetectable cTnI suggest that cTnT could be reexpressed similar to CKMB and LDH-1 in chronically damaged human skeletal muscle. Therefore, cTnI is probably the most heart-specific marker. Among the recently proposed new markers for early AMI diagnosis: glycogen phosphorylase isoenzyme BB (GPBB), fatty acid binding protein, phosphoglyceric acid mutase isoenzyme MB, enolase isoenzyme alpha beta, S100a0, and annexin V, GPBB is the most promising because it increases as early as 1 to 4 h from chest pain onset and its early release appears to be essentially dependent on ischemic myocardial injury.

Animals↗
PubMed1983

ATP-ADP-dependent phosphorylations of glycolysis metabolites, creatine and glycerol: their compartition and thermodynamic relationship in gastrocnemius muscle cell of exercised guinea pigs.

The concentrations of following metabolites were determined in freeze-clamped gastrocnemius muscle samples: glucose 1-phosphate, glucose 6-phosphate, glucose, fructose 1,6-diphosphate, fructose 6-phosphate, D-glyceraldehyde 3-phosphate. dihydroxyacetone phosphate, phosphoenolpyruvate, pyruvate, glycerol 3-phosphate, glycerol, creatine phosphate, creatine, glycerate 3-phosphate, glycerate 2-phosphate, adenosine monophosphate, adenosine diphosphate, adenosine triphosphate, inorganic phosphate. The results showed that within the limits of experimental error, concentration homeostasis for this metabolites is founded at least in some cases on equilibria between enzymic transformations. Discrepancies between constant mass ratios measured in this study and equilibrium constants allow the free energy variation delta G to keep creatine phosphate at high concentration to be calculated. For the phosphoglycerate mutase system, the equilibrium constant in controls and trained animals is unchanged and corresponds to that in vitro. Training hindered glycolysis and favoured phosphorylation of creatine by glycerol 3-phosphate. Metabolites of the pyruvate kinase and hexokinase system cannot be homogeneously distributed in one space. The creatine kinase system is also separated from the hexokinase und pyruvate kinase system. A compartition of glycolytic process in gastrocnemius muscle seems to be inferred from these results.

Adenosine Diphosphate↗
PubMed1992

Effects of vitamin B12-deficiency on testes tissue in rats.

The state of vitamin B12-deficiency in rats was evaluated by determination of hepatic vitamin B12-dependent enzyme activities after the animals had fed on a vitamin B12-deficient soybean protein diet for 150 days. The effect of vitamin B12-deficiency on testicular tissue was also studied by morphological observations. Growth of vitamin B12-deficient rats was retarded and marked increase in urinary methylmalonic acid was observed. Vitamin B12 contents in the organs were depressed distinctly by the deficiency, especially in testes, vitamin B12 content decreased to 2.5 ng/g. Hepatic methionine synthase and methylmalonyl-CoA mutase activities showed striking depression to 5% of the control rats and extreme vitamin B12-deficiency was confirmed. Testes weight also showed marked decrease together with their relative weight per 100 g body weight. Morphological observations of testes of vitamin B12-deficient rats revealed atrophy of the seminiferous tubules and aplasia of sperms and spermatids. The above results proved that vitamin B12-deficiency affected rat testes, and suggested that the rat could be the animal model for elucidation of the mechanism of B12 action on testicular functions.

Animals↗
PubMed2025

Identification of Differential Proteins in Thrombi of Cardioembolic and Atherothrombotic Etiology in Patients with Ischemic Stroke.

Knowing the precise etiology in ischemic stroke is necessary to ensure accurate diagnosis and decide on appropriate preventive treatments, especially in those of undetermined cause. Analysis of the thrombus protein composition could be useful to identify diagnostic biomarkers to help determine the stroke origin. Thrombi from 54 ischemic stroke patients with large vessel occlusion (LVO), of cardioembolic and atherothrombotic etiology, were analyzed using a proteomics approach. The proteome profile was compared between them to detect differential proteins of each etiology. Peptides of those differential proteins were quantified and related to the neurological function and clinical status of the patients. Of the 516 proteins identified, three showed significant differences between atherothrombotic and cardioembolic thrombi. These were fibronectin (FINC), 2,3-bisphosphoglycerate mutase (PMGE), and tropomyosin-1 (TPM1). Combining these proteins in a biomarker panel provided good sensitivity and high specificity for differentiating cardioembolic and atherothrombotic strokes. In addition, several of the quantified peptide levels correlated with clinical parameters related to stroke severity and prognosis. Three proteins differentially detected in ischemic stroke thrombi could be useful tools for accurately diagnosing ischemic stroke etiology, particularly in cases of undetermined cause. These biomarkers should be further analyzed in prospective multicenter studies to demonstrate their usefulness.

Humans↗
PubMed1986

Further studies on the biosynthesis of chlorothricin.

Feeding experiments with [U-13C3]- and (2R)-[1-2H2]glycerol showed that glycerol is incorporated intact into carbon atoms 22, 23 and 24 of the aglycone of chlorothricin. C-1 of glycerol gives rise to C-22 with retention of one atom of deuterium, which occupies the H-22R position. A mechanism for the assembly of the aglycone is proposed which invokes phosphoenolpyruvate as the direct precursor of the 3-carbon moiety and a Baeyer-Villiger oxidation as the mode of formation of the macrocyclic lactone functionality. A feeding experiment with [1,2-13C2]succinate suggests that the propionate units of the aglycone polyketide are formed entirely via the methylmalonyl-CoA mutase reaction. The formation of the two 2,6-dideoxy-D-rhamnose moieties of chlorothricin from glucose was shown to involve replacement of the 2-hydroxyl group of the sugar by hydrogen with inversion of configuration at C-2. This contrasts with the retention stereochemistry observed earlier for the analogous formation of the 2,6-dideoxyhexose moiety of the antibiotic granaticin.

Aminoglycosides↗
PubMed1995

The biosynthesis of monensin-A: thymine, beta-aminoisobutyrate and methacrylate metabolism in Streptomyces cinnamonensis.

Feeding experiments with isotopically labelled samples of [13C,2H3-methyl]-thymine, (R,S)-[I-13C]- and (R,S-[13C-methyl]-beta-aminoisobutyrates into monensin-A demonstrate that these metabolites can all contribute to the methylmalonyl-CoA pool in Streptomyces cinnamonensis, and implicate DNA catabolism as a contributory metabolic source of propionate carbon atoms for secondary metabolic biosynthesis. Further, these labelled compounds were unexpectedly incorporated into the butyrate unit of monensin-A, an observation which can be rationalised if beta-aminoisobutyrate is converted to methacrylyl-CoA and then reduced to isobutyryl-CoA prior to conversion to butyryl-Coa by the action of isobutyryl-CoA mutase. Feeding experiments with [I-13C]- and [13C-methyl]-methacrylates and [3-13C]-isobutyrate suggest that these metabolites partition similarly between the butyrate and propionate units of monensin-A consistent with the view that isobutyryl-CoA and methacrylyl-CoA have a close metabolic relationship.

Acyl Coenzyme A↗
PubMed1999

[Vitamin B12].

Vitamin B12 is unique among all the vitamins in that it contains not only a complex organic molecule but also an essential trace element, cobalt. Vitamin B12 is synthesized in some bacteria but not in animals and plants. Intestinal absorption and subsequent plasma transport of vitamin B12 are mediated by specific vitamin B12-binding proteins and their receptors in mammals. Vitamin B12 taken up by the cells is enzymatically converted to coenzyme forms of vitamin B12, methyl- and adenosyl-vitamin B12, which function as coenzymes of methionine synthase (EC 2.1.13), involved in methionine biosynthesis, and methylmalonyl-CoA mutase (EC 5.4.99.2), involved in oxidation of odd-numbered fatty acids and amino acids (valine, isoleucine, and threonine), respectively. Chemical properties, physiological function, and intracellular metabolism of vitamin B12 are summarized in this section.

Animals↗
PubMed2001

Early-onset combined methylmalonic aciduria and homocystinuria: neuroradiologic findings.

BACKGROUND AND PURPOSE: Combined methylmalonic aciduria and homocystinuria (MMA-HC) is caused by impaired hepatic conversion of dietary cobalamin to methylcobalamin and adenosylcobalamin, resulting in decreased activity of methylmalonyl-CoA mutase and methionine synthase. Patients with the early-onset variety present within 12 months of age with severe neurologic, hematologic, and gastrointestinal abnormalities. We describe the neuroradiologic features of early-onset MMA-HC and discuss related pathophysiological mechanisms. METHODS: Twelve infants with hypotonia, failure to thrive, poor feeding, and hematologic abnormalities were diagnosed with MMA-HC on the basis of a typical plasmatic and urinary metabolic profile and enzyme activity in fibroblastic cultures. Complementation studies were performed in two cases, and yielded a CblC result. MR imaging was performed at presentation in four cases and later in the others. All patients showed prompt biochemical improvement with intramuscular hydroxocobalamin administration, and most had moderate neurologic improvement. RESULTS: Diffuse supratentorial white matter edema and dysmyelination was the typical MR picture at presentation, whereas white matter bulk loss characterized later stages of the disease. Nucleocapsular areas of gliosis were an additional finding in one case. One patient had tetraventricular hydrocephalus at presentation. CONCLUSION: White matter damage is probably caused by reduced methyl group availability and nonphysiological fatty acids toxicity, whereas focal gliosis results from homocysteine-induced toxicity to the endothelium. Hydrocephalus may result from diffuse intracranial extracerebral arterial stiffness, known as reduced arterial pulsation hydrocephalus. MR imaging features at presentation and at follow-up are nonspecific.

Brain↗
PubMed2002

Changes in gene expression linked to methamphetamine-induced dopaminergic neurotoxicity.

The purpose of these studies was to examine the role of gene expression in methamphetamine (METH)-induced dopamine (DA) neurotoxicity. First, the effects of the mRNA synthesis inhibitor, actinomycin-D, and the protein synthesis inhibitor, cycloheximide, were examined. Both agents afforded complete protection against METH-induced DA neurotoxicity and did so independently of effects on core temperature, DA transporter function, or METH brain levels, suggesting that gene transcription and mRNA translation play a role in METH neurotoxicity. Next, microarray technology, in combination with an experimental approach designed to facilitate recognition of relevant gene expression patterns, was used to identify gene products linked to METH-induced DA neurotoxicity. This led to the identification of several genes in the ventral midbrain associated with the neurotoxic process, including genes for energy metabolism [cytochrome c oxidase subunit 1 (COX1), reduced nicotinamide adenine dinucleotide ubiquinone oxidoreductase chain 2, and phosphoglycerate mutase B], ion regulation (members of sodium/hydrogen exchanger and sodium/bile acid cotransporter family), signal transduction (adenylyl cyclase III), and cell differentiation and degeneration (N-myc downstream-regulated gene 3 and tau protein). Of these differentially expressed genes, we elected to further examine the increase in COX1 expression, because of data implicating energy utilization in METH neurotoxicity and the known role of COX1 in energy metabolism. On the basis of time course studies, Northern blot analyses, in situ hybridization results, and temperature studies, we now report that increased COX1 expression in the ventral midbrain is linked to METH-induced DA neuronal injury. The precise role of COX1 and other genes in METH neurotoxicity remains to be elucidated.

3,4-Dihydroxyphenylacetic Acid↗
PubMed1998

Cloning and Expression of aroG Gene of E. coli and Its Co-expression with pheA and tyrB Genes.

3-Deoxy-D-arabino-heptulonate-7-phosphate synthetase (DAHP) is one of the key enzymes in phenylalanine biosynthesis pathway. In E. coli, DAHP is encoded by aroG Gene. In this work, aroG was cloned from an E. coli mutant strain resistant to m-fluro-L-phenylalanine (mPF) and p-fluro-L-phenylalanine (pPF) by PCR. The gene was expressed under the control of lambda phage promoter p(R) in P2392 strain of E. coli. Distinct band was detected as the product of aroG on SDS-PAGE. The specific activity in crude extract of DAHP was raised to 1.7-fold. Based on the cloning and expression of pheA (encoding both chorsmate mutase CM and prephenate dehydratase PD) and tyrB (encoding phenylalanine aminotransferase PAT) genes, aroG, pheA and tyrB genes were constructed and expressed in P2392. The results showed that the specific activities of DAPH, CM/PD and PAT in crude extracts were increased by 1.7, 13.9/7.8 and 2.3-fold, respectively.

Journal Article↗
PubMed1992

Overexpression, site-directed mutagenesis, and mechanism of Escherichia coli acid phosphatase.

Site-directed mutagenesis was used to examine the catalytic importance of 2 histidine and 4 arginine residues in Escherichia coli periplasmic acid phosphatase (EcAP). The residues that were selected as targets for mutagenesis were those that were also conserved in a number of high molecular weight acid phosphatases from eukaryotic organisms, including human prostatic and lysosomal acid phosphatases. Both wild type EcAP and mutant proteins were overproduced in E. coli using an expression system based on the T7 RNA polymerase promoter, and the proteins were purified to homogeneity. Examination of the purified mutant proteins by circular dichroism and proton NMR spectroscopy revealed no significant conformational changes. The replacement of Arg16 and His17 residues that were localized in a conserved N-terminal RHGXRXP motif resulted in the complete elimination of EcAP enzymatic activity. Critical roles for Arg20, Arg92, and His303 were also established because the corresponding mutant proteins exhibited residual activities that were not higher than 0.4% of that of wild type enzyme. In contrast, the replacement of Arg63 did not cause a significant alteration of the kinetic parameters. The results are in agreement with a previously postulated distant relationship between acid phosphatases, phosphoglycerate mutases, and fructose-2,6-bisphosphatase. These and earlier results are also consistent with the conclusion that 2 histidine residues participate in the catalytic mechanism of acid phosphatases, with His17 playing the role of a nucleophilic acceptor of the phospho group, whereas His303 may act as a proton donor to the alcohol or phenol.

Acid Phosphatase↗
PubMedDate not supplied

Attenuation of oxidative stress-induced changes in thalassemic erythrocytes by vitamin E.

The oxidative stress status of the transfusion-dependent Ebeta- and beta-thalassemia patients were studied before and after treatment with vitamin E for a period of four weeks. The level of cellular vitamin antioxidants viz. ascorbic acid and vitamin E in the thalassemia patients were found to be considerably lower compared to normal subjects. The activities of enzymatic antioxidants viz. catalase, glutathione peroxidase and glutathione reductase were found to be drastically reduced in untreated Ebeta- and beta-thalassemic patients when compared to normal subjects. However, the activity of superoxide dis-mutase was found to be increased in both types of untreated thalassemic patients when compared to normal individuals. An increase in superoxide dismutase and a decrease in catalase activity reflects the presence of a severe oxidative stress situation in the erythrocytes of the untreated transfusion dependent Ebeta- and beta-thalassemia patients. Changes in erythrocyte membrane protein pattern in untreated Ebeta- and beta-thalassemia patients when compared to normal erythrocyte further confirm the presence of continued oxidative stress in the ailing thalassemic erythrocytes. All these changes in the antioxidant status as well as the changes in the erythrocyte membrane proteins are ameliorated to considerable extent when the transfusion-dependent Ebeta- and beta-thalassemia patients were treated with vitamin E at a dose of 10 mg/kg/day for a period of four weeks. The patients during the treatment period did not exhibit any side effects and gained in body weight indicating a healthy status. The present study reveals that the lipophilic antioxidant vitamin E could be useful in the management of transfusion-dependant Ebeta- and beta-thalassemia patients.

Adolescent↗
PubMed2005

A new domain family in the superfamily of alkaline phosphatases.

During the course of our large-scale genome analysis a conserved domain, currently detectable only in the genomes of Drosophila melanogaster, Caenorhabditis elegans and Anopheles gambiae, has been identified. The function of this domain is currently unknown and no function annotation is provided for this domain in the publicly available genomic, protein family and sequence databases. The search for the homologues of this domain in the non-redundant sequence database using PSI-BLAST, resulted in identification of distant relationship between this family and the alkaline phosphatase-like superfamily, which includes families of aryl sulfatase, N-acetylgalactosomine-4-sulfatase, alkaline phosphatase and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM). The fold recognition procedures showed that this new domain could adopt a similar 3-D fold as for this superfamily. Most of the phosphatases and sulfatases of this superfamily are characterized by functional residues Ser and Cys respectively in the topologically equivalent positions. This functionally important site aligns with Ser/Thr in the members of the new family. Additionally, set of residues responsible for a metal binding site in phosphatases and sulphtases are conserved in the new family. The in-depth analysis suggests that the new family could possess phosphatase activity.

Alkaline Phosphatase↗