Substrate specificity of ultraviolet DNA endonuclease (UVDE/Uve1p) from Schizosaccharomyces pombe

Schizosaccharomyces pombe ultraviolet DNA endonuclease (UVDE or Uve1p) has been shown to cleave 5' to UV light-induced cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts (6-4PP). This endonuclease is believed to function in the initial step in an alternative excision repair pathway for the removal of DNA damage caused by exposure to UV light. An active truncated form of this protein, Delta228-Uve1p, has been successfully overexpressed, affinity purified and partially characterized. In the present study we present data from a detailed substrate specificity trial. We have determined that the substrate range of Uve1p is much greater than was originally believed. We demonstrate that this DNA damage repair protein is capable of recognizing an array of UV-induced DNA photoproducts (cis-syn-, trans-syn I- and trans-syn II CPDs, 6-4PP and Dewar isomers) that cause varying degrees of distortion in a duplex DNA molecule. We also demonstrate that Uve1p recognizes non-UV-induced DNA damage, such as platinum-DNA GG diadducts, uracil, dihydrouracil and abasic sites. This is the first time that a single DNA repair endonuclease with the ability to recognize such a diverse range of lesions has been described. This study suggests that Uve1p and the alternative excision repair pathway may participate broadly in the repair of DNA damage.

Differentiation of isomeric photomodified oligodeoxynucleotides by fragmentation of ions produced by matrix-assisted laser desorption ionization and electrospray ionization

UV irradiation of oligodeoxynucleotides at 254 nm generates several different types of DNA photoproducts, including cis-syn cyclobutane pyrimidine dimers, pyrimidine[6-4] pyrimidone photoproducts and their Dewar valence isomers, and thymine-adenine photoproducts (TA*). Studies of photoproducts in oligodeoxynucleotides require the development of suitable structure determination methods such as mass spectrometry. In an earlier study (Vollmer et al. Int. J. Mass Spectrom. Ion Processes 1997, 165/166, 487-496), we showed that fast atom bombardment and tandem sector mass spectrometry can be used to locate the site of photomodification and identify most of the photoproducts of d(TATTAT). One goal of the present research was to expand the method to the more sensitive electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) methods. A second goal was to test the generality of the methods by investigating not only the photoproducts of d(TATTAT) but also those of three other oligodeoxynucleotides, d(GTATTAT), d(GGCTATAA), and d(AATTAA). The photoproducts of these sequences were separated by HPLC and gave characteristic fragment ions in postsource decompositions of MALDI-produced ions and collisionally activated decompositions of ESI-produced ions.

Contact hypersensitivity to mercury in amalgam restorations may mimic oral lichen planus

Oral lichenoid lesions caused by hypersensitivity to mercury in amalgam fillings may mimic oral lichen planus on clinical and histologic examination. A positive patch test reaction to more than one mercurial allergen increases confidence in the diagnosis and justifies the removal and replacement of all amalgam fillings with those made of other materials. A complete remission may be expected about 3 months after the last amalgam filling is removed.

Receptors for the 5-oxo class of eicosanoids in neutrophils

5-Hydroxy- and 5-oxo-eicosatetraenoate (5-HETE and 5-oxoETE) activate polymorphonuclear neutrophils (PMNs) through a common, receptor-like recognition system. To define this system, we examined the interaction of these eicosanoids with human PMNs. PMNs esterified 5-[3H]HETE to glycerolipids at 37 and 4 degreesC. At 37 but not 4 degreesC, the cells also hydroxylated the label to 5, 20-[3H]diHETE. The acyl:CoA synthetase blocker, triacsin C, inhibited esterification but also led to an increase in the hydroxylation of the label. PMNs processed 5-[3H]oxoETE through the same pathways but only or principally after reducing it to 5-[3H]HETE (37 or 4 degreesC). In the presence of these varying metabolic reactions, PMNs (37 or 4 degreesC; +/- triacsin C) could not be shown to receptor bind either radiolabel. Plasma membranes isolated from PMNs esterified but unlike whole cells did not reduce or hydroxylate 5-[3H]oxoETE. Triacsin C blocked esterification, thereby rendering the membranes unable to metabolize this radiolabel. Indeed, triacsin C-treated membranes bound (Kd = 3.8 nM) 5-[3H]oxoETE specifically and reversibly to 86 pmol of sites per 25 micrograms of membrane protein. 5-OxoETE, 5-HETE, and 5,15-diHETE displaced this binding at concentrations correlating with their potency in eliciting PMN Ca2+ transients. GTP and GTPgammaS, but not ATP or ATPgammaS, also reduced 5-[3H]oxoETE binding, whereas 15-HETE, leukotriene B4, platelet-activating factor, IL-8, C5a, and N-formyl-Met-Leu-Phe lacked this effect. We conclude that PMNs and their plasma membranes use an acyl:CoA synthetase-dependent route to esterify 5-HETE and 5-oxoETE into lipids. Blockade of the synthetase uncovers cryptic plasmalemma sites that bind 5-oxoETE with exquisite specificity. These sites apparently mediate responses to the 5-oxo class of eicosanoids and are likely members of the serpentine superfamily of G protein-linked receptors.

Contact dermatitis from polyvinyl chloride identification bands

One case of allergic contact dermatitis caused by polyvinyl chloride identification bands is reported. Patch tests in this case were positive for three of four bands tested, resorcinol monobenzoate, and benzoyl peroxide. Manufacturers could not confirm the presence of resorcinol monobenzoate and benzoyl peroxide in their respective bands. It is concluded that the patient's reaction was allergic and due to an unknown chemical(s) in the bands. Additives may comprise a significant portion of polyvinyl chloride bands. These components may be leachable, and thus lead to contact sensitization with subsequent allergy. Although patch testing is an excellent first step in determining the offending allergen, specialized chemical analysis may be required for exact identification.

Proton MR spectroscopy of pediatric brain tumors

Primary central nervous system tumors are the most common solid tumors in children. Their overall frequency is second only to that of leukemia. Many brain tumors in children are relatively benign and can be successfully treated with surgery or radiation therapy, but progress in treating the malignant forms of these neoplasms lags behind that for leukemias and other solid tumors. This article discusses how MR spectroscopy is used to manage the individualized treatment of children with brain tumors.

Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA

The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments. Structures of both sequences were derived from NOE restrained molecular dynamics/simulated annealing calculations using a fixed outer layer of water and an inner dynamic layer of water with sodium counterions. The resulting structures reveal a subtle distortion to the phosphodiester backbone in the dimer-containing sequence which includes a BII phosphate at the T9pA10 junction immediately 3' to the dimer. The BII phosphate, established experimentally by analysis of the 31P chemical shifts and interpretation of the 3JP-H3' values using an optimized Karplus relationship, enables the DNA helix to accommodate the dimer by destacking the base 3' to the dimer. Furthermore, the structures provide explanations for the unusually shifted T8-N3H imino, A16-H2 and T8-Me proton resonances and T9pA10 (31)P NMR resonance and are consistent with bending, unwinding, and thermodynamic data. The implications of the structural data for the mechanism by which cis-syn dimers are recognized by repair enzymes and bypassed by DNA polymerases are also discussed.

The ability of a variety of polymerases to synthesize past site-specific cis-syn, trans-syn-II, (6-4), and Dewar photoproducts of thymidylyl-(3'-->5')-thymidine

The role of photoproduct structure, 3' --> 5' exonuclease activity, and processivity on polynucleotide synthesis past photoproducts of thymidylyl-(3' --> 5')-thymidine was investigated. Both Moloney murine leukemia virus reverse transcriptase and 3' --> 5' exonuclease-deficient (exo-) Vent polymerase were blocked by all photoproducts, whereas Taq polymerase could slowly bypass the cis-syn dimer. T7 RNA polymerase was able to bypass all the photoproducts in the order cis-syn > Dewar > (6-4) > trans-syn-II. Klenow fragment could not bypass any of the photoproducts, but an exo- mutant could bypass the cis-syn dimer to a greater extent than the others. Likewise T7 DNA polymerase, composed of the T7 gene 5 protein and Escherichia coli thioredoxin, was blocked by all the photoproducts, but the exo- mutant Sequenase 2.0 was able to bypass them all in the order cis-syn > Dewar > trans-syn-II > (6-4). No bypass occurred with an exo- gene 5 protein in the absence of the thioredoxin processivity factor. Bypass of the cis-syn and trans-syn-II products by Sequenase 2.0 was essentially non-mutagenic, whereas about 20% dTMP was inserted opposite the 5'-T of the Dewar photoproduct. A mechanism involving a transient abasic site is proposed to account for the preferential incorporation of dAMP opposite the 3'-T of the photoproducts.

Thermodynamic and base-pairing studies of matched and mismatched DNA dodecamer duplexes containing cis-syn, (6-4) and Dewar photoproducts of TT

Cis-syn dimers, (6-4) products and their Dewar valence isomers are the major photoproducts of DNA and have different mutagenic properties and rates of repair. To begin to understand the physical basis for these differences, the thermal stability and base pairing properties of the corresponding photoproducts of the TT site in d(GAGTATTATGAG) were investigated. The (6-4) and Dewar products destabilize the duplex form by approximately 6 kcal/mol of free energy at 37 degreesC relative to the parent, whereas a cis-syn dimer only destabilizes the duplex form by 1.5 kcal/mol. Duplexes with G opposite the 3'-T of the (6-4) and Dewar products are more stable than those with A by approximately 0.4 kcal/mol, whereas the cis-syn dimer prefers A over G by 0.7 kcal/mol. Proton NMR suggests that wobble base pairing takes place between the 3'-T of the cis-syn dimer and an opposed G, whereas there is no evidence of significant H-bonding between these two bases in the (6-4) product. The thermodynamic and H-bonding data for the (6-4) product are consistent with a 4 nt interior loop structure which may facilitate flipping of the photoproduct in and out of the helix.

Structure and fragmentation mechanisms of isomeric T-rich oligodeoxynucleotides: a comparison of four tandem mass spectrometric methods

Understanding the product-ion spectra of T-rich tetradeoxynucleotides is a starting point in the development of a mass spectrometric scheme to determine the mutagenicity of individual types of DNA damage. We obtained product-ion spectra for electrospray-produced ions that were activated in the ion source (electrospray ionization-source collision-activated-dissociation) and by high-energy collisions in the MS/MS mode of a four-sector instrument. We also activated singly and doubly charged ions by low-energy collisions in an ion-trap mass spectrometer and investigated post source decompositions of matrix-assisted laser desorbed ions in a time-of-flight mass spectrometer. The various methods of extracting structural information give remarkably consistent results. The difference in the relative abundances of wn and dn ions of the singly charged oligonucleotides and the formation of [a3-B3] ions, where B3 is the base on the third position, are effective for identification and distinction of pairs of isomeric tetranucleotides. A sufficient number of tetramers and pentamers were studied to enable us to propose a charge-remote mechanism for the formation of site-specific [an-Bn] ion.

Template-directed photoligation of oligodeoxyribonucleotides via 4-thiothymidine

Non-enzymatic, template-directed ligation of oligonucleotides in aqueous solution has been of great interest because of its potential synthetic and biomedical utility and implications for the origin of life. Though there are many methods for template-directed chemical ligation of oligonucleotides, there are only three reported photochemical methods. In the first report, template-directed photoligation was effected by cyclobutane dimer formation between the 5'- and 3'-terminal thymidines of two oligonucleotides with >290 nm light, which also damages DNA itself. To make the photochemistry of native DNA more selective, we have replaced the thymidine at the 5'-end of one oligonucleotide with 4-thiothymidine (s4T) and show that it photoreacts at 366 nm with a T at the 3'-endof another oligonucleotide in the presence of a complementary template. When a single mismatch is introduced opposite either the s4T or its adjoining T, the ligation efficiency drops by a factor of five or more. We also show that by linking the two ends of the oligonucleotides together, photoligation can be used to form circular DNA molecules and to 'photopadlock' circular DNA templates. Thus, s4T-mediated photo-ligation may have applications to phototriggered antisense-based or antigene-based genetic tools, diagnostic agents and drugs, especially for those situations in which chemical or enzyme-mediated ligation isundesirable or impossible, for example inside a cell.

Bypass of a site-specific cis-Syn thymine dimer in an SV40 vector during in vitro replication by HeLa and XPV cell-free extracts

The key step in skin cancer induction by UV light is thought to be the mutagenic DNA synthesis past a DNA photoproduct in a proto-oncogene or tumor suppressor gene. To investigate this critical step, we have constructed an SV40 vector containing a cis-syn thymine dimer, the major DNA photoproduct induced by UVB light, within an AseI site at a location that would initially be replicated by leading strand synthesis. When the dimer-containing SV40 vector was incubated with cell-free HeLa extracts in the presence of TAg, and then digested with AseI, a 2325 bp fragment corresponding to inhibition of cleavage at the dimer site was observed, suggesting that the dimer had terminated synthesis and/or had been bypassed. When the reaction was limited to one round of replication and the products of restriction enzyme digestion were examined by denaturing gel electrophoresis, bands corresponding to both termination and bypass were observed in roughly a one-to-one ratio. Whereas increasing the dNTP concentration from 10 microM to 1 mM increased the ratio of bypass to termination from 0.6 to 2.6, it had no effect on the site of termination, which occurred exclusively one nucleotide before the dimer. Experiments in which dGTP was held constant at 25 microM and various combinations of the remaining nucleotides were raised from 25 microM to 1 mM showed substantial increases in the bypass-to-termination ratio, with the greatest effect seen for raising all three nucleotides to 1 mM. Replication by primary fibroblast XPV extracts was also investigated and found to be greatly stimulated by rhRPA, whereas the stimulatory effect for HeLa cell extracts was variable. In the presence of rhRPA, the XPV extracts were also found to bypass the cis-syn dimer, which contrasts with a recent report that could not detect dimer bypass in SV40 transformed XPV extracts in the absence of added replication factors [Cordeiro-Stone, M., et al. (1997) J. Biol. Chem. 272, 13945-13954].

North American Contact Dermatitis Group patch test results for the detection of delayed-type hypersensitivity to topical allergens

BACKGROUND

Allergic contact dermatitis is a significant cause of cutaneous disease affecting many individuals. Patch testing, when used properly, often provides support for the diagnosis of allergic contact dermatitis.

OBJECTIVE

This article reports patch testing results from July 1, 1994, to June 30, 1996, by the North American Contact Dermatitis Group (NACDG).

METHODS

Patients evaluated in our patch test clinics were tested with the same screening series of allergens by the use of a standardized patch testing technique. The data from these patients were recorded on a standard computer entry form and analyzed.

RESULTS

Forty-nine allergens were tested on 3120 patients. Budesonide was added to the series in July 1995 and tested on 1678 patients. Of these patients, 66.5% had positive allergic patch test reactions, and 57% had at least one allergic reaction that was felt to be clinically relevant to the present or past dermatitis. The 20 screening allergens commercially available to United States dermatologists in the Allergen Patch Test Kit, accounted for only 54.1% of the patients with positive allergic reactions. The additional 30 allergens on the NACDG screening series accounted for 47% of patients with positive allergic reactions. Had the Allergen Patch Test Kit alone been used, 12.4% of all patients tested may have had their disease misclassified as a nonallergic disorder, and an additional 34.4% of all tested patients would not have had their allergies fully defined. Among those patients with positive responses to the supplemental allergens, 81% of the responses were of present or past relevance. The 12 most frequent contact allergens were nickel sulfate, fragrance mix, thimerosal, quaternium-15, neomycin sulfate, formaldehyde, bacitracin, thiuram mix, balsam of Peru, cobalt chloride, para-phenylenediamine, and carba mix. The present relevance varied with the specific allergen from 10.7% (thimerosal) to 85.7% (quaternium-15). Among newer allergens, methyldibromoglutaronitrile/phenoxyethanol (cosmetic preservative) caused positive allergic reactions in 2% of the patients; tixocortol-21-pivalate and budesonide (corticosteroids), in 2.0% and 1.1% of the patients, respectively; and ethylene urea/melamine formaldehyde mix (textile resin), in 5% of the patients.

CONCLUSION

The usefulness of patch testing is enhanced with the number of allergens tested, because allergens not found on the commercially available screening series in the United States frequently give relevant allergic reactions.

Characterization of a novel cis-syn and trans-syn-II pyrimidine dimer glycosylase/AP lyase from a eukaryotic algal virus, Paramecium bursaria chlorella virus-1

Endonuclease V from bacteriophage T4, is a cis-syn pyrimidine dimer-specific glycosylase. Recently, the first sequence homolog of T4 endonuclease V was identified from chlorella virus Paramecium bursaria chlorella virus-1 (PBCV-1). Here we present the biochemical characterization of the chlorella virus pyrimidine dimer glycosylase, cv-PDG. Interestingly, cv-PDG is specific not only for the cis-syn cyclobutane pyrimidine dimer, but also for the trans-syn-II isomer. This is the first trans-syn-II-specific glycosylase identified to date. Kinetic analysis demonstrates that DNAs containing both types of pyrimidine dimers are cleaved by the enzyme with similar catalytic efficiencies. Cleavage analysis and covalent trapping experiments demonstrate that the enzyme mechanism is consistent with the model proposed for glycosylase/AP lyase enzymes in which the glycosylase action is mediated via an imino intermediate between the C1' of the sugar and an amino group in the enzyme, followed by a beta-elimination reaction resulting in cleavage of the phosphodiester bond. cv-PDG exhibits processive cleavage kinetics which are diminished at salt concentrations greater than those determined for T4 endonuclease V, indicating a possibly stronger electrostatic attraction between enzyme and DNA. The identification of this new enzyme with broader pyrimidine dimer specificity raises the intriguing possibility that there may be other T4 endonuclease V-like enzymes with specificity toward other DNA photoproducts.

An ultrahigh-vacuum chamber for surface X-ray diffraction

An ultrahigh-vacuum environmental chamber for surface X-ray diffraction on Station 9.4 at the Synchrotron Radiation Source, Daresbury Laboratory, is described. Film growth can be monitored by simultaneously recording the Auger signal and the X-ray intensity at a particular point in reciprocal space. Such in situ measurements are essential for understanding the dynamic processes that occur during adsorption. An example is given in which the specularly reflected X-ray signal is correlated with Auger plots, during growth of Tl on Cu(001). In addition, the diffractometer and chamber combination allow large reconstructions to be investigated as shown by the in-plane structural analysis of the c(4x4) InSb surface. A study of the layer structure of Cr on Ag(001), in which an extended out-of-plane detector assembly was used, is also presented.

Latex allergy update: four vignettes

Four vignettes of occupational natural rubber latex (NRL) allergy are presented. Each had contact urticaria, 2 of 4 had systemic symptoms, 3 were allergic to cross-reacting fruit, and 2 had pollen and tree allergy. Recent information on latex cross-reactivity with fruit and pollen is discussed along with an update on latex radioallergosorbent tests and control of NRL allergy.

Errors in corticospinal axon guidance in mice lacking the neural cell adhesion molecule L1

BACKGROUND

Neural cell adhesion molecules of the immunoglobulin superfamily (IgCAMs) have been implicated in both the fasciculation and guidance of axons, but direct genetic evidence of a role for neural IgCAMs in axon guidance in vertebrates is lacking. The L1 subfamily of vertebrate neural IgCAMs function as both homophilic and heterophilic receptors for a variety of cell-surface and extracellular ligands and may signal through intracellular kinases or by recruitment of the fibroblast growth factor receptor. L1 itself has been implicated in many neural processes and is expressed widely in the embryonic and adult nervous systems. In humans, mutations in the L1 gene are linked with a spectrum of brain disorders, including loss of the corticospinal tract, but the mechanistic basis for these disorders is unknown.

RESULTS

We show that mice that do not express L1 have defects in the guidance of axons of the corticospinal tract, a major motor control pathway projecting from the cortex to the spinal cord. Although the pathway to the caudal medulla appears normal, a substantial proportion of axons fail to cross the midline to the opposite dorsal column as normal. In adults, this results in a reduced decussation and in large numbers of axons projecting ipsilaterally. There is also a varying, but reduced, number of corticospinal axons in the dorsal columns of the spinal cord. These do not project beyond cervical levels. We show that these are defects in axon guidance, because they arise during the early stages of the development of the decussation. The presence of a ligand for L1, CD24, specifically at the point of decussation suggests a mechanism in which L1 functions to guide corticospinal axons across the midline.

CONCLUSIONS

L1 function is necessary for the guidance of corticospinal axons across the pyramidal decussation in mice. Some of the defects in the corticospinal tract of humans with mutations in L1 could be due to errors in axon guidance at the pyramidal decussation.

Reaction mechanism of (6-4) photolyase

The (6-4) photolyase catalyzes the photoreversal of the (6-4) dipyrimidine photoproducts induced in DNA by ultraviolet light. Using the cloned Drosophila melanogaster (6-4) photolyase gene, we overproduced and purified the recombinant enzyme. The binding and catalytic properties of the enzyme were investigated using natural substrates, T[6-4]T and T[6-4]C, and the Dewar isomer of (6-4) photoproduct and substrate analogs s5T[6-4]T/thietane, mes5T[6-4]T, and the N-methyl-3'T thietane analog of the oxetane intermediate. The enzyme binds to the natural substrates and to mes5T[6-4]T with high affinity (KD approximately 10(-9)-10(-10) M) and produces a DNase I footprint of about 20 base pairs around the photolesion. Several lines of evidence suggest that upon binding by the enzyme, the photoproduct flips out of the duplex. Of the four substrates that bind with high affinity to the enzyme, T[6-4]T and T[6-4]C are repaired with relatively high quantum yields compared with the Dewar isomer and the mes5T[6-4]T which are repaired with 300-400-fold lower quantum yield than the former two photoproducts. Reduction of the FAD cofactor with dithionite increases the quantum yield of repair. Taken together, the data are consistent with photoinduced electron transfer from reduced FAD to substrate, in a manner analogous to the cyclobutane pyrimidine dimer photolyase.

Chiasmatic specificity in the regenerating mammalian optic nerve

The mammalian central nervous system is capable of regenerating; however, there is no evidence that the regenerating axons can navigate along their normal pathways and reestablish topographically organized projections: essential for functional return of vision. Here retinal ganglion cells in the opossum Monodelphis were birthdated with tritiated thymidine on the sixth postnatal day (P6), before being lesioned in the temporal retina at P8. Retrograde tracing with horseradish peroxidase injected into the ipsilateral optic tract at P24 showed that the temporal crescent had reformed behind the retinal lesion. By comparisons of cell and thymidine counts from lesioned and control regions of retina, it was estimated that about 40% of the normal number of ganglion cells are able to regenerate into the ipsilateral optic tract following a lesion in the temporal retina at P8. A clear line of decussation (separation of ipsilateral and contralateral projections) reformed in the lesioned temporal retina and regenerating ganglion cells labeled with DiI were turned at appropriate points on passing through the optic chiasm. This is evidence of chiasmatic specificity with regard to lesioned retinal ganglion cells regenerating into the ipsilateral optic tract.

Regeneration in the developing optic nerve: correlating observations in the opossum to other mammalian systems

Regeneration of severed axons within the central nervous system of adult mammals does not normally occur with any degree of success. During development, however, newly forming projections must send axons to distant sites and form appropriate connections with their targets: successful regeneration has been observed during this critical period. The opossum central nervous system develops during early postnatal life and has provided a useful experimental model to investigate this specialized mode of axonal regeneration in mammals. The presence of a clear decision point at the optic chiasm has also provided a useful site at which to investigate the navigational capacity of retinal ganglion cells regenerating along the optic nerve during this critical period. Regeneration failure occurs as the central nervous system progresses from this permissive, developing state to a mature, non-permissive adult state. Studies into the behaviour of glial and neuronal elements around this transition period can help elucidate some of the factors that need to be overcome if regeneration is ever to become successful in adult mammals. The regeneration characteristics of a lesioned projection are dependent upon its developmental stage and are also related to the proximity of axotomy along its pathway. A system of staging is proposed to correlate observations in the opossum optic nerve to other mammalian systems.