The ribonucleotide reductases — A unique group of metalloenzymes essential for cell proliferation

Stability of the Herpesvirus Ribonucleotide Reductase-Inhibiting Nonapeptide YAGAVVNDL in Extracts of HSV-1-Infected Cells

The nonapeptide YAGAVVNDL has previously been shown to specifically inhibit ribonucleotide reductase (RR) induced by herpes simplex virus (HSV) and other herpesviruses. The stability of this peptide has been examined in extracts of HSV-infected cells. It was found to be rapidly modified to yield free tyrosine and the octapeptide AGAWNDL. Modification could be inhibited by several protease inhibitors, suggesting that it arises through cleavage of the amino-terminal tyrosine peptide bond. The implications of these results for the development of a therapeutically useful drug based on the nonapeptide are discussed.

Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis

Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, thereby threatening economic and dairy industries worldwide. Currently there is no effective drug or vaccine available against Cp. To identify new targets, we adopted a novel integrative strategy, which began with the prediction of the modelome (tridimensional protein structures for the proteome of an organism, generated through comparative modeling) for 15 previously sequenced C. pseudotuberculosis strains. This pan-modelomics approach identified a set of 331 conserved proteins having 95-100% intra-species sequence similarity. Next, we combined subtractive proteomics and modelomics to reveal a set of 10 Cp proteins, which may be essential for the bacteria. Of these, 4 proteins (tcsR, mtrA, nrdI, and ispH) were essential and non-host homologs (considering man, horse, cow and sheep as hosts) and satisfied all criteria of being putative targets. Additionally, we subjected these 4 proteins to virtual screening of a drug-like compound library. In all cases, molecules predicted to form favorable interactions and which showed high complementarity to the target were found among the top ranking compounds. The remaining 6 essential proteins (adk, gapA, glyA, fumC, gnd, and aspA) have homologs in the host proteomes. Their active site cavities were compared to the respective cavities in host proteins. We propose that some of these proteins can be selectively targeted using structure-based drug design approaches (SBDD). Our results facilitate the selection of C. pseudotuberculosis putative proteins for developing broad-spectrum novel drugs and vaccines. A few of the targets identified here have been validated in other microorganisms, suggesting that our modelome strategy is effective and can also be applicable to other pathogens.

Spectroscopic techniques and cyclic voltammetry with synthesis: manganese(II) coordination stability and its ligand field parameters effect on macrocyclic ligands

Manganese(II) macrocyclic complexes are prepared with different macrocyclic ligands, containing cyclic skeleton bearing organic components which have different chromospheres like N, O and S donor atoms and stereochemistry. Thus, six macrocyclic ligands, were prepared and their capacity to retain the manganese(II) ion in solid as well as in aqueous solution was determined and characterized by elemental analyses, molar conductance measurements, magnetic susceptibility measurements, mass, (1)H NMR, IR, electronic spectral and cyclic voltammetric studies. The electronic spectrum of this system showed a dependence that may be consistent with the formation of stable complexes and coordination behaviour of the ions. ESR spectra of all the complexes are recorded in solid as well as solution, which show the oxidation state of the manganese(II). Spin Hamiltonian manganese(II), which can be defined as the magnetic field vector (H): H = gBeta(e)HS + D[S(2)(z) - 35/12] + E[S(2)(z) - S(2)(y)] + ASI + (1/6)a [S(4)(x) + S(4)(y) + S(4)(z) - 707/16] + (1/180)F[(35S(2)(z) - 475)/(2S(2)(z) + 3255/10)] Significant distortion of the manganese(II) ion in observed geometry is evident from the angle subtended by the different membered chelate rings and the angles spanned by trans donor atoms octahedral geometry. Cyclic voltammetric studies indicate that complexes with all ligands undergoes one electron oxidation from manganese(II) to manganese(III) followed by a further oxidation to manganese(IV) at a significantly more positive potential.

The genome of Gryllus bimaculatus nudivirus indicates an ancient diversification of baculovirus-related nonoccluded nudiviruses of insects

The Gryllus bimaculatus nudivirus (GbNV) infects nymphs and adults of the cricket Gryllus bimaculatus (Orthoptera: Gryllidae). GbNV and other nudiviruses such as Heliothis zea nudivirus 1 (HzNV-1) and Oryctes rhinoceros nudivirus (OrNV) were previously called "nonoccluded baculoviruses" as they share some similar structural, genomic, and replication aspects with members of the family Baculoviridae. Their relationships to each other and to baculoviruses are elucidated by the sequence of the complete genome of GbNV, which is 96,944 bp, has an AT content of 72%, and potentially contains 98 predicted protein-coding open reading frames (ORFs). Forty-one ORFs of GbNV share sequence similarities with ORFs found in OrNV, HzNV-1, baculoviruses, and bacteria. Most notably, 15 GbNV ORFs are homologous to the baculovirus core genes, which are associated with transcription (lef-8, lef-9, lef-4, vlf-1, and lef-5), replication (dnapol), structural proteins (p74, pif-1, pif-2, pif-3, vp91, and odv-e56), and proteins of unknown function (38K, ac81, and 19kda). Homologues to these baculovirus core genes have been predicted in HzNV-1 as well. Six GbNV ORFs are homologous to nonconserved baculovirus genes dnaligase, helicase 2, rr1, rr2, iap-3, and desmoplakin. However, the remaining 57 ORFs revealed no homology or poor similarities to the current gene databases. No homologous repeat (hr) sequences but fourteen short direct repeat (dr) regions were detected in the GbNV genome. Gene content and sequence similarity suggest that the nudiviruses GbNV, HzNV-1, and OrNV form a monophyletic group of nonoccluded double-stranded DNA viruses, which separated from the baculovirus lineage before this radiated into dipteran-, hymenopteran-, and lepidopteran-specific clades of occluded nucleopolyhedroviruses and granuloviruses. The accumulated information on the GbNV genome suggests that nudiviruses form a highly diverse and phylogenetically ancient sister group of the baculoviruses, which have evolved in a variety of highly divergent host orders.

Complete genome sequence analysis of an iridovirus isolated from the orange-spotted grouper, Epinephelus coioides

Orange-spotted grouper iridovirus (OSGIV) was the causative agent of serious systemic diseases with high mortality in the cultured orange-spotted grouper, Epinephelus coioides. Here we report the complete genome sequence of OSGIV. The OSGIV genome consists of 112,636 bp with a G+C content of 54%. 121 putative open reading frames (ORF) were identified with coding capacities for polypeptides varying from 40 to 1168 amino acids. The majority of OSGIV shared homologies to other iridovirus genes. Phylogenetic analysis of the major capsid protein, ATPase, cytosine DNA methyl transferase and DNA polymerase indicated that OSGIV was closely related to infectious spleen and kidney necrosis virus (ISKNV) and rock bream iridovirus (RBIV), but differed from lymphocytisvirus and ranavirus. The determination of the genome of OSGIV will facilitate a better understanding of the molecular mechanism underlying the pathogenesis of the OSGIV and may provide useful information to develop diagnosis method and strategies to control outbreak of OSGIV.

Mixed-valent [FeIV(mu-O)(mu-carboxylato)2FeIII]3+ core

The symmetrically ligated complexes 1, 2, and 3 with a (mu-oxo)bis(mu-acetato)diferric core can be one-electron oxidized electrochemically or chemically with aminyl radical cations [*NR3][SbCl6] in acetonitrile yielding complexes which contain the mixed-valent [(mu-oxo)bis(mu-acetato)iron(IV)iron(III)]3+ core: [([9]aneN3)(2FeIII2)(mu-O)(mu-CH3CO2)2](ClO4)2 (1(ClO4)2), [(Me3[9]aneN3)(2FeIII2)(mu-O)(mu-CH3CO2)2](PF6)2 (2(PF6)(2)), and [(tpb)(2FeIII2)(mu-O)(mu-CH3CO2)2] (3) where ([9]aneN3) is the neutral triamine 1,4,7-triazacyclononane and (Me3[9]aneN3) is its tris-N-methylated derivative, and (tpb)(-) is the monoanion trispyrazolylborate. The asymmetrically ligated complex [(Me3[9]aneN3)FeIII(mu-O)(mu-CH3CO2)2FeIII(tpb)](PF6) (4(PF6)) and its one-electron oxidized form [4ox]2+ have also been prepared. Finally, the known heterodinuclear species [(Me3[9]aneN3)CrIII(mu-O)(mu-CH3CO2)2Fe([9]aneN3)](PF6)2 (5(PF6)(2)) can also be one-electron oxidized yielding [5ox]3+ containing an iron(IV) ion. The structure of 4(PF6).0.5CH3CN.0.25(C2H5)2O has been determined by X-ray crystallography and that of [5ox]2+ by Fe K-edge EXAFS-spectroscopy (Fe(IV)-O(oxo): 1.69(1) A; Fe(IV)-O(carboxylato) 1.93(3) A, Fe(IV)-N 2.00(2) A) contrasting the data for 5 (Fe(III)-O(oxo) 1.80 A; Fe(III)-O(carboxylato) 2.05 A, Fe-N 2.20 A). [5ox]2+ has an St = 1/2 ground state whereas all complexes containing the mixed-valent [FeIV(mu-O)(mu-CH3CO2)2FeIII]3+ core have an St = 3/2 ground state. Mössbauer spectra of the oxidized forms of complexes clearly show the presence of low spin FeIV ions (isomer shift approximately 0.02 mm s(-1), quadrupole splitting approximately 1.4 mm s(-1) at 80 K), whereas the high spin FeIII ion exhibits delta approximately 0.46 mm s(-1) and DeltaE(Q) approximately 0.5 mm s(-1). Mössbauer, EPR spectral and structural parameters have been calculated by density functional theoretical methods at the BP86 and B3LYP levels. The exchange coupling constant, J, for diiron complexes with the mixed-valent FeIV-FeIII core (H = -2J S1.S2; S(1) = 5/2; S2 = 1) has been calculated to be -88 cm(-1) (intramolecular antiferromagnetic coupling) and for the reduced diferric form of -75 cm(-1) in reasonable agreement with experiment (J = -120 cm(-1)).

Radiation inactivation of ribonucleotide reductase, an enzyme with a stable free radical

Herpes simplex virus ribonucleotide reductase (RR) is a tetrameric enzyme composed of two homodimers of large R1 and small R2 subunits with a tyrosyl free radical located on the small subunit. Irradiation of the holoenzyme yielded simple exponential decay curves and an estimated functional target size of 315 kDa. Western blot analysis of irradiated holoenzyme R1 and R2 yielded target sizes of 281 kDa and 57 kDa (approximately twice their expected size). Irradiation of free R1 and analysis by all methods yielded a single exponential decay with target sizes ranging from 128-153 kDa. For free R2, quantitation by enzyme activity and Western blot analyses yielded simple inactivation curves but considerably different target sizes of 223 kDa and 19 kDa, respectively; competition for radioligand binding in irradiated R2 subunits yielded two species, one with a target size of approximately 210 kDa and the other of approximately 20 kDa. These results are consistent with a model in which there is radiation energy transfer between the two monomers of both R1 and R2 only in the holoenzyme, a radiation-induced loss of free radical only in the isolated R2, and an alteration of the tertiary structure of R2.

Understanding the molecular mechanism of viral resistance to peptidomimetic inhibitors of ribonucleotide reductase

Herpes simplex virus (HSV) encodes a ribonucleotide reductase which provides high levels of deoxynucleotides necessary for replication of viral DNA in infected cells. The enzyme is composed of two distinct subunits, R1 and R2, whose association is required for enzymatic activity. Compounds that mimic the C-terminal amino acids of the HSV ribnucleotide reductase R2 subunit inhibit the enzyme by preventing the association of R1 and R2. Moderate resistance to one of these inhibitors, BILD 733, has been generated in cell culture. This resistance is the result of two point mutations in R1, P1090L and A1091S. Here we report on the binding of additional peptidomimetic inhibitors with altered functional groups to these mutants. This study has made it possible, in the absence of a crystal structure for this enzyme, to define the molecular mechanism by which these two mutations cause the observed resistance. Mutation of proline 1090 to leucine causes a conformational shift in the R1 inhibitor binding site. Mutation of alanine 1091 to serine weakens a specific binding interaction with the hydrophobic carboxy terminus of both R2 and inhibitors. Potential limitations on the degree of viral resistance possible by each resistance mechanism are discussed.

Ribonucleotide reductase in Bacillus subtilis--evidence for a Mn-dependent enzyme

The reduction of 2'-ribonucleotides to 2'-deoxyribonucleotides, a unique step in DNA formation, is catalyzed by ribonucleotide reductase (RRase), an allosterically regulated, cell cycle-dependent enzyme. This work reports a reversible impairment of DNA formation and ribonucleotide reduction upon manganese depletion in Bacillus subtilis demonstrated through in vivo labeling with necleic acid precursors and enzyme assays with ether-permeabilized cells. No deoxyadenosylcobalamin-dependent reduction of ribonucleotides was detected in the cytosol, and the properties of a partially purified enzyme fraction, i.e., sensitivity towards EDTA and hydroxyurea (HU), indicated a metal-dependent type of RRase. The enzyme was enriched by gel filtration on Superose 12 from glycerol- or fumarate-grown cells and submitted to Q-band electron paramagnetic resonance (EPR) spectroscopy for further characterization of the metal center. A distinct Mn(II) signal was obtained in both preparations characteristic of a protein-bound mangaenese in a mononuclear metal center with axial symmetry. The intensity of this Mn signal was not affected by addition of the radical scavenger HU (10 mM) but reduced in the presence of 2.5 mM EDTA. On the basis of these results, we suggest that Bacillus subtilis has a Mn-dependent ribonucleotide reductase.

Cloning, sequencing and expression of ribonucleotide reductase R2 from Trypanosoma brucei

Ribonucleotide reductase (RR) is an attractive drug target molecule. The gene of the R2 protein of Trypanosoma brucei RR (nrd B) has been cloned. It encodes a protein of 337 residues which shows about 60% identity with other eukaryotic R2 proteins. All residues which bind the iron center, the tyrosyl radical or are supposed to participate in the radical transfer are conserved in the trypanosomal protein sequence. Overexpression of the gene in E. coli resulted in 2-5 mg pure R2 protein from 100 ml bacterial cell culture. Northern blot analysis revealed a transcript of 1.85 kb in bloodstream and procyclic forms of the parasite.

Equilibrium and kinetic studies of iron(II) and iron(III) complexes of some alpha (N)-heterocyclic thiosemicarbazones. Reduction of the iron(III) complexes of 2-formylpyridine thiosemicarbazone and 2-acetylpyridine thiosemicarbazone by cellular thiol-like reducing agents

alpha (N)-heterocyclic thiosemicarbazones have been shown to possess antitumor properties in mammalian cells through the inhibition of DNA synthesis; the ability to provide the inhibitory action is probably due to coordination of iron. This paper deals with equilibrium and kinetic studies involving 2-formylpyridine thiosemicarbazone (HFPT) and 2-acetylpyridine thiosemicarbazone (HAPT) coordinated to Fe(II) and Fe(III) cations in aqueous solution. The formation constants of all species present in equilibrium were determined. Kinetic measurements of the reduction of the Fe(III) complex of both ligands by thiolic reducing agents, that can act as structural models of cellular thiols, i.e., N-acetyl-L-cysteine (ACCIS) and dithiothreitol (DTT), were carried out. The experimental data lead to a rate law of the type v = k1[A] + k2[A] [B], where [A] represents the concentration of the complex and [B] that of the reducing agent, indicating the coexistence of two reaction pathways. One pathway depends only on the complex concentration and occurs even in the absence of the reducing agent, and the other involves both the complex and ACCIS or DTT.

The relationship of intracellular iron chelation to the inhibition and regeneration of human ribonucleotide reductase

The depletion of cellular iron can lead to the inhibition of ribonucleotide reductase, preventing new DNA synthesis and hence inhibiting cell proliferation. Electron paramagnetic resonance (EPR) spectroscopy has been used to examine simultaneously for the first time the relationship between chelation of intracellular iron and the rate of removal and regeneration of the tyrosyl radical of ribonucleotide reductase within intact human leukemia K562 cells. The different physiochemical characteristics of relatively hydrophobic low molecular weight bidentate hydroxypyridinone chelators and the higher molecular weight hexadentate ferrioxamine have been exploited to elucidate these interactions further. The base-line concentration of EPR-detectable mononuclear nonheme iron complexes was 3.15 =/- 1.05 microM, rising on incubation with chelators more rapidly with hydroxypyridinones than with desferrioxamine. Hydroxypyridinones also removed the tyrosyl radical more rapidly, apparently as a consequence of depletion of the intracellular iron pools necessary to regenerate the active enzyme and compatible with their reportedly greater cell toxicity. The radical decay rate is consistent with previous models, suggesting that iron is spontaneously removed from mammalian ribonucleotide reductase. Upon removal of extracellular chelator the regeneration of the tyrosyl radical was significantly faster for hydroxypyridinones than for desferrioxamine, consistent with their differential effects on cell cycle synchronization.

Detection of a stable free radical in the B2 subunit of the manganese ribonucleotide reductase (Mn-RRase) of Corynebacterium ammoniagenes

Ribonucleotide reductases catalyze the irreversible reductive formation of 2'-deoxyribonucleotides required for DNA replication and cell proliferation, and a radical mechanism was assumed to be involved in this reaction. In order to search for a radical in the aerobic manganese ribonucleotide reductase (Mn-RRase) by electron paramagnetic resonance (EPR) the native metal-containing 100 kDa B2 subunit was deliberately prepared from the wild type strain Corynebacterium ammoniagenes ATCC 6872. Enrichment by 2'5'-ADP Sepharose 4B affinity chromatography, fast protein liquid chromatography (FPLC) with SuperoseTM12 and concentration by vacuum evaporation allowed for the first time the detection of a stable free radical by EPR spectroscopy at 77 K. The EPR spectrum exhibits an easily saturable doublet of 1.8 mT splitting and a line width of 1.3 mT at g = 2.0040. The EPR signal intensity showed a clear correlation with the enzymatic activity upon long-time storage at ambient temperature (294 K) and inactivation by the specific RRase inhibitor hydroxyurea (HU). This leads to the assumption of a protein-linked radical, with functional significance, in the metal-containing 100 kDa B2 subunit of the MnRRase of Corynebacterium ammoniagenes.

Reduction of the tyrosyl radical and the iron center in protein R2 of ribonucleotide reductase from mouse, herpes simplex virus and E. coli by p-alkoxyphenols

The rate of reduction of the tyrosyl radical in the small subunit of ribonucleotide reductase (protein R2) from E. coli, mouse, and herpes simplex virus (HSV-2) by a series of p-alkoxyphenols with different alkyl chains, have been studied by stopped-flow UV-vis and stopped-flow EPR spectroscopy. The reduction and release of iron in R2 by the inhibitors was followed using bathophenanthroline as chelator of Fe2+. p-Alkoxyphenols reduce the mouse R2 tyrosyl radical 1-2 orders of magnitude faster than the HSV-2 and E. coli radical. In contrast to E. coli, the iron center in R2 from mouse and HSV-2 is reduced by the inhibitors. For mouse R2, the rate of reduction of the tyrosyl radical increases in parallel with increasing alkyl chain length of the inhibitor, an observation which may be important for the design of new antiproliferative drugs.

The critical C-terminus of the small subunit of herpes simplex virus ribonucleotide reductase is mobile and conformationally similar to C-terminal peptides

The C-terminus of the small subunit of class I ribonucleotide reductases is essential for subunit association and enzymatic activity. 1H NMR analysis of the small subunit (2 x 38 kDa as a homodimer) of herpes simplex virus ribonucleotide reductase shows that this critical binding site is mobile and exposed in relation to the rest of the protein. Assignments of six C-terminal amino acids are made by comparing the TOCSY and NOESY spectra of the small subunit with the spectra of an identical protein truncated by seven amino acids at the C-terminus and the spectra of an analogous 15 amino acid peptide. The mobility of the C-terminus may be important for subunit recognition and could be general for other ribonucleotide reductases. The spectral comparisons also suggest that the six C-terminal amino acids of the small subunit and peptide are conformationally similar. This observation may be important for the design of inhibitors of ribonucleotide reductase subunit association.

D-mannitol, a specific hydroxyl free radical scavenger, reduces the developmental toxicity of hydroxyurea in rabbits

Hydroxyurea (HU) is a potent mammalian teratogen. Within 2-4 hours after maternal injection, HU causes 1) a rapid episode of embryonic cell death and 2) profound inhibition of embryonic DNA synthesis. A variety of antioxidants delays the onset of embryonic cell death and reduces the incidence of birth defects. Antioxidants do not block the inhibition of DNA synthesis, indicating that early embryonic cell death is not caused by inhibited DNA synthesis. We have suggested that some HU molecules may react within the embryo to produce H2O2 and subsequent free radicals, including the very reactive hydroxyl free radical. The free radicals could cause the early cell death; antioxidants are believed to terminate the aberrant free radical reactions resulting in lessened developmental toxicity. To investigate whether hydroxyl free radicals cause the early episode of cell death, pregnant New Zealand white rabbits were injected subcutaneously on gestational day 12 with a teratogenic dose of HU (650 mg/kg) in the presence or absence of 550 mg/kg of D-mannitol (Man), a specific scavenger of hydroxyl free radicals. Osmotic control rabbits received HU plus 550 mg/kg of xylose (Xyl, a nonactive aldose). At term, the teratologic effects of HU were ameliorated by Man as evidenced by decreased incidences of the expected limb malformations. Xyl exerted no demonstrable effect on HU teratogenesis. Histological examination of limb buds at 3-8 hours after maternal injection, showed that Man delayed the onset of HU-induced cell death by as much as 4 hours. Xyl had no effect. That Man acts within the embryo was shown by performing intracoelomic injections on alternate implantation sites with Man, Xyl, or saline followed by subcutaneous injection of the pregnant doe with HU. Embryos were harvested 3-8 hours later. Limb buds from saline- and Xyl-injected embryos exhibited the typical pattern of widespread HU-induced cell death at 3-4 hours, whereas Man-injected embryos did not exhibit cell death until 5-8 hours. These results are consistent with those reported for antioxidant-mediated amelioration of HU-induced developmental toxicity and with the hypothesis that hydroxyl free radicals are the proximate reactive species in HU-induced early embryonic cell death.

Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion

The Escherichia coli nrd operon contains the genes encoding the two subunits of ribonucleoside diphosphate reductase. The regulation of the nrd operon has been observed to be very complex. The specific binding of two proteins to the nrd regulatory region and expression of mutant nrd-lac fusions that do not bind these proteins are described. A partially purified protein from an E. coli cell extract was previously shown to bind to the promoter region and to regulate transcription of the nrd operon (C. K. Tuggle and J. A. Fuchs, J. Bacteriol. 172:1711-1718, 1990). We have purified this protein to homogeneity by affinity chromatography and identified it as the E. coli factor for inversion stimulation (Fis). Cu-phenanthroline footprinting experiments showed that Fis binds to a site centered 156 bp upstream of the start of nrd transcription. Mutants with deletion and site-directed mutations that do not bind Fis at this site have two- to threefold-lower expression of an nrd-lac fusion. The previously reported negative regulatory nature of this site (C. K. Tuggle and J. A. Fuchs, J. Bacteriol. 172:1711-1718, 1990) was found to be due to a change in polarity in the vectors used to construct promoter fusions. Two nine-base sequences with homology to the DnaA consensus binding sequence are located immediately upstream of the nrd putative -35 RNA polymerase binding site. Binding of DnaA to these sequences on DNA fragments containing the nrd promoter region was confirmed by in vitro Cu-phenanthroline footprinting. Footprinting experiments on fragments with each as well as both of the mutated 9-mers suggests cooperativity between the two sites in binding DnaA. Assay of in vivo expression from wild-type and DnaA box-mutated nrd promoter fragments fused to lacZ on single-copy plasmids indicates a positive effect of DnaA binding on expression of nrd.

Ribonucleotide reductases and their occurrence in microorganisms: a link to the RNA/DNA transition

The evolution of a deoxyribonucleotide synthesizing ribonucleotide reductase might have initiated the transition from the ancient RNA world into the prevailing DNA world. At least five classes of ribonucleotide reductases have evolved. The ancient enzyme has not been identified. A reconstruction of the first ribonucleotide reductase requires knowledge of contemporary enzymes and of microbial evolution. Experimental work on the former focuses on few organisms, whereas the latter is now well understood on the basis of ribosomal RNA sequences. Deoxyribonucleotide formation has not been investigated in many evolutionary important microorganisms. This review covers our knowledge on deoxyribonucleotide synthesis in microorganisms and the distribution of ribonucleotide reductases in nature. Ecological constraints on enzyme evolution and knowledge deficiencies emerge from complete coverage of the phylogenetic groups.

8-Azidoadenosine and ribonucleotide reductase

Inhibitors of ribonucleotide reductase are potential antiproliferative agents, since they deplete cells from DNA precursors. Substrate nucleoside analogues, carrying azido groups at the base moiety, are shown to have strong cytostatic properties, as measured by the inhibition of the incorporation of thymidine into DNA. One compound, 8-azidoadenosine, inhibits CDP reduction in cytosolic extracts from cancer cells. The corresponding diphosphate behaves as a substrate for ribonucleotide reductase while the triphosphate is an allosteric effector.

A possible new class of ribonucleotide reductase from Methanobacterium thermoautotrophicum

The ribonucleotide reductase from the strictly anaerobic methanogen Methanobacterium thermoautotrophicum has been partially purified by ion-exchange and gel-filtration chromatography. Its molecular weight is estimated to be 100,000 by the latter step. Unlike all previously studied ribonucleotide reductases, the enzyme does not employ dithiol compounds such as dithiothreitol as artificial electron donors in in vitro assays. Inhibition of the enzyme by S-adenosylmethionine, oxygen, and azide further distinguishes it from the Escherichia coli anaerobic enzyme, the iron- and manganese-containing, and the adenosylcobalamin-dependent enzymes. Our preliminary results suggest that this enzyme has an activation mechanism different from the known classes of ribonucleotide reductases.

Adenosylcobalamin and cob(II)alamin as prosthetic groups of 2-methyleneglutarate mutase from Clostridium barkeri

The ultraviolet/visible spectrum of the pure pink-orange 2-methyleneglutarate mutase from Clostridium barkeri between 300-600 nm showed the presence of cobalamins; notably the peaks at 470 and 528 nm were indicative of oxygen-stable cob(II)alamin and adenosylcobalamin (coenzyme B12), respectively. Using the absorption coefficients of the isosbestic points at 340, 393 and 489 nm, the total cobalamin content was estimated as 3.7 +/- 0.3 mol/mol tetrameric enzyme (m = 300 kDa). Denaturation with 8 M urea in the presence of 2 mM dithiothreitol followed by gel chromatography and renaturation afforded an inactive enzyme which contained 40-50% of the initially bound cobalamin. This preparation could be reactivated to 95-100% by addition of adenosylcobalamin. The cobalamins were removed to 85% from the mutase by denaturation with 8 M urea in the presence of 1 M cyanide (pH 12) with irreversible loss of activity. 2-Methyleneglutarate mutase was inactivated by incubation with aquo-, cyano- or methylcobalamin; up to 50% of the activity was recovered by addition of adenosylcobalamin. Upon incubation of the mutase with [5'-3H]adenosylcobalamin about 30% of the total cobalamin was exchanged by the tritium-labelled cofactor without loss of activity. During aerobic catalysis the enzyme became sensitive towards oxygen which was accompanied by loss of activity and formation of aquocobalamin from adenosylcobalamin. EPR spectroscopy demonstrated the presence of 0.8 mol base-on cob(II)alamin/mol enzyme. Upon addition of 2-methyleneglutarate a second EPR signal of about equal intensity at g = 2.13 arose. The question of whether the oxygen-stable cob(II)alamin participates in catalysis or its complex with the enzyme represents an inactive form is currently under investigation.

In situ studies on incorporation of nucleic acid precursors into Chlamydia trachomatis DNA

Chlamydiae are obligate intracellular bacteria that are dependent on eukaryotic host cells for ribonucleoside triphosphates. The purpose of the present study was to determine whether Chlamydia trachomatis obtains deoxyribonucleotides from the host cell. The study was aided by the finding that host and parasite DNA synthesis activity could be distinguished by their differing sensitivities to aphidicolin and norfloxacin. Results from isotope incorporation experiments indicated that any nucleobase or ribonucleoside that could serve as a precursor for host DNA synthesis could also be utilized by C. trachomatis for DNA replication. C. trachomatis utilized only those precursors which the host cell converted to the nucleotide level. Pyrimidine deoxyribonucleotides were efficient precursors for host DNA synthesis; however, they were not used by C. trachomatis. On the other hand, purine deoxyribonucleosides are rapidly catabolized by host cells, it is necessary to regulate their metabolism to determine whether they serve as direct precursors for C. trachomatis DNA synthesis. This was partially achieved by using a hypoxanthine-guanine phosphoribosyltransferase-negative cell line and using deoxycoformycin and 8-aminoguanosine as inhibitors of (deoxy)adenosine deaminase and purine nucleoside phosphorylase, respectively. The results indicated that purine deoxyribonucleosides are efficiently utilized for host cell DNA synthesis even if degradation pathways are inhibited and salvage to ribonucleotides is minimized. In sharp contrast, the purine deoxyribonucleosides were utilized by C. trachomatis as precursors for DNA synthesis only when host catabolic pathways and salvage reactions were intact. High-pressure liquid chromatographic analysis of nucleotide pools extracted from host cells pulsed with radiolabeled precursors suggests that infected cells transport and phosphorylate all deoxynucleosides as effectively as mock-infected control cultures. In aggregate, these results show that chlamydiae do not take up deoxyribonucleotides from the host cells.

Isolation and initial characterization of a series of Chlamydia trachomatis isolates selected for hydroxyurea resistance by a stepwise procedure

Chlamydiae are obligate intracellular bacteria that are dependent on eukaryotic host cells for ribonucleoside triphosphates but not deoxyribonucleotide triphosphates. Ribonucleotide reductase is the only enzyme known to catalyze the direct conversion of a ribonucleotide to a deoxyribonucleotide. Hydroxyurea inhibits ribonucleotide reductase by inactivating the tyrosine free radical present in the small subunit of the enzyme. In this report, we show that Chlamydia trachomatis growth is inhibited by hydroxyurea in both wild-type mouse L cells and hydroxyurea-resistant mouse L cells. Hydroxyurea was used as a selective agent in culture to isolate, by a stepwise procedure, a series of C. trachomatis isolates with increasing levels of resistance to the cytotoxic effects of the drug. One of the drug-resistant C. trachomatis isolates (L2HR-10.0) was studied in more detail. L2HR-10.0 retained its drug resistance phenotype even after passage in the absence of hydroxyurea for 10 growth cycles. In addition, L2HR-10.0 was cross resistant to guanazole, another inhibitor of ribonucleotide reductase. Results obtained from hydroxyurea inhibition studies using various host cell-parasite combinations indicated that inhibition of host cell and C. trachomatis DNA synthesis by hydroxyurea can occur but need not occur simultaneously. Crude extract prepared from highly purified C. trachomatis reticulate bodies was capable of reducing CDP to dCDP. The CDP reductase activity was not inhibited by monoclonal antibodies to the large and small subunits of mammalian ribonucleotide reductase, suggesting that the activity is chlamydia specific. The CDP reductase activity was inhibited by hydroxyurea. Crude extract prepared from drug-resistant L2HR-10.0 reticulate bodies contained an elevation in ribonucleotide reductase activity. In total, our results indicate that C. trachomatis obtains the precursors for DNA synthesis as ribonucleotides with subsequent conversion to deoxyribonucleotides catalyzed by a chlamydia-specific ribonucleotide reductase.

Ribonucleotide reductase in melanoma tissue. EPR detection in human amelanotic melanoma and quenching of the tyrosine radical by 4-hydroxyanisole

The characteristic EPR doublet of tyrosine radicals of the growth-regulating enzyme ribonucleotide reductase was detected in human melanoma tissue grown in nude mice. This was possible through the use of an amelanotic melanoma that does not exhibit disturbing EPR signals from melanin. The content of tyrosine radicals is higher in young tumor tissues than in older ones. The clinically applied antimelanotic drug, 4-hydroxyanisole, inhibits ribonucleotide reductase in Ehrlich ascites tumor cells as demonstrated by a pronounced quenching of tyrosine radicals (IC50 = 5 microM). In amelanotic melanoma tissue tyrosine radicals of the enzyme are also quenched by 4-hydroxyanisole in concentrations down to 50 microM. Thus, the inactivation of ribonucleotide reductase, which provides deoxyribonucleotides for DNA synthesis, may be a hitherto unexpected mechanism for the antitumor action of 4-hydroxyanisole.

Vaccinia virus encodes a protein with similarity to glutaredoxins

Recently, we have reported the complete nucleotide sequence of vaccinia virus (Goebel, S. J., Johnson, G. P., Perkus, M. E., Davis, S. W., Winslow, J. P., and Paoletti, E. 1990, Virology 179, 247-266). Approximately 2.2 kbp leftward of the large subunit of ribonucleotide reductase resides a 108-amino acid open reading frame, O2L (nt 62,851-62,528) with significant similarity to known glutaredoxins. The deduced amino acid sequence of open reading frame O2L is 28.7% identical to the yeast and Escherichia coli proteins and greater than 40% identical to various mammalian glutaredoxins. Similar patterns of hydrophobicity as well as alpha-helix and beta-sheet potentials suggest that O2L and the glutaredoxins share a similar secondary structure. Furthermore, a common function is inferred by the presence of a highly conserved redox-active site.

Deoxyribonucleotide metabolism in hydroxyurea-resistant V79 hamster cells

V79 hamster cells were made resistant against hydroxyurea by continuous culture at stepwise increasing drug concentrations. Two cell lines were cloned, resistant to 0.4 mM (V79/H0.4) and 4 mM (V79/H4) hydroxyurea, with a fivefold and a 20-fold increase in soluble ribonucleotide reductase activity. We investigated how the increased amount of enzyme affected the in situ activity of ribonucleotide reductase and deoxyribonucleotide metabolism, in particular substrate cycles between pyrimidine deoxyribonucleosides and their 5'-phosphates. The in situ activity of the reductase was only moderately elevated (1.3-fold in V79/H4 cells). In the fully resistant line, the steady-state level of dATP was increased fourfold, and that of dTTP twofold. These nucleotides are negative allosteric effectors of the reductase and we propose that the increased pools inhibit the enzyme and thereby maintain the in situ activity of the reductase at only a slightly increased level. The surplus deoxyribonucleotides was excreted from the cells as thymidine and deoxycytidine via substrate cycles. The data support and extend our previous model for the regulation of deoxyribonucleotide synthesis via the allosteric properties of ribonucleotide reductase and substrate cycles that link salvage and degradation of deoxyribonucleotides.

Purification and characterization of recombinant mouse and herpes simplex virus ribonucleotide reductase R2 subunit

Overexpression of recombinant mouse and herpes simplex virus ribonucleotide reductase small subunit (protein R2) has been obtained by using the T7 RNA polymerase expression system. Both proteins, which constitute about 30% of the soluble Escherichia coli proteins, have been purified to homogeneity by a rapid and simple procedure. At this stage, few of the molecules contain the iron-tyrosyl free-radical center necessary for activity; however, addition of ferrous iron and oxygen under controlled conditions resulted in a mouse R2 protein containing 0.8 radical and 2 irons per polypeptide chain. In this reaction, one oxygen molecule was needed to generate each tyrosyl radical. Both proteins had full enzymatic activity. EPR spectroscopy showed that iron-center/radical interactions are considerably stronger in both mouse and viral proteins than in E. coli protein R2. CD spectra showed that the bacterial protein contains 70% alpha-helical structure compared to only about 50% in the mouse and viral proteins. Light absorption spectra between 310 and 600 nm indicate close similarity of the mu-oxo-bridged binuclear iron centers in all three R2 proteins. Furthermore, the paramagnetically shifted iron ligand proton NMR resonances show that the antiferromagnetic coupling and ligand arrangement in the iron center are nearly identical in all three species.

Development of the "activated" high resolution 1H MR spectrum in murine T cells and B cells occurs in G1 phase of the cell cycle

T and B lymphocytes stimulated with mitogens develop 1H MR spectra characteristic of triglycerides in an isotropic environment. These distinctive signals, which are also observed in malignant cells, cannot be suppressed by compounds which inhibit progression through the cell cycle. Cellular proliferation is thus not essential for the development and maintenance of high resolution lipid spectra in activated cells.

EPR studies on the oxidation of hydroxyurea to paramagnetic compounds by oxyhemoglobin

N. Hydroxyurea forms methemoglobin from oxyhemoglobin with concomitant formation of the aminocarbonylaminooxyl radical H2N-CO-NHO., as detected with electron paramagnetic resonance spectroscopy (EPR). This radical could be detected for several hours in a low steady-state concentration. Approximately 1 hr after the reaction had been started, the EPR spectra of two additional paramagnetic intermediates could be detected at low temperature (77 degrees K), a low-spin ferric methemoglobin complex with hydroxyurea (MetHb-NHOH-CO-NH2) and the hemoglobin-nitric oxide adduct (Hb2(+)-NO). The intensities of their EPR spectra increased steadily over the range of more than 64 hr. The low-spin ferric methemoglobin complex was immediately formed when hydroxyurea was dissolved in a methemoglobin whereas the nitric oxide complex was possibly an oxidation product of the MetHb-hydroxyurea adduct. Its oxidative degradation is known to lead to the very toxic compounds nitric oxide and nitrogen dioxide which can therefore contribute to the toxic action of hydroxyurea.

Identification of a free radical and oxygen dependence of ribonucleotide reductase in yeast

Ribonucleotide reductase is a key enzyme for DNA biosynthesis. The enzymes isolated from animal and plant cells possess a stable tyrosyl free radical which is essential for catalysis. Fungal ribonucleotide reductases are little known; the partially characterized enzyme from yeast cells proved exceptionally shortlived, and a free radical could not as yet be demonstrated. We here show that a doublet ESR signal centered at g = 2.0046 can be measured below 60 degrees K in rapidly purified protein samples which is very similar to the ESR spectra of the tyrosine radicals present in other eukaryotic ribonucleotide reductases in structure, microwave saturation, and quenching by hydroxyurea. Because generation of these radicals requires oxygen, anaerobic yeast cultures were also studied. No change in ribonucleotide reductase was observed at 50 ppm residual oxygen in the gas phase, but cell proliferation ceased entirely under complete anaerobiosis.

Quenching of tyrosine radicals of M2 subunit from ribonucleotide reductase in tumor cells by different antitumor agents: an EPR study

The inhibition of ribonucleotide reductase (RR) of intact Ehrlich ascites tumor cells by different antitumor agents was compared using EPR spectroscopy. The inactivation of M2 subunit was measured via quenching of the functionally essential tyrosine radical. Inhibitors of different classes, for example, hydroxyurea, pyrogallol, and thiosemicarbazones, differ in their efficiency by three orders of magnitude. Most effective inhibition was found for isoquinoline-1-aldehyde-thiosemicarbazone (IQ-1) with an IC50 value of 0.18 microM. Inhibition of RR inside tumor cells is comparable with that reported for isolated enzymes.

New crystal forms of the small subunit of ribonucleotide reductase from Escherichia coli

The small subunit of ribonucleotide reductase from Escherichia coli has been crystallized in two new crystal forms. The form most suitable for X-ray analysis belongs to the orthorhombic space group P2(1)2(1)2(1). It has the cell dimensions 74.3 A, 85.5 A, 115.7 A and diffracts to about 2.1 A resolution. The asymmetric unit most probably contains one dimer. Absorption spectra of single crystals confirm that the crystals contain a binuclear iron center. Crystals of the iron-depleted apoenzyme have also been obtained.