DNA repair nucleases

Stability of DNA largely depends on accuracy of repair mechanisms, which remove structural anomalies induced by exogenous and endogenous agents or introduced by DNA metabolism, such as replication. Most repair mechanisms include nucleolytic processing of DNA, where nucleases cleave a phosphodiester bond between a deoxyribose and a phosphate residue, thereby producing 5-terminal phosphate and 3-terminal hydroxyl groups. Exonucleases hydrolyse nucleotides from either the 5 or 3 end of DNA, while endonucleases incise internal sites of DNA. Flap endonucleases cleave DNA flap structures at or near the junction between single-stranded and double-stranded regions. DNA nucleases play a crucial role in mismatch repair, nucleotide excision repair, base excision repair and double-strand break repair. In addition, nucleolytic repair functions are required during replication to remove misincorporated nucleotides, Okazaki fragments and 3 tails that may be formed after repair of stalled replication forks.Received 12 June 2003; received after revision 29 July 2003; accepted 16 September 2003     

Hotspots of homologous recombination

Homologous recombination occurs at higher than average frequency at and near hotspots. Hotspots are special nucleotide sequences recognized by proteins that promote, directly or indirectly, a rate limiting step of recombination. This review focuses on two well-studied examples, the Chi sites of the bacteriumEscherichia coli and the M26 site of the fission yeastSchizosaccharomyces pombe. Chi, 5 G-C-T-G-G-T-G-G 3, is recognized by the RecBCD enzyme, which nicks the DNA near Chi and produces a 3-ended single-stranded DNA tail; this tail is a potent substrate for homologous pairing by RecA and single-stranded DNA binding proteins. M26, 5 A-T-G-A-C-G-T 3, is recognized by a heterodimeric protein and stimulates, by an as-yet-unknown mechanism, meiotic recombination at and near theade6 gene. Additional hotspots in bacteria, fungi, and mammals enhance recombination directly or indirectly via a variety of mechanisms. Although hotspots are widespread among organisms, the biological role of their localized enhancement of recombination remains a matter of speculation.     

Removal of 5-bromo-2-deoxyuridine incorporated in liver DNA of newborn and young adult rats

Summary 5-bromo-2-deoxyuridine (BUdR) removal from liver DNA in newborn and young adult rats has been demonstrated: it forms the basis of a reliable method to measure DNA repair in tissues provided with detectable DNA synthetic activity.This work was supported by a grant from Consiglio Nazionale delle Ricerche, Rome, and Donazione Teston, Bologna, Italy.     

Repercussions de l'hyperthyroïdie sur le contenu total en ADN du cervelet de rat âgé de 6 et 35 jours. Effets comparés de la LT3 et de la DLT4

Summary The total cerebellar proteins RNA and DNA contents from DLT4- and LT3-treated rats was studied at 6 and 35 days of age. The effect of injections of 5 g/j of DLT4 is comparable to that of 25 g of LT3 at birth, followed by 0.5 g every 2 days. On the other hand, injection of 0.5 g of LT3 every 2 days does not induce any significant modification of the total DNA contents in the cerebellum.     

Alternariol,a dibenzopyrone mycotoxin ofAlternaria spp., is a new photosensitizing and DNA cross-linking agent

Summary The mycotoxin alternariol (3,4,5-trihydroxy-6-methyldibenzo [a] pyrone) but not alternariol monomethyl ether (3,4-dihydroxy-5-methoxy-6-methyldibenzo [a] pyrone) is phototoxic toEscherichia coli in the presence of near UV light (320–400 nm). The phototoxicity bioassays with a DNA repair-deficient mutant ofE. coli suggested that DNA may be the molecular target for photo-induced toxicity of alternariol. Interactions between alternariol and double-stranded, supercoiled DNA suggest that alternariol interacts with DNA by intercalation. No DNA breakage was detected in this system; however, alternariol forms a complex and cross-links double-stranded DNA in near UV light. These results suggest that alternariol is a new phototoxic, DNA-intercalating agent and is a DNA cross-linking mycotoxin in near UV light.Acknowledgment. Dr Albert Stoessl (Agriculture Canada, London, Ontario, Canada) generously provided a mixture of alternariol and alternariol monomethyl ether, and made many helpful suggestions. Dr Ashwood-Smith (University of Victoria, Victoria, British Columbia, Canada) kindly supplied the microorganisms through Dr G.H.N. Towers (University of British Columbia, Vancouver). We gratefully acknowledge the gifts. It is a pleasure to acknowledge the able assistance of Mr S. Tallevi.     

Protecting the terminus: t-loops and telomere end-binding proteins

Telomeric DNA is composed of a region of duplex telomeric tract followed by a single-strand overhang on the 3 G-rich strand. The DNA is packaged by proteins that associate directly with the single- and double-strand regions of the telomeric tract and by their associated proteins. This review discusses the evidence that G-strand overhangs are present on both ends of eukaryotic chromosomes and the steps needed to generate these overhangs. The overhangs are protected by specialized G-overhang-binding protein and/or invasion by the overhang of the duplex region of the telomeric tract to form a structure called a t-loop. The G-overhang-binding proteins identified from different species are described, and their properties compared. The data supporting the existence of t-loops at native telomeres is discussed, and the conditions required to promote their in vitro formation are presented.     

Expression of the mutant gene for L-gulono-γ-lactone oxidase in scurvy-prone rats

A mutant strain of Wistar rats with L-gulono--lactone oxidase deficiency has recently been established. To investigate this deficiency by DNA and RNA blot hybridization analyses, a fragment of a previously cloned cDNA encoding rat L-gulono--lactone oxidase was used as a probe. When genomic DNA of the mutant rat was digested with several restriction enzymes, the probe hybridized to fragments of the same sizes as those produced from DNA of normal rats. Poly(A)⁺RNA from the liver of the mutant rat was found to contain an L-gulono--lactone oxidase-specific mRNA of a normal size at a comparable level to that of normal rats. An in vitro translation experiment revealed that the mRNA programmed the synthesis of an enzyme protein which had the same molecular weight as that of the translational product of the normal mRNA, although the amount synthesized was markedly reduced as compared with that synthesized with the normal mRNA. In accordance with this observation, a very low but definite degree of L-gulono--lactone oxidase activity was detected in the microsomes of the mutant rat by a newly developed, highly sensitive method.Acknowledgments. The authors thank Dr Susumu Makino, Shionogi Research Laboratories, Shionogi & Co., Ltd, Japan, for his kind donation of normal (ODS- +/+) and ODS (ODS-od/od) rats. This work was supported in part by Grant-in-Aid (59570103) for Scientific Research from the Ministry of Education, Science and Culture of Japan.     

The biochemistry of ancient DNA in bone

The amount of DNA in ancient bone was determined by ethidium bromide staining after the removal of the potent Taq inhibitor, fulvic acid. A complete decalcification and a perfusion protocol were used to recover DNA from bone. A variety of purification techniques including molecular sieve, hydroxyapatite binding and Magic preparations yielded DNA that spanned from 3.4g/g of bone to below detectable limits. Fulvic acid was shown to interfere with the quantification of DNA derived from ancient human skeletal material one hundred to over seven thousand years old. Scanning UV in the 300 to 230 nm range is a simple and sensitive technique for documenting fulvic acid contamination in ancient bone extracts.     

In vitro reconstitution of homologous recombination reactions

The proteins essential to homologous recombination inE. coli have been purified and their individual activities have been identified, permitting biochemical reconstitution of steps that comprise the cellular recombination process. This review focuses on the biochemical events responsible for the initiation and homologous pairing steps of genetic recombination. The properties of an in vitro recombination reaction that requires the concerted action of recA, recBCD, and SSB proteins and that is stimulated by the recombination hotspot, Chi(), are described. The recBCD enzyme serves as the initiator of this reaction; its DNA helicase activity produces single-stranded DNA that is used by the recA protein to promote homologous pairing and DNA strand invasion of supercoiled (recipient) DNA. The SSB protein acts to trap the single-stranded DNA produced by recBCD enzyme and to facilitate pairing by the recA protein. The regulatory sequence acts incis by attenuating the nuclease, but not the helicase, activity of recBCD enzyme. This attenuation assures the preservation of ssDNA produced by the DNA helicase activity and is responsible for the simulation in vitro and, presumably, in vivo. The attenuation of nuclease activity by results in the loss or functional inactivation of the recD subunit.     

Inter- and intrapopulation studies of ancient humans

For a genetic analysis of ancient human populations to be useful, it must be demonstrated that the DNA samples under investigation represent a single human population. Toward that end, we have analyzed human DNA from the Windover site (7000–8000 BP). MHC-I analysis, using allele-specific oligonucleotide hybridization to PCR amplified Windover DNA, microsatellite analysis by PCR of the APO-A2 repeat and mtD-loop 3 region sequencing on multiple individuals spanning nearly the full range of estimated burial dates all confirm the hypothesis that there is a persistence of both nuclear and mitochondrial haplotypes at Windover throughout its entire period of use. Thus, Windover can be considered a single population. Neighbor-joining tree analysis of mtDNA sequences suggests that some mitochondrial types are clearly related to extant Amerind types, whereas others, more distantly related, may reflect genetically distinct origins. A more complete sequence analysis will be required to firmly resolve this issue. Calibrating genetic relationships deduced by tree analysis, radiocarbon dates and burial position, yields a human mtD-loop DNA rate of evolution of 3700 to 14,000 years per percent change. Both values are within the range of recent, independently calculated values using estimates of evolutionary divergence or theoretical population genetics. Thus we are beginning to relaize the promise of ancient DNA analysis to experimentally answer heretofore unapproachable questions regarding human prehistory and genetic change.     

Differential sensitivity to ethidium bromide of replicative DNA synthesis and bleomycin-induced unscheduled DNA synthesis in permeable mouse sarcoma cells1

Summary Replicative DNA synthesis in permeable mouse sarcoma cells was more sensitive to ethidium bromide (EtBr) than bleomycin-induced unscheduled DNA synthesis (UDS). A similar difference in sensitivity to EtBr was observed between DNA polymerases and . The difference in sensitivity to EtBr of replicative DNA synthesis and UDS in the present system seems to reflect mainly the sensitivity difference between DNA polymerases and .Acknowledgments. The authors wish to thank Nippon Kayaku Co. (Tokyo, Japan) for providing copper-free bleomycin A₂. This research was supported in part by a grant from the Japan Ministry of Education, Science and Culture.     

Stimulation of polydnavirus replication by 20-hydroxyecdysone

During oviposition the endoparasitic waspCampoletis sonorensis, introduces a polydnavirus into parasitized insects where viral gene expression is required for endoparasite survival. The polydnavirus is integrated into wasp chromosomal DNA and replicates only in the ovary. Ecdysteroids regulate the developmental expression of many insect genes and may regulate polydnavirus replication. Direct verification of viral replication was performed by dot blot hybridization and by amplifying DNA sequences containing the viral integration site; this junction fragment cannot be amplified from integrated virus. Thoracic ligations and in vitro ecdysteroid treatments of wasp ovaries support the hypothesis that polydnavirus DNA replication is regulated by ecdysteroid during parasite development.     

Biochemical aspects of radiation biology

Summary In order to analyze the mechanisms of biological radiation effects, the events after radiation energy absorption in irradiated organisms have to be studied by physico-chemical and biochemical methods. The radiation effects in vitro on biomolecules, especially DNA, are described, as well as their alterations in irradiated cells. Whereas in vitro, in aqueous solution, predominantly OH radicals are effective and lead to damage in single moieties of the DNA, in vivo the direct absorption of radiation energy leads to locally multiply-damaged sites, which produce DNA double-strand breaks and locally denatured regions. DNA damage will be repaired in irradiated cells. Error free repair leads to the original nucleotide sequence in the genome by excision or by recombination. Error prone repair (mutagenic repair), leads to mutation. However, the biochemistry of these processes, regulated by a number of genes, is poorly understood. In addition, more complex reactions, such as gene amplification and transposition of mobile gene elements, are responsible for mutation or malignant transformation.     

Paradoxical effect of 1-β-D-arabinofuranosyl cytosine triphosphate on bleomycin-induced unscheduled DNA synthesis in permeable sarcoma cells

Summary 1--D-Arabinofuranosyl cytosine-5-triphosphate (araCTP), an inhibitor of DNA synthesis, paradoxically enhanced unscheduled DNA synthesis (USD) induced by bleomycin in permeable mouse sarcoma cells. A greater enhancing effect of araCTP on bleomycin-induced USD was observed with lower concentrations of dCTP in the assay mixture. USD measured without bleomycin in nuclei isolated from mouse sarcoma cells was not enhanced, but inhibited by araCTP.Acknowledgments. The authors wish to thank Nippon Kayaku Co. (Tokyo, Japan) for providing copper-free bleomycin A₂. This research was supported in part by a grant from the Japan Ministry of Education, Science and Culture.     

S-adenosyl-L-homocysteine: A non-cytotoxic hypomethylating agent

The cytotoxic effect caused by the hypomethylating agent S-adenosyl-L-homocysteine (SAH) was compared with that of two drugs commonly used to induce DNA hypomethylation, 5-azacytidine and 5-aza-2-deocycytidine. Two in vitro cytotoxicity tests, the tetrazolium MTT assay and the intracellular lactate dehydrogenase (LDH) activity test, suggest that SAH induces hypomethylation without causing any cytotoxic effect. We propose the use of SAH as a non-cytotoxic agent which may be more suitable for inducing experimental DNA hypomethylation.     

Molecular ecology of a Neolithic meadow: The DNA of the grass remains from the archaeological site of the Tyrolean Iceman

The paper reports on the molecular analysis of samples of approximately 5,300-year-old grass found at the alpine archaeological site where the so-called Tyrolean Iceman was discovered. The grass comes from a cloak made of long grass blades and/or the stuffing of the snow footwear worn by the Iceman. The results show that while the largest fraction of the DNA extractable from the grass is of foreign origin, a much smaller part belongs to the original genetic material of the grass itself, and can be used as a valuable taxonomic clue to the plant species utilized by neolithic men to manufacture their equipment. On the other hand, the foreign DNA, or at least a portion of it, comes from microorganisms-mainly filamentous fungi and unicellular algae-which seem to have been associated with the grass since the time the grass was harvested.     

Structure and morphogenesis of bacteriophage T4

Bacteriophage T4 is one of the most complex viruses. More than 40 different proteins form the mature virion, which consists of a protein shell encapsidating a 172-kbp double-stranded genomic DNA, a tail, and fibers, attached to the distal end of the tail. The fibers and the tail carry the host cell recognition sensors and are required for attachment of the phage to the cell surface. The tail also serves as a channel for delivery of the phage DNA from the head into the host cell cytoplasm. The tail is attached to the unique portal vertex of the head through which the phage DNA is packaged during head assembly. Similar to other phages, and also herpes viruses, the unique vertex is occupied by a dodecameric portal protein, which is involved in DNA packaging.Received 18 February 2003; received after revision 16 April 2003; accepted 9 May 2003     

Absence of low molecular weight DNA polymerase activity from the nuclei ofAmoeba discoides

Summary Amoeba discoides nuclear protein partially purified by passage through Sephadex G-200 showed 3 high-mol.-wt DNA polymerase activities which eluted in and just following the void volume. No low-mol.-wt (45,000 daltons) DNA polymerase activity was detected. Nuclear protein layered on 5–20% sucrose gradients also showed an absence of lowmol.-wt DNA polymerase . The void volume enzyme showed deoxyribonuclease activity, but no low-mol.-wt nuclease activity was detected.     

Visualization of DNA in various phages (T4, χ, T7, ϕ 29) by ethidium bromide epi-fluorescent microscopy

Summary DNA-containing areas in various phages (T4, , T7 and 29) could be observed at the light microscopic level using ethidium bromide epi-fluorescent microscopy. The fluorescent intensity per phage was in linear proportion to the DNA content in each phage.Acknowledgements. This work was supported in part by the grant No. 521708 and No. 511212 from the Japan Ministry of Education, Science and Culture.     

Epidermal growth factor (EGF) accelerates the maturation of fetal mouse intestinal mucosa in utero

Summary Pregnant Swiss ICR mice were injected i.p. with 0.5 g of epidermal growth factor (EGF) per g b. wt at 15, 16 and 17 days of gestation and fetuses were removed at 18 days of gestation. EGF treatment had no effect on the weight of the fetuses and on the length of the small intestine. No modification of the protein and DNA contents was noted. However brush border alkaline phosphatase and trehalase activities were significantly increased as well as endoplasmic reticulum membrane-bound glucose-6-phosphatase.Supported by grant MA-6069 from the Medical Research Council of Canada. Dr D. Ménard is a chercheur boursier du Fonds de la recherche en santé du Québec