Nonaheme cytochrome c, a new physiological electron acceptor for [Ni,Fe] hydrogenase in the sulfate-reducing bacterium Desulfovibrio desulfuricans Essex: primary sequence, molecular parameters, and redox properties

A nonaheme cytochrome c was purified to homogeneity from the soluble and the membrane fractions of the sulfate-reducing bacterium Desulfovibrio desulfuricans Essex. The gene encoding for the protein was cloned and sequenced. The primary structure of the multiheme protein was highly homologous to that of the nonaheme cytochrome c from D. desulfuricans ATCC 27774 and to that of the 16-heme HmcA protein from Desulfovibrio vulgaris Hildenborough. The analysis of the sequence downstream of the gene encoding for the nonaheme cytochrome c from D. desulfuricans Essex revealed an open reading frame encoding for an HmcB homologue. This operon structure indicated the presence of an Hmc complex in D. desulfuricans Essex, with the nonaheme cytochrome c replacing the 16-heme HmcA protein found in D. vulgaris. The molecular and spectroscopic parameters of nonaheme cytochrome c from D. desulfuricans Essex in the oxidized and reduced states were analyzed. Upon reduction, the pI of the protein changed significantly from 8.25 to 5.0 when going from the Fe(III) to the Fe(II) state. Such redox-induced changes in pI have not been reported for cytochromes thus far; most likely they are the result of a conformational rearrangement of the protein structure, which was confirmed by CD spectroscopy. The reactivity of the nonaheme cytochrome c toward [Ni,Fe] hydrogenase was compared with that of the tetraheme cytochrome c(3); both the cytochrome c(3) and the periplasmic [Ni,Fe] hydrogenase originated from D. desulfuricans Essex. The nonaheme protein displayed an affinity and reactivity toward [Ni,Fe] hydrogenase [K(M) = 20.5 +/- 0.9 microM; v(max) = 660 +/- 20 nmol of reduced cytochrome min(-1) (nmol of hydrogenase)(-1)] similar to that of cytochrome c(3) [K(M) = 12.6 +/- 0.7 microM; v(max) = 790 +/- 30 nmol of reduced cytochrome min(-1) (nmol of hydrogenase)(-1)]. This shows that nonaheme cytochrome c is a competent physiological electron acceptor for [Ni,Fe] hydrogenase.

Ras-related GTPase Rhob represses NF-kappaB signaling

rhoB encoding a Ras-related GTPase is immediate-early inducible by genotoxic treatments, indicating that it is part of the cellular stress response. Here, we investigated the influence of RhoB on signal pathways that are rapidly evoked by genotoxic compounds. The data obtained show that wild-type RhoB neither affects activation of mitogen-activated protein kinases nor AP-1-dependent gene expression. However, RhoB inhibited both basal and genotoxic agent-stimulated activity of the transcription factor nuclear factor kappaB (NF-kappaB). Thus, RhoB attenuated alkylation-induced increase in the DNA binding activity of NF-kappaB and abrogated NF-kappaB-driven gene expression. Furthermore, RhoB inhibited decrease in the cellular amount of IkappaBalpha after genotoxic stress as well as after tumor necrosis factor alpha and 12-O-tetradecanoylphorbol acetate treatment. This indicates that RhoB represses NF-kappaB activation by inhibiting dissociation and subsequent degradation of IkappaBalpha. On the basis of the data, we suggest that RhoB is a novel negative regulator of NF-kappaB signaling.

Transcriptional activation of the small GTPase gene rhoB by genotoxic stress is regulated via a CCAAT element

The gene encoding the Ras-related GTPase RhoB-specific is immediate-early inducible by genotoxic treatments. Regulation of transcriptional activation of rhoB is still unclear. Here we show that cells lacking either p53 or c-Fos are not different from wild-type cells with respect to the level of rhoB induction upon UV irradiation, indicating that these transcription factors are not crucial for stimulation of rhoB mRNA expression. Extracts from UV-irradiated and non-irradiated cells revealed similar DNA-binding activities to a 0.17 kb rhoB promoter fragment harboring the functional element(s) necessary for stimulation of rhoB by UV light. By means of immunoprecipitation we found that an ATF-2-specific antibody co-precipitates the (32)P-labeled 0.17 kb rhoB fragment, whereas an anti-AP1 antibody did not. Since no consensus sequence for binding of ATF-2 is present within the rhoB promoter, ATF-2 is likely to be associated with another factor that binds to the minimal promoter. Deletion analysis and site-directed mutagenesis of the 0.17 kb rhoB fragment revealed a CCAAT box to be an essential requirement for stimulation of rhoB by UV light and methyl methanesulfonate. Moreover, immunoprecipitation experiments showed that the CCAAT-binding factor NF-YA is complexed with ATF-2. Overall, the data strongly indicate that transcriptional activation of the rhoB gene by genotoxic stress is regulated via a CCAAT box and that interaction of CCAAT-binding factor and ATF-2 triggers the stress-inducible expression of rhoB.

Crystallization and preliminary X-ray analysis of adenylylsulfate reductase from Archaeoglobus fulgidus

A group of anaerobic microorganisms use sulfate as the terminal electron acceptor for energy conservation. The process of sulfate reduction involves several enzymatic steps. One of them is the conversion of adenylyl sulfate (adenosine-5'-phosphosulfate) to sulfite, catalyzed by adenylylsulfate reductase. This enzyme is composed of a FAD-containing alpha-subunit and a beta-subunit harbouring two [4Fe-4S] clusters. Adenylylsulfate reductase was isolated from Archaeoglobus fulgidus under anaerobic conditions and crystallized using the hanging-drop vapour-diffusion method using PEG 4000 as precipitant. The crystals grew in space group P2(1)2(1)2(1), with unit-cell parameters a = 72.4, b = 113.2, c = 194.0 A. The asymmetric unit probably contains two alphabeta units. The crystals diffract beyond 2 A resolution and are suitable for X-ray structure analysis.

Inhibition of protein isoprenylation impairs rho-regulated early cellular response to genotoxic stress

Activation of c-Jun N-terminal kinases (JNKs) and nuclear factor-kappaB (NF-kappaB) are early cellular responses to genotoxic stress involved in the regulation of gene expression. Pretreatment of cells with the hydroxymethyl glutaryl-CoA reductase inhibitor lovastatin blocked stimulation of JNK1 activity by UV irradiation and by treatment with the alkylating compound methyl methanesulfonate but did not affect activation of extracellular signal-regulated kinase 2 by UV light. Lovastatin also attenuated UV-induced degradation of the NF-kappaB inhibitor IkappaBalpha. The effects of lovastatin on UV-triggered stimulation of JNK1 as well as on IkappaBalpha degradation were reverted by cotreatment with geranylgeranylpyrophosphate but not with farnesylpyrophosphate. Both a geranylgeranyltransferase type I inhibitor and a farnesyltransferase inhibitor blocked JNK1 stimulation by UV irradiation without impairing signaling to NF-kappaB. This indicates that different types of isoprenylated proteins impair UV-induced signaling to JNK1 and NF-kappaB, respectively. Since lovastatin caused a rapid decrease in the level of membrane-bound Rho GTPases, we hypothesize that Rho signaling is inhibited by lovastatin. In line with this hypothesis, Rho-inactivating toxin B from Clostridium difficile abolished both JNK1 activation and IkappaBalpha degradation evoked by UV irradiation. In summary, lovastatin-mediated inhibition of protein isoprenylation abrogates cellular stress responses involving JNK- and NF-kappaB-regulated pathways, which seems to be caused by inactivation of Rho GTPases.

Formation of organosilicon compounds 117:1 C-brominated 1,3,5-trisilacyclohexanes and their reactions with BuLi

The photobromination of 1,1,3,3,5,5-hexamethyl-1,3,5-trisilacyclohexane (1) almost exclusively attacks CH2 groups and results in 2,2-dibromo-trisilacyclohexane (2) as well as 2,2,4,4-tetrabromo-trisilacyclohexane (3) in high yields. Starting from a mixture of C-brominated trisilacyclohexanes the isomeric 2,2,9-tribromo-1,3,3,5,5,8,8,10,10,13,13-undecamethyl-1,3,5,8,10,13-hexasilabicyclo[7.2.2]tridec-6-yne (6) had been obtained in very low yield in an attempt to establish a preparative route to adamantanes with a C4Si6 skeleton, i.e., with C bridgeheads and SiR2 bridges. By ICl-cleavage of a Si—methyl bond in 2 and subsequent substitution with Br3CLi, the trisilacyclohexane 4 with functional groups in opposite positions of the ring can be obtained. Linking the step-by-step synthesized Cl-Me2Si-C=C-SiMe2-CH2-SiMe2-Ph to the CBr3 group of 4 results after HBr-cleavage of the Si—Ph bond in (ω-bromo-octynyl)-trisilacyclohexane (12). A ring closure of 12 would result in an isomeric hexasila bicyclo[7.2.2]tridec-6-yne. The compounds were characterized by 1H, 13C, and 29Si NMR spectra. Additionally, the molecular structures of 4 and 6 were confirmed by X-ray single crystal investigations.Key words: 1,1,3,3,5,5-hexamethyl-1,3,5-trisilacyclohexane, bromination, 2,2,9-tribromo-1,3,3,5,5,8,8,10,10,13,13-undecamethyl-1,3,5,8,10,13-hexasilabicyclo[7.2.2]tridec-6-yne, carbosilane synthesis, NMR data, crystal structure investigation.

Solving the generalized indirect Fourier transformation (GIFT) by Boltzmann simplex simulated annealing (BSSA)

The structure of colloidal particles can be studied with small-angle X-ray and neutron scattering (SAXS and SANS). In the case of randomly oriented systems, the indirect Fourier transformation (IFT) is a well established technique for the calculation of model-free real-space information. Interaction leads to an overlap of inter- and intraparticle scattering effects, preventing most detailed interpretations. The recently developed generalized indirect Fourier transformation (GIFT) technique allows these effects to be separated by assuming various models for the interaction,i.e.the so-called structure factors. The different analytical behaviour of these structure factors from that of the form factors, describing the intraparticle scattering, allows this separation. The mean-deviation surface is defined by the quality of the fit for different parameter sets of the structure factor. Its global minimum represents the solution. The former non-linear least-squares approach has proved to be inefficient and not very reliable. In this paper, the incorporation of the completely different Boltzmann simplex simulated annealing (BSSA) algorithm for finding the global minimum of the hypersurface is presented. This new method increases not only the calculation speed but also the reliability of the evaluation.

Human APE/Ref-1 protein

Human apurinic (apyrimidinic) endonuclease/redox-factor 1 (APE/Ref-1) is an ubiquitously expressed multifunctional protein of 36.5 kDa which is encoded by a approximately 3 kb gene localized on chromosome 14. APE/Ref-1 is involved in the repair of DNA damage as well as in the transcriptional regulation of genes. The repair function of the protein is located on its C-terminal region. Activation of transcription factors, which occurs via a redox-based mechanism, pertains to a approximately 6 kDa N-terminal fragment with Cys-65 being of essential importance. APE/Ref-1 is part of the cellular response to oxidative stress and protects cells from the genotoxic and cytotoxic effect of oxidizing agents. Thus, specific downmodulation of APE/Ref-1 activity in tumors might be considered as a novel therapeutic approach in tumor therapy.

Comparison of HOCl traps with myeloperoxidase inhibitors in prevention of low density lipoprotein oxidation

In this study, the production of the highly toxic oxidant hypochlorous acid (HOCl) by the phagocytic enzyme myeloperoxidase (MPO) was quantitated and the concomitant alterations of low density lipoprotein (LDL) were analyzed in view of the potential role of LDL in atherosclerosis. Using the monochlorodimedone assay, it was found that HOCl is produced in micromolar concentrations. The kinetics of the decrease of tryptophan fluorescence appeared to be a sensitive method to monitor LDL alterations under near in vivo conditions. Therefore, this method was used to subsequently compare the effectiveness of MPO inhibitors that block production of HOCl with compounds that act as HOCl traps. The efficiency of MPO inhibitors to prevent LDL damage increased in the series benzohydroxamic acid < salicylhydroxamic acid < 3-amino-1,2,4-triazole < sodium azide < potassium cyanide < p-hydroxy-benzoic acid hydrazide, while for the HOCl traps the protective efficiency increased in the series glycine < taurine < methionine. We conclude that HOCl traps may have high potential therapeutic impact in vivo due to their low toxicity, although high concentrations of them would have to reach sites of inflammation. In contrast, only low concentrations of a specific MPO inhibitor would be required to irreversibly inhibit the enzyme.

Adenylylsulfate reductases from archaea and bacteria are 1:1 alphabeta-heterodimeric iron-sulfur flavoenzymes--high similarity of molecular properties emphasizes their central role in sulfur metabolism

Highly active adenylylsulfate (APS) reductase was isolated under N(2)/H(2) from sulfate-reducing and sulfide-oxidizing bacteria and archaea. It was a 1:1 alphabeta-heterodimer of molecular mass approximately 95 kDa, and two subunits (alpha approximately 75, beta approximately 20 kDa). The specific activity was 11-14 micromol (min mg)(-1); cofactor analysis revealed 0.96+/-0.05 FAD, 7.5+/-0.1 Fe and 7.9+/-0.25 S(2-). The photochemically reduced enzyme had a multiline EPR spectrum resulting from two interacting [4Fe-4S] centers. The properties of the different APS reductases were remarkably similar, although the enzyme is involved in different metabolic pathways and was isolated from phylogenetically far separated organisms. A structural model is proposed, with FAD bound to the alpha-subunit, and two [4Fe-4S] centers located in close proximity on the beta-subunit.

Helicobacter pylori prevalence in Leipzig's 1998 school entries: methodology and first results

The non-invasive, stable-isotope-aided Helicobacter pylori (H. pylori) tests--breath and equivalent urine tests--were offered on a voluntary basis as part of the mandatory school entry medical examination to the 1998 school entry cohort of the City of Leipzig (480,000 residents). Parents of participating subjects were asked to fill out a detailed epidemiologic questionnaire. The response rate was 94% (n = 2228 of 2369 school starters born in 1991/92). Parent-completed questionnaires were returned by 1890 (80%) children. The overall H. pylori positive prevalence was 7.2%. The prevalence among children with a test and a parent-completed questionnaire was 6.5%. Prevalences among subsequently tested family members of the positive tested children was 65, 60 and 39% for mothers, fathers and siblings respectively. Though studies have shown that the direct transmission of the bacterium (oral-oral and fecal-oral) is a dominant pathway of infection, the questionnaire analyses indicate associations between H. pylori colonisation and living as well as environmental conditions.

Ras-related GTPase RhoB forces alkylation-induced apoptotic cell death

rhoB encoding a Ras-related GTPase is immediate-early inducible by genotoxic treatments. To address the question of the physiological role of RhoB in cellular defense, cells stably overexpressing wild-type RhoB protein were generated. Overexpression of RhoB renders cells hypersensitive to the killing effect of alkylating agents including antineoplastic drugs but not to UV-light and doxorubicin. As compared to control cells, RhoB overexpressing cells revealed an increase in the frequency of alkylation-induced apoptotic cell death. This indicates that RhoB is involved in modulating apoptotic signaling. Furthermore, overexpression of RhoB resulted in a prolonged transient block to DNA replication upon MMS treatment. UV-induced replication blockage was not affected by RhoB. Based on the data we suggest RhoB to be a novel regulatory factor which takes influence on the level of cytotoxicity of DNA damaging drugs and forces cells to alkylation-induced apoptosis. The data indicate that this might be due to RhoB mediated delay in cell cycle progression upon alkylation treatment.

Rho GTPases are over-expressed in human tumors

Small GTPases of the Rho family are involved in the regulation of a variety of cellular processes, such as the organization of the microfilamental network, cell-cell contact and malignant transformation. To address the question of whether Rho proteins are involved in carcinogenesis in man, we compared their expression in tumors from colon, breast and lung with that of the corresponding normal tissue originating from the same patient. As shown by Rho-specific 32P-ADP-ribosylation, as well as Western-blot analysis, the amount of RhoA protein was largely increased in all 3 types of tumors tested. The most dramatic differences in the expression of Rho GTPases were observed in breast tissue. All breast tumors analyzed showed high levels of RhoA, Rac and Cdc42 proteins, whereas in the corresponding normal tissue these Rho proteins were hardly or not detectable. Progression of breast tumors from WHO grade I to grade III was accompanied by a significant average increase in RhoA protein. Overall, increase in the amount of Rho GTPases, in particular RhoA, appears to be a frequent event in different types of human tumors. This supports the view that Rho GTPases are involved in human carcinogenesis.

Rho GTPases are over-expressed in human tumors

Small GTPases of the Rho family are involved in the regulation of a variety of cellular processes, such as the organization of the microfilamental network, cell-cell contact and malignant transformation. To address the question of whether Rho proteins are involved in carcinogenesis in man, we compared their expression in tumors from colon, breast and lung with that of the corresponding normal tissue originating from the same patient. As shown by Rho-specific 32P-ADP-ribosylation, as well as Western-blot analysis, the amount of RhoA protein was largely increased in all 3 types of tumors tested. The most dramatic differences in the expression of Rho GTPases were observed in breast tissue. All breast tumors analyzed showed high levels of RhoA, Rac and Cdc42 proteins, whereas in the corresponding normal tissue these Rho proteins were hardly or not detectable. Progression of breast tumors from WHO grade I to grade III was accompanied by a significant average increase in RhoA protein. Overall, increase in the amount of Rho GTPases, in particular RhoA, appears to be a frequent event in different types of human tumors. This supports the view that Rho GTPases are involved in human carcinogenesis.

Characterization of Enzymatically Induced Aggregation of Casein Micelles in Natural Concentration by in Situ Static Light Scattering and Ultra Low Shear Viscosimetry

The aggregation of casein micelles in undiluted skim milk after the addition of chymosin was studied by static light scattering and ultra low shear viscometry. The static light scattering measurements were made with two different sample thicknesses, 72 and 16 µm. The scattering data were analyzed by indirect Fourier transformation and by the polydispersity inversion technique which led to pair distance distribution functions and size distribution function, respectively. The minimum scattering angle was 1 degrees, which allows for the determination of particle sizes up to a maximum diameter of 12 µm. The fractal dimension determined from double logarithmic plots of intensity versus scattering vector resulted in values between 1.9 and 2.0. The influence of multiple scattering was determined by comparison of the measurements with the different sample thicknesses. The measurements show no significant influence of multiple scattering when the transmission is above 0.85. Due to the very complex and porous structure of the casein aggregates the Rayleigh-Debye-Gans scattering theory has been used in the data analysis. Measurements with a new instrument using ultra low shear showed good agreement with theory. Copyright 1999 Academic Press.

Cell and tissue-type specific expression of Ras-related GTPase RhoB

Ras-homologous (Rho) GTPases are involved in the regulation of a variety of cellular processes such as the organization of the actin cytoskeleton, malignant transformation and genotoxic stress-induced signaling. Here we show that, among the family of Rho GTPases, specifically rhoB mRNA expression is rapidly induced upon UV-irradiation, whereas the level of rac 1 and cdc42 mRNA is not affected. Increase in rhoB mRNA was accompanied by a approximately 4-fold increase in the amount of membrane-bound RhoB protein. Basal expression of rhoB mRNA appears to be cell-type specific with low amounts in rodent NIH 3T3, V79, H4IIE, CHO and human HaCat cells and comparably high amounts in monkey COS, human HeLa and HepG2 cells. In rabbit tissues, exceptionally high levels of rhoB mRNA and RhoB protein were found in lung whereas its expression was quite low in heart, liver, spleen and kidney. Variations in rhoB mRNA expression level are not due to cell-type specific differences in rhoB mRNA stability as shown by inhibitor experiments. However, transiently transfected rhoB promoter CAT construct was expressed at significantly higher level in HeLa and HepG2 as compared to NIH 3T3 and CHO cells. Thus, cell-type specific differences in the level of rhoB mRNA are likely to be due to variations in the transcriptional activity of the rhoB gene. The data indicate that, among the family of Rho GTPases, only the expression of rhoB is rapidly stimulated by genotoxic stress. Furthermore basal rhoB expression appears to be regulated in a cell and tissue-type specific manner. This may be related to yet unknown tissue-specific physiological function of RhoB.

Activation of c-Jun N-terminal kinase 1 by UV irradiation is inhibited by wortmannin without affecting c-iun expression

Activation of c-Jun N-terminal kinases (JNKs)/stress-activated protein kinases is an early response of cells upon exposure to DNA-damaging agents. JNK-mediated phosphorylation of c-Jun is currently understood to stimulate the transactivating potency of AP-1 (e.g., c-Jun/c-Fos; c-Jun/ATF-2), thereby increasing the expression of AP-1 target genes. Here we show that stimulation of JNK1 activity is not a general early response of cells exposed to genotoxic agents. Treatment of NIH 3T3 cells with UV light (UV-C) as well as with methyl methanesulfonate (MMS) caused activation of JNK1 and an increase in c-Jun protein and AP-1 binding activity, whereas antineoplastic drugs such as mafosfamide, mitomycin C, N-hydroxyethyl-N-chloroethylnitrosourea, and treosulfan did not elicit this response. The phosphatidylinositol 3-kinase inhibitor wortmannin specifically blocked the UV-stimulated activation of JNK1 but did not affect UV-driven activation of extracellular regulated kinase 2 (ERK2). To investigate the significance of JNK1 for transactivation of c-jun, we analyzed the effect of UV irradiation on c-jun expression under conditions of wortmannin-mediated inhibition of UV-induced stimulation of JNK1. Neither the UV-induced increase in c-jun mRNA, c-Jun protein, and AP-1 binding nor the activation of the collagenase and c-jun promoters was affected by wortmannin. In contrast, the mitogen-activated protein kinase/ERK kinase inhibitor PD98056, which blocked ERK2 but not JNK1 activation by UV irradiation, impaired UV-driven c-Jun protein induction and AP-1 binding. Based on the data, we suggest that JNK1 stimulation is not essential for transactivation of c-jun after UV exposure, whereas activation of ERK2 is required for UV-induced signaling leading to elevated c-jun expression.

Phosphorylation of the DNA repair protein APE/REF-1 by CKII affects redox regulation of AP-1

The DNA repair protein apurinic endonuclease (APE/Ref-1) exerts several physiological functions such as cleavage of apurinic/apyrimidinic sites and redox regulation of the transcription factor AP-1, whose activation is part of the cellular response to DNA damaging treatments. Here we demonstrate that APE/Ref-1 is phosphorylated by casein kinase II (CKII). This was shown for both the recombinant APE/Ref-1 protein (Km=0.55 mM) and for APE/Ref-1 expressed in COS cells. Phosphorylation of APE/Ref-1 did not alter the repair activity of the enzyme, whereas it stimulated its redox capability towards AP-1, thus promoting DNA binding activity of AP-1. Inhibition of CKII mediated phosphorylation of APE/Ref-1 blocked mutagen-stimulated increase in AP-1 binding. It also abrogated the induction of c-Jun protein and rendered cells more sensitive to induced DNA damage. Thus, phosphorylation of APE/Ref-1 appears to be involved in regulating the different physiological activities of the enzyme. CKII mediated phosphorylation of APE/Ref-1 and concomitant increase in AP-1 binding activity appears to be a novel mechanism of cellular stress response, forcing transcription of AP-1 target gene(s) the product(s) of which may exert protective function.

Probing the structure of the human Ca2+- and Zn2+-binding protein S100A3: spectroscopic investigations of its transition metal ion complexes, and three-dimensional structural model

A large-scale procedure was developed for the anaerobic purification of the human recombinant Ca2+- and Zn2+-binding protein S100A3 for spectroscopic studies. S100A3 eluted as a non-covalently bound dimer (20.8 kDa). It contained 7.5+/-0.1 free thiol groups/monomer, and bound Ca2+ with a Kd of approximately 4 mM, which corresponds to a tenfold increase in affinity compared to the aerobically purified protein. The transition metal ions Co2+, Zn2+ and Cd2+ were used as spectroscopic probes to investigate the role of the 10 cysteine residues per monomer S100A3 in metal binding. Spectrophotometric titrations suggest the formation of dinuclear thiolate-bridged clusters consisting of a Me2+(S(Cys))4 and a Me2+(S(Cys))3(N(His)) site as described for zinc finger proteins. A three-dimensional structural model of S100A3 was proposed on the basis of the NMR structure of the structurally related rabbit S100A6 protein, and taking into account the structural influence of cysteine residues.