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B Demple

Publications and source records attributed to B Demple.

At least 37 records · Page 2Linked to original sources
PubMed1999

Genetic responses against nitric oxide toxicity.

The threat of free radical damage is opposed by coordinated responses that modulate expression of sets of gene products. In mammalian cells, 12 proteins are induced by exposure to nitric oxide (NO) levels that are sub-toxic but exceed the level needed to activate guanylate cyclase. Heme oxygenase 1 (HO-1) synthesis increases substantially, due to a 30- to 70-fold increase in the level of HO-1 mRNA. HO-1 induction is cGMP-independent and occurs mainly through increased mRNA stability, which therefore indicates a new NO-signaling pathway. HO-1 induction contributes to dramatically increased NO resistance and, together with the other inducible functions, constitutes an adaptive resistance pathway that also defends against oxidants such as H2O2. In E. coli, an oxidative stress response, the soxRS regulon, is activated by direct exposure of E. coli to NO, or by NO generated in murine macrophages after phagocytosis of the bacteria. This response is governed by the SoxR protein, a homodimeric transcription factor (17-kDa subunits) containing [2Fe-2S] clusters essential for its activity. SoxR responds to superoxide stress through one-electron oxidation of the iron-sulfur centers, but such oxidation is not observed in reactions of NO with SoxR. Instead, NO nitrosylates the iron-sulfur centers of SoxR both in vitro and in intact cells, which yields a form of the protein with maximal transcriptional activity. Although nitrosylated SoxR is very stable in purified form, the spectroscopic signals for the nitrosylated iron-sulfur centers disappear rapidly in vivo, indicating an active process to reverse or eliminate them.

Animals↗
PubMed1999

Transcriptional regulation via redox-sensitive iron-sulphur centres in an oxidative stress response.

Genetic responses to oxidative stress are triggered by excessive levels of agents such as superoxide. The soxRS regulon of Escherichia coli includes at least a dozen oxidative-stress and antibiotic-resistance genes that are activated by the SoxS protein, the synthesis of which is controlled by the redox-sensing SoxR protein. SoxR is a homodimer of 17 kDa subunits, each of which contains a [2Fe-2S] cluster. Transcriptional activation by SoxR is controlled by the oxidation state of these metal centres. In the absence of oxidative stress, the [2Fe-2S] centres are in the reduced form and the protein is inactive, although it still binds the soxS promoter. Agents that generate superoxide in the cell (e.g. paraquat) cause rapid oxidation of the metal centres, which triggers the transcriptional activity of SoxR; removal of the oxidative stress is followed by rapid re-reduction of the [2Fe-2S] centres. This facile mechanism links oxidation state to control of protein activity and may be used widely to allow cells to respond to oxidative stress.

Allosteric Regulation↗
PubMed1998

Thiol-mediated disassembly and reassembly of [2Fe-2S] clusters in the redox-regulated transcription factor SoxR.

SoxR, a transcription factor containing [2Fe-2S] clusters, governs the cellular response to oxidative stress in Escherichia coli. The oxidation state of the iron-sulfur clusters regulates the SoxR transcriptional activity. When the reduced iron-sulfur clusters become oxidized ([2Fe-2S]2+ state), SoxR is activated to stimulate transcription of the soxS gene, whose product in turn switches on a group of genes encoding various proteins that defend against oxidative stress and antibiotics. A previous study showed that the oxidized [2Fe-2S] clusters of SoxR are destroyed by a free-radical-dependent process in vitro during aerobic exposure to the biological thiol glutathione. Here, we show that different thiols have differing effects on the SoxR [2Fe-2S] clusters. Like reduced glutathione, N-acetyl-L-cysteine, L-cysteine methyl ester, and L-cysteine ethyl ester disrupted the SoxR [2Fe-2S] clusters in aerobic solution. This disruption was blocked by L-cysteine, which was effective at concentrations 100-fold lower (1-10 microM) than the disrupting thiols (1 mM). In view of a previous observation that superoxide dismutase and catalase block the disruption process, this result suggests that L-cysteine may quench reactive SoxR or thiol intermediates involved in the cluster disruption reaction, the detailed mechanism of which remains unknown. In contrast, bifunctional thiols such as dithiothreitol or dithioerythritol promoted the aerobic assembly of the functional [2Fe-2S] clusters into apo-SoxR in the presence of Fe2+ and inorganic sulfide. The dithiol protein thioredoxin-A of E. coli acted catalytically in vitro in the presence of thioredoxin reductase and NADPH to promote [2Fe-2S] cluster assembly into apo-SoxR. The regulatory activity of SoxR in vivo, assessed by monitoring the paraquat-mediated induction of a soxS'::lacZ reporter fusion, was significantly lower in a strain lacking both thioredoxin-A and glutathione reductase, which maintains reduced glutaredoxins. Thus, cellular monothiols and dithiol proteins may contribute to SoxR regulation by affecting the disassembly and reassembly of the [2Fe-2S] clusters.

Apoproteins↗
PubMed1998

Dynamics of the interaction of human apurinic endonuclease (Ape1) with its substrate and product.

We investigated the interaction dynamics of human abasic endonuclease, the Ape1 protein (also called Ref1, Hap1, or Apex), with its DNA substrate and incised product using electrophoretic assays and site-specific amino acid substitutions. Changing aspartate 283 to alanine (D283A) left 10% residual activity, contrary to a previous report, but complementation of repair-deficient bacteria by the D283A Ape1 protein was consistent with its activity in vitro. The D308A, D283/D308A double mutant, and histidine 309 to asparagine proteins had 22, 1, and approximately 0. 02% of wild-type Ape1 activity, respectively. Despite this range of enzymatic activities, all the mutant proteins had near-wild-type binding affinity specific for DNA containing a synthetic abasic site. Thus, substrate recognition and cleavage are genetically separable steps. Both the wild-type and mutant Ape1 proteins bound strongly to the enzyme incision product, an incised abasic site, which suggested that Ape1 might exhibit product inhibition. The use of human DNA polymerase beta to increase Ape1 activity by eliminating the incision product supports this conclusion. Notably, the complexes of the D283A, D308A, and D283A/D308A double mutant proteins with both intact and incised abasic DNA were significantly more stable than complexes containing wild-type Ape1, which may contribute to the lower turnover numbers of the mutant enzymes. Wild-type Ape1 protein bound tightly to DNA containing a one-nucleotide gap but not to DNA with a nick, consistent with the proposal that substrate recognition by Ape1 involves a space bracketed by duplex DNA, rather than mere flexibility of the DNA.

Amino Acid Substitution↗
PubMed1998

Rapid dissociation of human apurinic endonuclease (Ape1) from incised DNA induced by magnesium.

Repair of apurinic/apyrimidinic (AP) sites is initiated by AP endonucleases, such as the human Ape1 protein (also called Hap1, Apex, and Ref1). This and related enzymes show strong dependence on divalent cations, particularly magnesium. Here we explore the role of this metal in different stages of the Ape1 reaction: substrate binding, cleavage, and product release. We examined DNA binding using an electrophoretic approach and DNA cleavage in single-turnover and steady-state reactions. Magnesium at low to moderate concentrations accelerated both substrate and product release by wild-type Ape1 protein. For a mutant Ape1 protein with an aspartate to alanine substitution at residue 308, substrate in preformed protein-DNA complexes was more efficiently cleaved before release in contrast to wild-type Ape1, whereas product release was accelerated dramatically. The magnesium dependence of steady-state AP endonuclease reactions was sigmoidal for both wild-type and the aspartate 308 to alanine protein but was not sigmoidal for an aspartate 283 to alanine derivative of Ape1. These results show that magnesium affects both DNA interactions with and phosphodiester cleavage by Ape1 and can change the rate-limiting step of the reaction. Structural studies will need to be interpreted in the context of these diverse effects of the metal.

Carbon-Oxygen Lyases↗
PubMed1998

Excision of C-4'-oxidized deoxyribose lesions from double-stranded DNA by human apurinic/apyrimidinic endonuclease (Ape1 protein) and DNA polymerase beta.

Oxidative damage to DNA deoxyribose generates oxidized abasic sites (OAS) that may constitute one-third of ionizing radiation damage. The antitumor drug bleomycin produces exclusively OAS in the form of C-4-keto-C-1-aldehydes in unbroken DNA strands and 3'-phosphoglycolate esters terminating strand breaks. We investigated whether two human DNA repair enzymes can mediate OAS excision in vitro: Ape1 protein (the main human abasic endonuclease (also called Hap1, Apex, or Ref1)) and DNA polymerase beta, which carries out both the abasic excision and the resynthesis steps. We used a duplex oligonucleotide substrate with one main target for bleomycin-induced damage. Ape1 catalyzed effective incision at the C-4-keto-C-1-aldehyde sites at a rate that may be only a few-fold lower than incision of hydrolytic abasic sites at the same location. Consistent with several previous studies, Ape1 hydrolyzed 3'-phosphoglycolates 25-fold more slowly than C-4-keto-C-1-aldehydes. DNA polymerase beta excised the 5'-terminal OAS formed by Ape1 incision at a rate similar to its removal of unmodified abasic residues. Polymerase beta-mediated excision of 5'-terminal OAS was stimulated by Ape1 as it is for unmodified abasic sites. Escherichia coli Fpg (MutM) protein also excised 5'-terminal OAS, but in our hands, the RecJ protein did not. These observations help define mammalian pathways of OAS repair, point to interactions that might coordinate functional steps, and suggest that still unknown factors may contribute to removal of 3'-phosphoglycolate esters.

Base Sequence↗
PubMed1998

Complex genetic response of human cells to sublethal levels of pure nitric oxide.

NO is a biologically generated free radical that serves diverse roles in mammalian cell signaling and immune-mediated cell killing. Because mammalian cells might be exposed to varying levels of NO, we tested for possible defense genes and proteins induced upon treatment of cells with sublethal fluxes of pure NO. Two-dimensional gel analysis was performed for human embryonic lung fibroblasts (IMR-90) exposed for 90 min to pure NO at approximately 280 nM/s, which revealed the reproducible induction of at least 12 proteins. Among these, a prominent polypeptide had Mr approximately 32,000, similar to the well-known oxidative stress protein heme oxygenase-1 (HO-1). Northern blot analysis of IMR-90 and HeLa cells demonstrated the NO-mediated induction of HO-1 mRNA up to 70-fold over the levels in untreated cells. HO-1 induction depended on the NO dose and subsequent expression time and was maximal 3-5 h after a 1-h exposure to NO at a constant flux of approximately 280 nM/s. The mRNA encoding a tyrosine/threonine phosphatase (CL100/MKP-1) was also NO inducible (approximately 20 fold), whereas there was no increase in expression of the mRNA encoding manganese-containing superoxide dismutase. Induction of HO-1 mRNA was independent of the guanylate cyclase signaling pathway; addition of the analogue 8-bromo-cyclic GMP did not induce the HO-1 transcript, and the soluble guanylate cyclase inhibitor LY-83583 did not block HO-1 induction by NO in IMR-90 cells. Luciferase reporter constructs containing up to 4.7 kb of DNA upstream of the HO-1 transcription start site showed < or = 2.5-fold induction in IMR-90 or HeLa cells exposed to NO. However, HO-1 mRNA was dramatically stabilized after exposure of IMR-90 cells to NO. Even a transient NO exposure produced elevated levels of HO-1 protein for > or = 10 h, whereas continuous low-level NO treatment (35 nM/s) maintained elevated HO-1 mRNA expression for > or = 8 h. These results reveal a complex mammalian response to NO that involves a new level of posttranscriptional control in response to this radical.

Cell Cycle Proteins↗
PubMed1998

The redox-regulated SoxR protein acts from a single DNA site as a repressor and an allosteric activator.

The SoxR protein of Escherichia coli responds to redox signals by activating the transcription of soxS, which encodes another transcription activator that directly stimulates oxidative stress genes. We show here that transcription of the soxR gene, which is positioned head-to-head with soxS in the chromosome, initiates in the intergenic region and is itself repressed by SoxR protein in in vitro transcription experiments. Analysis of single-copy operon fusions to soxR, combined with the results of Northern blotting experiments, verified this regulation and the transcription start site in vivo. The structure of the overlapping promoters is such that the single SoxR-binding site is located in the -10/-35 spacer of the soxS promoter, but just downstream of the -10 element of the soxR promoter. Activated and non-activated SoxR bind this site equally well, exerting nearly constant repression of soxR; activated SoxR simultaneously stimulates the soxS promoter >/=30-fold. The functional soxR promoter depresses soxS transcription when SoxR is not activated and enhances soxS transcription when SoxR is activated, as shown by comparing the expression of soxS'::lacZ fusions with and without the soxR -35 element (induction ratio only approximately 7-fold). SoxR thus represents a highly polar, redox-regulated transcriptional switch that maximizes the change in expression of soxS.

Allosteric Regulation↗
PubMed1998

A bridge to control.

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Amino Acid Substitution↗
PubMed1997

NF kappa B-independent transcriptional induction of the human manganous superoxide dismutase gene.

Numerous conditions induce expression of manganese-containing superoxide dismutase (MnSOD) in mammalian cells. The reported inducers of MnSOD are all agents that activate two transcription factors, AP-1 and NF kappa B, but several reports have suggested that MnSOD induction relies solely on NF kappa B. We investigated the contribution of the individual transcription factors by using antioxidants and metal chelators to modulate MnSOD transcriptional activation in response to phorbol esters or hydrogen peroxide. The results indicate substantial transcriptional induction of the MnSOD gene independent of NF kappa B. The metal chelator and antioxidant pyrrolidine dithiocarbamate (PDTC) at 60 or 100 microM induced the MnSOD transcript in HeLa cells while diminishing expression of the NF kappa B-responsive transcript I kappa B-alpha. Induction of the MnSOD mRNA by phorbol-12-myristate-13-acetate (PMA) was only slightly diminished in the presence of PDTC, which in contrast virtually eliminated induction of the NF kappa B-dependent transcript I kappa B-alpha by PMA. MnSOD RNA induction by H2O2 was only approximately 1.5-fold, compared to a ca. 3-fold activation of I kappa B-alpha expression. Two other antioxidants, N-acetyl-L-cysteine and butylated hydroxyanisole, failed to block induction of the MnSOD transcript by PMA, which is consistent with a role for AP-1. In vitro DNA binding studies confirmed strong AP-1 activation under conditions where NF kappa B is blocked but the MnSOD transcript is strongly induced (e.g., PMA treatment in the presence of PDTC).

Antioxidants↗
PubMed1997

In vivo kinetics of a redox-regulated transcriptional switch.

SoxR is a transcription activator governing a cellular response to superoxide and nitric oxide in Escherichia coli. SoxR protein is a homodimer, and each monomer has a redox-active [2Fe-2S] cluster. Oxidation and reduction of the [2Fe-2S] clusters can reversibly activate and inactivate SoxR transcriptional activity. Here, we use electron paramagnetic resonance spectroscopy to follow the redox-switching process of SoxR protein in vivo. SoxR [2Fe-2S] clusters were in the fully reduced state during normal aerobic growth, but were completely oxidized after only 2-min aerobic exposure of the cells to superoxide-generating agents such as paraquat. The oxidized SoxR [2Fe-2S] clusters were rapidly re-reduced in vivo once the oxidative stress was removed. The in vivo kinetics of SoxR [2Fe-2S] cluster oxidation and reduction exactly paralleled the increase and decrease of transcription of soxS, the target gene for SoxR. The kinetic analysis also revealed that an oxidative stress-linked decrease in soxS mRNA stability contributes to the rapid attainment of a new steady state after SoxR activation. Such a redox stress-related change in soxS mRNA stability may represent a new level of biological control.

Bacterial Proteins↗
PubMed1997

Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway.

Mutagenic abasic (AP) sites are generated directly by DNA-damaging agents or by DNA glycosylases acting in base excision repair. AP sites are corrected via incision by AP endonucleases, removal of deoxyribose 5-phosphate, repair synthesis, and ligation. Mammalian DNA polymerase beta (Polbeta) carries out most base excision repair synthesis and also can excise deoxyribose 5-phosphate after AP endonuclease incision. Yeast two-hybrid analysis now indicates protein-protein contact between Polbeta and human AP endonuclease (Ape protein). In vitro, binding of Ape protein to uncleaved AP sites loads Polbeta into a ternary complex with Ape and the AP-DNA. After incision by Ape, only Polbeta exhibits stable DNA binding. Kinetic experiments indicated that Ape accelerates the excision of 5'-terminal deoxyribose 5-phosphate by Polbeta. Thus, the two central players of the base excision repair pathway are coordinated in sequential reactions.

DNA Polymerase I↗
PubMed1997

Cysteine-to-alanine replacements in the Escherichia coli SoxR protein and the role of the [2Fe-2S] centers in transcriptional activation.

The Escherichia coli soxRS regulon activates oxidative stress and antibiotic resistance genes in two transcriptional stages. SoxR protein becomes activated in cells exposed to excess superoxide or nitric oxide and then stimulates transcription of the soxS gene, whose product in turn activates>/=10 regulon promoters. Purified SoxR protein is a homodimer containing a pair of [2Fe-2S] centers essential for soxS transcription in vitro . The [2Fe-2S] centers are thought to be anchored by a C-terminal cluster of four cysteine residues in SoxR. Here we analyze mutant SoxR derivatives with individual cysteines replaced by alanine residues (Cys-->Ala). The mutant proteins in cell-free extracts bound the soxS promoter with wild-type affinity, but upon purification lacked Fe or detectable transcriptional activity for soxS in vitro . Electron paramagnetic resonance measurements in vivo indicated that the Cys-->Ala proteins lacked the [2Fe-2S] centers seen for wild-type SoxR. The Cys-->Ala mutant proteins failed to activate soxS expression in vivo in response to paraquat, a superoxide- generating agent. However, when expressed to approximately 5% of the cell protein, the Cys-->Ala derivatives increased basal soxS transcription 2-4-fold. Overexpression of the Cys119-->Ala mutant protein strongly interfered with soxS activation by wild-type SoxR in response to paraquat. These studies demonstrate the essential role of the [2Fe-2S] centers for SoxR activation in vivo ; the data may also indicate oxidant-independent mechanisms of transcriptional activation by SoxR.

Alanine↗
PubMed1997

Spacing of promoter elements regulates the basal expression of the soxS gene and converts SoxR from a transcriptional activator into a repressor.

SoxR protein of Escherichia coli governs a global response against superoxide-generating agents (such as paraquat) or nitric oxide, and provides broad antibiotic resistance. A redox signal activates SoxR post-translationally to trigger transcription of a second regulatory gene, soxS. Activated and non-activated SoxR bind the soxS promoter with the same high affinity, but only the activated protein stimulates soxS transcription. SoxR acts by an unusual mechanism of positive control: the protein binds the soxS promoter between near-consensus -10 and -35 elements that are separated by an unusually long 19 bp (versus the optimal 17 bp). We have constructed and analyzed site-specific deletions that alter the promoter element spacing. Reducing the spacer length to 16-18 bp dramatically elevated basal expression of soxS in vivo and in vitro, and nearly eliminated additional activation by SoxR in response to paraquat. More strikingly, shortening the spacer converted SoxR from an activator into a repressor regardless of paraquat treatment. Gel mobility-shift assays show that repression by SoxR of the promoters with 17 and 16 bp spacers is due to interference with binding by RNA polymerase. Thus, activated SoxR remodels the unusual configuration of the wild-type soxS promoter into a highly active form, probably by compensating for the suboptimal distance between the -10 and the -35 elements.

Bacterial Proteins↗
PubMed1997

Abasic site binding by the human apurinic endonuclease, Ape, and determination of the DNA contact sites.

The mutagenic and lethal effects of abasic sites in DNA are averted by repair initiated by 'class II' apurinic (AP) endonucleases, which cleave immediately 5'to abasic sites. We examined substrate binding by the human AP endonuclease, Ape protein (also called Hap1, Apex or Ref-1). In electrophoretic mobility-shift experiments, Ape bound synthetic DNA substrates containing single AP sites or tetrahydrofuran (F) residues. No complexes were detected with single-stranded substrates or unmodified duplex DNA. In EDTA, the concentration of Ape required to shift 50% of duplex F-DNA was approximately 50 nM, while the addition of 10 mM MgCl2 nearly eliminated detectable F-DNA@Ape complexes. Filter-binding studies demonstrated a half-life of approximately 50 s at 0 degrees C for F-DNA@Ape complexes in the presence of EDTA, and <15 s after the addition of Mg2+. The DNA recovered from F-DNA@Ape complexes was intact but was rapidly cleaved upon addition of Mg2+, which suggests that these protein-DNA complexes are on the catalytic pathway for incision. Methylation and ethylation interference experiments identified DNA contacts critical for Ape binding, and Cu-1, 10-phenanthroline footprinting suggested an Ape-induced structural distortion at the abasic site prior to cleavage.

Binding Sites↗
PubMed1997

Redox signal transduction: mutations shifting [2Fe-2S] centers of the SoxR sensor-regulator to the oxidized form.

SoxR is a [2Fe-2S] transcription factor triggered by oxidative stress and activated in vitro by one-electron oxidation or assembly of the iron-sulfur centers. To distinguish which mechanism operates in cells, we studied constitutively active SoxR (SoxRc) proteins. Three SoxRc proteins contained [2Fe-2S] centers required for in vitro transcription and, like wild-type SoxR, were inactivated by chemical reduction. However, in vivo spectroscopy showed that even without oxidative stress, the three SoxRc proteins failed to accumulate with reduced [2Fe-2S] (< or = 4% compared to > or = 40% for wild type). One SoxRc protein had a redox potential 65 mV lower than wild type, consistent with its accumulation in the oxidized (activated) form in vivo. These results link in vitro and in vivo approaches showing novel redox regulation that couples an iron-sulfur oxidation state to promoter activation.

Aerobiosis↗
PubMed1997

Study of redox-regulated transcription factors in prokaryotes.

Several prokaryotic regulatory proteins that respond to changes in oxygen tension or the presence of oxidative agents have now been identified. The Fnr protein governs the expression of numerous genes during anaerobic growth, both as a transcriptional activator and as a repressor. OxyR protein responds to cellular exposure to H2O2 to stimulate transcription of several defense proteins. SoxR protein is triggered by superoxide or nitric oxide to activate a multigene regulon for antioxidant defense and antibiotic resistance. Each of these proteins has been purified and characterized for DNA binding and transcriptional activity in vitro. Fnr, OxyR, and SoxR all seem to respond directly to redox signals generated in the cell, and their in vitro properties support this view: Fnr has an oxygen-sensitive [4Fe-4S] center essential for DNA binding; OxyR may be activated via oxidation of a key cysteine residue; and SoxR activation depends on redox-sensitive [2Fe-2S] centers. Basic methods for genetic and biochemical analysis in these systems are presented, with emphasis on detailed methods for SoxR that illustrate general approaches for all the systems.

Bacteria↗