Base excision repair in nuclear and mitochondrial DNA.

Base excision repair mechanisms have been analyzed in nuclear and mitochondrial DNA. We measured the size and position of the newly incorporated DNA repair patch in various DNA substrates containing single oxidative lesions. Repair of 8-oxoguanine and of thymine glycol is almost exclusively via the base excision repair (BER) pathway with little or no involvement of nucleotide excision repair (NER). The repair mode is generally via the single-nucleotide replacement pathway with little incorporation into longer patches. Extension of these studies suggests that DNA polymerase beta plays a critical role not only in the short-patch repair process but also in the long-patch, PCNA-dependent pathway. Mitochondria are targets for a heavy load of oxidative DNA damage. They have efficient BER repair capacity, but cannot repair most bulky lesions normally repaired by NER. In vitro experiments performed using rat and human mitochondrial extracts suggest that the repair incorporation during the removal of uracil in DNA occurs via the short-patch repair BER pathway. Oxidative DNA damage accumulates with age in mitochondrial DNA, but this cannot be explained by an attenuation of DNA repair. In contrast, we observe that mitochondrial incision of 8-oxoG increases with age in rodents.

DNA repair and mutagenesis in Werner syndrome.

Werner syndrome (WS) is the hallmark premature aging syndrome in which the patients appear much older than their actual chronological age. The disorder is associated with significantly increased genome instability and with transcriptional deficiencies. There has been some uncertainty about whether WS cells are defective in DNA repair. We thus examined repair in vitro in nuclear and mitochondrial DNA. Whereas cellular studies so far do not show significant DNA repair deficiencies, biochemical studies with the Werner protein clearly indicate that it plays a role in DNA repair.

Purification and characterization of a novel UV lesion-specific DNA glycosylase/AP lyase from Bacillus sphaericus.

The purification and characterization of a pyrimidine dimer-specific glycosylase/AP lyase from Bacillus sphaericus (Bsp-pdg) are reported. Bsp-pdg is highly specific for DNA containing the cis-syn cyclobutane pyrimidine dimer, displaying no detectable activity on oligonucleotides with trans-syn I, trans-syn II, (6-4), or Dewar photoproducts. Like other glycosylase/AP lyases that sequentially cleave the N--glycosyl bond of the 5' pyrimidine of a cyclobutane pyrimidine dimer, and the phosphodiester backbone, this enzyme appears to utilize a primary amine as the attacking nucleophile. The formation of a covalent enzyme-DNA imino intermediate is evidenced by the ability to trap this protein-DNA complex by reduction with sodium borohydride. Also consistent with its AP lyase activity, Bsp-pdg was shown to incise an AP site-containing oligonucleotide, yielding beta- and delta-elimination products. N-terminal amino acid sequence analysis of this 26 kDa protein revealed little amino acid homology to any previously reported protein. This is the first report of a glycosylase/AP lyase enzyme from Bacillus sphaericus that is specific for cis-syn pyrimidine dimers.

Two glycosylase/abasic lyases from Neisseria mucosa that initiate DNA repair at sites of UV-induced photoproducts.

Diverse organisms ranging from Escherichia coli to humans contain a variety of DNA repair proteins that function in the removal of damage caused by shortwave UV light. This study reports the identification, purification, and biochemical characterization of two DNA glycosylases with associated abasic lyase activity from Neisseria mucosa. These enzymes, pyrimidine dimer glycosylase I and II (Nmu-pdg I and Nmu-pdg II), were purified 30,000- and 10,000-fold, respectively. SDS-polyacrylamide gel electrophoresis analysis indicated that Nmu-pdg I is approximately 30 kDa, whereas Nmu-pdg II is approximately 19 kDa. The N-terminal amino acid sequence of Nmu-pdg II exhibits 64 and 66% identity with E. coli and Hemophilus parainfluenzae endonuclease III, respectively. Both Nmu-pdg I and Nmu-pdg II were found to have broad substrate specificities, as evidenced by their ability to incise DNA containing many types of UV and some types of oxidative damage. Consistent with other glycosylase/abasic lyases, the existence of a covalent enzyme-DNA complex could be demonstrated for both Nmu-pdg I and II when reactions were carried out in the presence of sodium borohydride. These data indicate the involvement of an amino group in the catalytic reaction mechanism of both enzymes.

Role of specific amino acid residues in T4 endonuclease V that alter nontarget DNA binding.

Endonuclease V is a pyrimidine dimer-specific DNA glycosylase-apurinic (AP)1 lyase which, in vivo or at low salt concentrations in vitro, binds nontarget DNA through electrostatic interactions and remains associated with that DNA until all dimers have been recognized and incised. On the basis of the analyses of previous mutants that effect this processive nicking activity, and the recently published cocrystal structure of a catalytically deficient endonuclease V with pyrimidine dimer-containing DNA [Vassylyev, D. G., et al. (1995) Cell 83, 773-782], four site-directed mutations were created, the mutant enzymes expressed in repair-deficient Escherichia coli, and the enzymes purified to homogeneity. Steady-state kinetic analyses revealed that one of the mutants, Q15R, maintained an efficiency (k(cat)/Km) near that of the wild-type enzyme, while R117N and K86N had a 5-10-fold reduction in efficiency and K121N was reduced almost 100-fold. In addition, K121N and K86N exhibited a 3-5-fold increase in Km, respectively. All the mutants experienced mild to severe reduction in catalytic activity (k(cat)), with K121N being the most severely affected (35-fold reduction). Two of the mutants, K86N and K121N, showed dramatic effects in their ability to scan nontarget DNA and processively incise at pyrimidine dimers in UV-irradiated DNA. These enzymes (K86N and K121N) appeared to utilize a distributive, three-dimensional search mechanism even at low salt concentrations. Q15R and R117N displayed somewhat diminished processive nicking activities relative to that of the wild-type enzyme. These results, combined with previous analyses of other mutant enzymes and the cocrystal structure, provide a detailed architecture of endonuclease V-nontarget DNA interactions.

Detection of Theileria parva in the salivary glands of Rhipicephalus appendiculatus: evaluation of staining methods.

A comparison of ten methods for staining tick salivary glands for detection of Theileria parva infection from ticks fed on rabbits for various periods was undertaken. Staining with azure without hydrochloric acid hydrolysis was found to be the most reliable method for detection of the presporozoite stages (sporoblasts) of T. parva in the salivary gland acini of unfed Rhipicephalus appendiculatus and could be applied to field ticks. All the stains proved suitable for the detection and quantitation of sporozoites in ticks fed for 4 days on rabbits. The capacity of the stains to allow detection of early stages of T. parva differed, but it became more reliable during tick feeding as sporoblasts developed and matured. Giemsa's stain and Feulgen's stain followed by superimposition of Giemsa's stain were superior to other stains for the detection and quantitation of immature salivary gland stages in feeding ticks.

In vitro feeding of instars of the ixodid tick Amblyomma variegatum on skin membranes and its application to the transmission of Theileria mutans and Cowdria ruminatium.

An in vitro feeding method using rabbit or cattle skin membranes, applied successfully to all stages (larvae, nymphae and adults) of the ioxodid tick, Amblyomma variegatum, is described. The feeding apparatus consisted of a blood container with a membrane placed on top of a tick containment unit. A carbon dioxide atmosphere of between 5 and 10% and a temperature of 37 degrees C were used as stimulants for the attachment of the ticks. High CO2 concentrations in the atmosphere improved the feeding success of all instars. The effect of anticoagulation methods for the bloodmeal was investigated, and heparinized blood was found to be the most suitable for tick feeding. When the bloodmeal was replaced by tissue culture medium for feeding nymphs the subsequent moulting success was reduced. Adult ticks of both sexes remained attached for up to 16 days, until completion of their bloodmeals. All stages of the tick fed on whole blood in the artificial feeding system and all reached engorged weights less than those achieved by control ticks fed on experimental animals. A large proportion of ticks, fed artificially on whole blood, moulted or laid eggs successfully. The method was successfully applied for the transmission of Theileria mutans and Cowdria ruminantium to cattle.

Chlorella virus PBCV-1 encodes a homolog of the bacteriophage T4 UV damage repair gene denV.

The bacteriophage T4 denV gene encodes a well-characterized DNA repair enzyme involved in pyrimidine photodimer excision. We have discovered the first homologs of the denV gene in chlorella viruses, which are common in fresh water. This gene functions in vivo and also when cloned in Escherichia coli. Photodamaged virus DNA can also be photoreactivated by the host chlorella. Since the chlorella viruses are continually exposed to solar radiation in their native environments, two separate DNA repair systems, one that functions in the dark and one that functions in the light, significantly enhance their survival.

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.