Expression of PCAF, p300 and Gcn5 and more highly acetylated histone H4 in pediatric tumors.

Any deregulation of histone acetyltransferases (HATs) could affect several processes in tumors. In this paper, the expression of the PCAF, p300 and Gcn5 HATs by RT-PCR in 34 tumor samples was evaluated. Samples of both central nervous system tumors (CNST, 13 cases) and Wilm's tumors (WT, 11 cases) over-expressed PCAF up to 1.6-, and Gcn5 up to 1.3-fold, respectively. In 9 out of 10 samples of benign tumors (BT), PCAF was not expressed. The p300 gene was the least expressed in all tumors. The medians of expression of PCAF (124.0 DU) and Gcn5 (127.0 DU) genes were higher in CNST than in both WT (102.0 and 101.0 DU, respectively) and BT (70.0 and 82.4 DU, respectively). There was a trend to decrease the expression of PCAF and Gcn5 genes in CNST, according to: chemotherapy (110.0 and 96.0 DU, respectively), chemo plus radiotherapy (124.0 and 115.0 DU, respectively) or no treatment (134.0 and 142.0 DU, respectively) in the tumors. A similar trend was observed in WT. Finally, we revealed more highly acetylated forms of histone H4 in CNST and WT. The over-expression of PCAF could represent a new molecular tumor marker in malignant tumors, especially in CNST in pediatric patients.

Effect of sodium butyrate on pro-matrix metalloproteinase-9 and -2 differential secretion in pediatric tumors and cell lines.

Matrix metalloproteinases (MMPs) are enzymes responsible for extracellular matrix degradation and contribute to local and distant cell invasion during cancer progression or metastasis. The effects of chromatin structure on gene expression and the use of histone deacetylase inhibitors such as sodium butyrate (NaBu) may directly influence pro-MMPs secretion. In the present study, we evaluated the effect of NaBu on pro-MMP-9 and pro-MMP-2 secretion in human Jurkat and HT1080 cells, and in 36 pediatric solid tumors. Cell lines and samples were exposed to 8 mM of NaBu and proteinase activity was evaluated in the supernatant by gelatin zymograms. Our results showed, for Jurkat cells treated with NaBu, increases of 2-fold and 1.5-fold in pro-MMP-9 and pro-MMP-2 secretion, respectively. A 50% decrease in pro-MMP-9 secretion due to NaBu was observed in HT1080 cells. NaBu induced a 0.62 reduction in levels of pro-MMP-9 secretion in untreated tumors. For cell lines and some NaBu-treated tumors we found histone H4 hyperacetylation. We conclude that pro-MMPs gene expression and their secretion can be epigenetically mis-regulated in tumoral processes.

Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing.

Xylanases are hemicellulases that hydrolyze the internal beta-1,4-glycoside bonds of xylan. The extracellular thermostable endo-1,4-beta-xylanase (EC 3.2.1.8; XT6) produced by the thermophilic bacterium Geobacillus stearothermophilus T-6 was shown to bleach pulp optimally at pH 9 and 338 K and was successfully used in a large-scale biobleaching mill trial. The xylanase gene was cloned and sequenced. The mature enzyme consists of 379 amino acids, with a calculated molecular weight of 43 808 Da and a pI of 9.0. Crystallographic studies of XT6 were performed in order to study the mechanism of catalysis and to provide a structural basis for the rational introduction of enhanced thermostability by site-specific mutagenesis. XT6 was crystallized in the primitive trigonal space group P3(2)21, with unit-cell parameters a = b = 112.9, c = 122.7 A. A full diffraction data set for wild-type XT6 has been measured to 2.4 A resolution on flash-frozen crystals using synchrotron radiation. A fully exchanged selenomethionyl XT6 derivative (containing eight Se atoms per XT6 molecule) was also prepared and crystallized in an isomorphous crystal form, providing full selenium MAD data at three wavelengths and enabling phase solution and structure determination. The structure of wild-type XT6 was refined at 2.4 A resolution to a final R factor of 15.6% and an R(free) of 18.6%. The structure demonstrates that XT6 is made up of an eightfold TIM-barrel containing a deep active-site groove, consistent with its 'endo' mode of action. The two essential catalytic carboxylic residues (Glu159 and Glu265) are located at the active site within 5.5 A of each other, as expected for 'retaining' glycoside hydrolases. A unique subdomain was identified in the carboxy-terminal part of the enzyme and was suggested to have a role in xylan binding. The three-dimensional structure of XT6 is of great interest since it provides a favourable starting point for the rational improvement of its already high thermal and pH stabilities, which are required for a number of biotechnological and industrial applications.

Stereotactically-guided biopsies of brainstem tumors.

INTRODUCTION: More than 10 years ago, the goal of our work had been to obtain a tissue sample of infiltrating lesions of the brainstem that had been diagnosed using computerized axial tomography (CAT). At that time, biopsies were believed to be indispensable when starting treatment of tumors. With time our objectives changed. Biopsies remained necessary, since until 1 year before the writing of this article we had not had the benefits of magnetic resonance imaging (MRI) at our Hospital. We also decided that carrying out sound statistics, confirmed by biopsies, was in itself a good procedure, especially in a country in which, to date, no serial studies of brainstem tumors had been undertaken. METHODS: We analyzed all of the patients diagnosed with posterior fossa tumors between March 1989 and March 2002 at the Hospital Infantil de México Federico Gómez (HIM). A preoperative TAC of the cranium was performed on every patient. Stereotactically-guided biopsies during tomography allowed precise control of penetration. Material obtained was sent to the Department of Pathology for analysis. RESULTS: Fifty patients were diagnosed with infiltrating tumors of the brainstem: 30 cases of low-grade astrocytomas, 13 cases of high-grade astrocytomas, 2 cases of primitive neuroectodermic tumors, 2 cases of rhabdoid tumors, 1 case of ependymoma, and 2 patients had non-specified tumors. The most frequent symptoms and signs were ataxia and disturbances of the cranial nerves. There was no mortality caused by penetration, and follow-up studies of more than 5 years were carried out. DISCUSSION: The results from our series were similar to those in the literature. In our case, follow-up studies were undertaken for longer periods. In the first section of our work, we suggest the need for stereotactic biopsies in order to arrive at a precise diagnosis in environments in which MRI may be unavailable. CONCLUSION: At present, presumptive diagnosis of infiltrating brainstem lesions may be adequately undertaken with imaging methods, such as MRI. However, we believe that a stereotactically-guided biopsy provides an accurate method for diagnosing lesions of the brainstem. In our case, this procedure has been carried out entirely in the tomography room, without any complications of disease or mortality.

Formation of a tyrosyl radical intermediate in Proteus mirabilis catalase by directed mutagenesis and consequences for nucleotide reactivity.

Proteus mirabilis catalase (PMC) belongs to the family of NADPH binding catalases. The function of NADPH in these enzymes is still a matter of debate. This study presents the effects of two independent phenylalanine mutations (F194 and F215), located between NADPH and heme in the PMC structure. The phenylalanines were replaced with tyrosines which we predicted could carry radicals in a NADPH-heme electron transfer. The X-ray crystal structures of the two mutants indicated that neither the binding site of NADPH nor the immediate environment of the residues was affected by the mutations. Measurements using H2O2 as a substrate confirmed that the variants were as active as the native enzyme. With equivalent amounts of peroxoacetic acid, wild-type PMC, F215Y PMC, and beef liver catalase (BLC) formed a stable compound I, while the F194Y PMC variant produced a compound I which was rapidly transformed into compound II and a tyrosyl radical. EPR studies showed that this radical, generated by the oxidation of Y194, was not related to the previously observed radical in BLC, located on Y369. In the presence of excess NADPH, compound I was reduced to a resting enzyme (k(obs) = 1.7 min(-1)) in a two-electron process. This was independent of the enzyme's origin and did not require any thus far identified tyrosyl radicals. Conversely, the presence of a tyrosyl radical in F194Y PMC greatly enhanced the oxidation of reduced beta-nicotinamide mononucleotide under a steady-state H2O2 flow with observable compound II. This process could involve a one-electron reduction of compound I via Y194.

Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.

Isopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase catalyses a crucial activation step in the isoprenoid biosynthesis pathway. This enzyme is responsible for the isomerization of the carbon-carbon double bond of IPP to create the potent electrophile DMAPP. DMAPP then alkylates other molecules, including IPP, to initiate the extraordinary variety of isoprenoid compounds found in nature. The crystal structures of free and metal-bound Escherichia coli IPP isomerase reveal critical active site features underlying its catalytic mechanism. The enzyme requires one Mn(2+) or Mg(2+) ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site. Two critical residues, C67 and E116, face each other within the active site, close to the metal-binding site. The structures are compatible with a mechanism in which the cysteine initiates the reaction by protonating the carbon-carbon double bond, with the antarafacial rearrangement ultimately achieved by one of the glutamates involved in the metal coordination sphere. W161 may stabilize the highly reactive carbocation generated during the reaction through quadrupole- charge interaction.

Preliminary structural studies of Escherichia coli isopentenyl diphosphate isomerase.

Escherichia coli isopentenyl diphosphate isomerase, an enzyme catalyzing a key step in isoprenoid biosynthesis, has been produced in selenomethionyl form. The protein was purified and crystallized by the hanging-drop vapour-diffusion method. Crystals display trigonal symmetry, with unit-cell parameters a = b = 71.3, c = 61.7 A, and diffract to 1.45 A resolution.

Crystallization and preliminary X-ray diffraction analysis of a [2Fe-2S] ferredoxin (FdVI) from Rhodobacter capsulatus.

A [2Fe-2S] ferredoxin found in the photosynthetic bacterium Rhodobacter capsulatus has been purified in recombinant form from Escherichia coli. This protein, called FdVI, resembles ferredoxins involved in iron-sulfur cluster biosynthesis in various prokaryotic and eukaryotic cells. Purified recombinant FdVI was recovered in high yields and appeared to be indistinguishable from the genuine R. capsulatus ferredoxin based on UV-visible absorption and EPR spectroscopy and mass spectrometry. FdVI has been crystallized in the oxidized state by a sitting-drop vapour-diffusion technique using sodium formate as precipitant. Seeding larger drops from a previous hanging-drop-grown small crystal resulted in the formation of long red-brown prismatic needles. Preliminary X-ray diffraction analysis indicated that FdVI crystals are orthorhombic and belong to the space group P2(1)2(1)2(1), with unit-cell parameters a = 45.87, b = 49.83, c = 54.29 A.

Interruption of the internal water chain of cytochrome f impairs photosynthetic function.

The structure of cytochrome f includes an internal chain of five water molecules and six hydrogen-bonding side chains, which are conserved throughout the phylogenetic range of photosynthetic organisms from higher plants, algae, and cyanobacteria. The in vivo electron transfer capability of Chlamydomonas reinhardtii cytochrome f was impaired in site-directed mutants of the conserved Asn and Gln residues that form hydrogen bonds with water molecules of the internal chain [Ponamarev, M. V., and Cramer, W. A. (1998) Biochemistry 37, 17199-17208]. The 251-residue extrinsic functional domain of C. reinhardtii cytochrome f was expressed in Escherichia coli without the 35 C-terminal residues of the intact cytochrome that contain the membrane anchor. Crystal structures were determined for the wild type and three "water chain" mutants (N168F, Q158L, and N153Q) having impaired photosynthetic and electron transfer function. The mutant cytochromes were produced, folded, and assembled heme at levels identical to that of the wild type in the E. coli expression system. N168F, which had a non-photosynthetic phenotype and was thus most affected by mutational substitution, also had the greatest structural perturbation with two water molecules (W4 and W5) displaced from the internal chain. Q158L, the photosynthetic mutant with the largest impairment of in vivo electron transfer, had a more weakly bound water at one position (W1). N153Q, a less impaired photosynthetic mutant, had an internal water chain with positions and hydrogen bonds identical to those of the wild type. The structure data imply that the waters of the internal chain, in addition to the surrounding protein, have a significant role in cytochrome f function.

Bile acid secretion during rat liver carcinogenesis.

Retro-differentiation of liver parenchyma during neoplastic processes is characterized by the expression of tumor antigens, such as alpha-fetoprotein and the placental isoenzyme of glutathione-S-transferase (GST-P). To investigate whether this may also affect a typical liver function such as bile acid secretion was the aim of this work. Rat hepatocarcinogenesis was induced by diethylnitrosamine (i.p., 200 mg/Kg body weight at day 0) and promoted by two-thirds partial hepatectomy (at day 21) plus 2-acetamidofluorene administration (50 mg/Kg body weight, subcutaneously, twice a week from day 14 to day 35). In order to carry out planimetric measurements of neoplastic tissue after immunohistochemical staining, a novel monoclonal antibody (MAb 14.1.3) against GST-P with no cross-reactivity against the major liver isoform of GST (GST-H) was raised. Analysis of total biliary bile acid output using the 3alpha-hydroxysteroid dehydrogenase method indicated that a significant reduction (-26%) occurred during the formation of GST-P-positive foci (12 wk). This was restored to normal values during adenoma formation (16-20 wk), but decreased again during carcinoma transformation (32 wk). These changes were not parallel to that observed in bile flow, which was progressively but slightly decreased throughout the whole period under study. HPLC analysis of bile samples collected for 1 h at different time points during hepatocarcinogenesis revealed that in contrast to what happens during cholestatic disease, a continuous and progressive increase in the cholic acid-to-chenodeoxycholic acid ratio (from 4.4+/-0.5 in control animals to 15.1+/-1.9 in rats with hepatocellular carcinoma) occurs. A significant and transient increase at 16 wk (+120%) in the proportion of bile acids amidated with glycine as compared to those conjugated with taurine was also observed. These results indicate that the mechanisms accounting for the secretion of major bile acids are modified differently at various steps of rat liver tumor development.

Purification, crystallization and preliminary X-ray analysis of catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa.

The catabolic ornithine carbamoyltransferase (OTCase) from Pseudomonas aeruginosa exhibits allosteric behaviour, with two conformational states of the molecule: an active R form and an inactive T form. The enzyme is a dodecamer with a molecular mass of 455700 Da. Three crystal forms have been obtained. Crystals of allosteric state T are rhombohedral, belonging to the R3 space group, with hexagonal unit-cell parameters a = b = 180.6, c = 122.0 A. They diffract to a resolution of 4.5 A. Two crystal forms for allosteric state R have been obtained, with hexagonal and cubic symmetries. Hexagonal crystals, which diffract to a resolution of 3. 4 A, belong to the space group P6(3) with unit-cell parameters a = b = 140.8, c = 145.6 A. The cubic crystals belong to space group I23, with unit-cell parameter a = 134.32 A and diffract to a resolution better than 2.5 A. In all crystal forms, the dodecamer exhibits a 23 point-group symmetry.

Allosteric regulation in Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase revisited: association of concerted homotropic cooperative interactions and local heterotropic effects.

The allosteric catabolic ornithine carbamoyltransferase (OTCase) from Pseudomonas aeruginosa, a dodecamer build up of four trimers of identical subunits, shows strong carbamoylphosphate homotropic co-operativity. Its activity is allosterically inhibited by spermidine and activated by AMP. Modified forms of the enzyme exhibiting substantial alterations in both homotropic and heterotropic interactions were recently obtained. We report here the first detailed kinetic characterization of homotropic and heterotropic modulations in allosteric wild-type and in engineered OTCases. Homotropic co-operativity for the saturation either by citrulline or arsenate was also observed when arsenate was utilised as an alternate substrate of the reverse reaction. Amino acid substitution of glutamate 105 by a glycine produces an enzyme devoid of homotropic interactions between the catalytic sites for carbamoylphosphate. This mutant, which is blocked in an active conformation, is still sensitive to the allosteric effector AMP, which increases affinity with respect to the substrate, carbamoylphosphate. It is also observed that homotropic co-operative interactions do not reappear in the E105G enzyme upon strong inhibition by the allosteric inhibitor of the wild-type enzyme, spermidine.Replacement of residues 34 to 101 of the native enzyme by the homologous amino acids of anabolic Escherichia coli OTCase produces a trimeric enzyme which retains reduced homotropic co-operativity. Activation by AMP and inhibition by spermidine of this chimaeric OTCase do not affect carbamoylphosphate homotropic co-operativity. AMP acts by reducing the concentration of substrate at half maximum velocity while spermidine acts in the inverse way. These observations indicate that in the two mutant forms of OTCase, homotropic and heterotropic interactions can be uncoupled and therefore must involve different molecular mechanisms. Furthermore, the results of stimulation of enzyme activity by phosphate, arsenate, pyrophosphate and phosphonoacetyl-l-ornithine on wild-type and mutant OTCases suggest that the physiological substrate phosphate, besides acting at the catalytic site, may act at an allosteric site. On the other hand, pyrophosphate and phosphonoacetyl-l-ornithine activation results exclusively from interactions of this effector with the active site residues.

Kinetic studies of allosteric catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa.

The pseudo-reverse reaction of Pseudomonas aeruginosa catabolic ornithine carbamoyltransferase in which arsenate is first coupled to citrulline followed by elimination of carbamylarsenate has been studied. Arsenate and citrulline saturation curves are sigmoidal. The different responsiveness of the transcarbamoylase to isosteric and allosteric ligands was examined both in the forward reaction, the carbamoylation of ornithine, and in the pseudo-reverse reaction, the arsenolytic cleavage of citrulline. Nucleoside monophosphates and polyamines that act as allosteric activators and inhibitors, respectively, on the carbamoylation reaction have the same effect on the rate of the arsenolytic cleavage of citrulline. ATP and other nucleoside triphosphates were found to stimulate enzyme activity at low carbamoylphosphate concentration with little influence on the carbamoylphosphate concentration at half-maximum velocity as well as on the cooperative index. When measuring the initial rate of the reverse reaction, the arsenolytic cleavage of citrulline, ATP was found to be a weak inhibitor, whereas CTP still stimulates the reaction and UTP was without influence. This unidirectional inhibition or activation phenomenon is likely apparent since initial studies were conducted and no consideration was given to equilibrium conditions. Regulation of catabolic OTCase by nucleoside triphosphates is without physiological meaning. In contrast, stimulation by nucleoside monophosphates may indicate that energy limitation could promote the synthesis and activity of the catabolic enzyme.

Bile secretion by the rat liver during synchronized regeneration.

Simultaneous coexistence of differentiated, proliferating and redifferentiated hepatocytes occurs during normal liver regeneration (LR). The aim of the present work was to study the time course of the capacity of the liver to form bile during synchronized LR. Following two-thirds partial hepatectomy (PH) in rats, i.v. administration of the ribonucleotide reductase reversible inhibitor hydroxyurea (HU) was used to transiently block liver cells at G1/S boundary. Experiments were performed at 0 and 4 hours, and 1, 3 or 7 days after releasing HU-induced inhibition. Bile acid pool size was determined by collecting bile samples over 24 hours. Initial (first hour) bile flow and bile acid output were increased early on during synchronized LR as compared with the values found in non-hepatectomized control animals. These values were thereafter (1 day) reduced, but increased again at 3 days after halting HU infusion. The time course of bile acid depletion and changes in bile flow were very similar in control and synchronized LR, except that in the latter a more important early reduction in bile flow and bile acid output was found. Shortly after PH, part of the bile acid pool was lost, but this was quickly restored, soon (1 day) reaching a net bile acid pool size very similar to that found in control rats. The highest pool size relative to liver weight was found on day 1, when bile acid output and bile flow reached their lowest values. Additional experiments were performed using in situ perfused regenerating rat livers in which stepwise infusion of taurocholate (TC) was carried out. PH alone modified neither the bile acid-independent (BAIF) nor the bile acid-dependent fraction of bile flow (BADF). However, in normal LR, the BAIF decreased on day 1 and recovered at 7 days, while in synchronized LR it remained depressed up to 7 days. The BADF was only reduced during the early phase of normal LR and did not change significantly in synchronized LR. The maximal secretion rate (SRmax) for TC, as expressed per gram of remaining liver tissue, was not affected immediately after PH, but a marked reduction was observed on day 1 in both normal and synchronized LR. Afterwards, SRmax was quickly restored in both synchronized LR and, although in a slower way, normal LR. These results suggest that synchronization of LR involves changes in the time required to the recovery of specific liver functions such as bile formation.

Bile acid secretion during synchronized rat liver regeneration.

One major difficulty in interpreting the changes occurring during liver regeneration is the co-existence of non-activated cells and proliferating hepatocytes at all stages of differentiation. The aim of this study was to investigate bile acid (BA) secretion into bile during normal (NLR) and synchronized (SLR) liver regeneration in rats. Regeneration was synchronized by reversible inhibition of ribonucleotide reductase by 10 h treatment with hydroxyurea (HU) shortly after two-third partial hepatectomy. Total BA output as measured by GC-MS increased immediately after partial hepatectomy. This was followed by a further transient enhancement during the next day in the NLR. HU treatment did not significantly modify total BA output, but after releasing synchronized regeneration a marked reduction was observed. This was followed by a recovery to reach values close to those of NLR on day 7 of the regenerative process in SLR. Amidated BA output as measured by HPLC analysis revealed an early enhancement in the proportion of non-conjugated BAs in bile in NLR. However, the profile of conjugated BAs, which was not affected by HU treatment, matched that of total BAs during the first stage of SLR. By contrast, the increase in BA output observed on day 3 of the regenerative process in this group was accounted for by an enhancement in non-conjugated BA secretion. On day 7 of the regenerative process, the proportion of conjugated BA in bile was restored to approximately 100% in this group. Most BA molecules were conjugated with taurine rather than with glycine in all experimental groups, during both NLR and SLR. GC-MS determinations indicated that the magnitude of the cholic acid predominance in all bile samples was significantly modified during liver regeneration. This was increased early after partial hepatectomy and declined toward control values after few (2-3) days. Enhancement in the cholic acid predominance was due to a reduction in the proportion of all other major BAs, above all ursocholic acid and omega-muricholic acid. By contrast, minor BAs in normal control rat bile such as allo-cholic acid were increased during both NLR and SLR, and remained at detectable levels up to day 7. Changes in the proportion of secreted BA species were similar in SLR and NLR except that the early reduction in the proportion of BAs other than cholic acid was more pronounced in SLR and the quantitative importance of the diversity in BA species was recovered earlier in SLR than in NLR. In summary, these results indicate that profound changes in BA secretion during rat liver regeneration do occur. Most of them are probably related to the existence of retro-differentiation/re-differentiation processes which are speeded up by hydroxyurea-induced synchronization of the wave of hepatocyte proliferation.