A pachytene map of the mouse spermatocyte

Pachytene chromomere maps of early and mid/late mouse spermatocytes have been prepared which permit exact identification of each bivalent. The average total number of chromomeres on the autosomal bivalents was 248 in the early cells and 184 in the mid/late. There was close correspondence between early and mid/late chromomeres in 122 locations. Comparisons of early pachytene chromomeres with published prometaphase dark G bands revealed 1.6 more chromomeres in the meiotic autosomal bivalents, with close correspondence of larger chromomeres and major mitotic bands. Fewer chromomeres were found in pachytene spermatocytes than had been seen in a previous study of pachytene oocytes. Comparisons of chromomeres of spermatocytes and oocytes revealed several differences.     

Steady-state kinetics of mouse DNA polymerase beta.

DNA polymerase beta from mouse myeloma has been purified to near homogeneity, and its properties have been examined. The enzyme did not catalyze a detectable level of dNTP turnover, pyrophosphate exchange, pyrophosphorolysis, 3'-exonuclease degradation, or 5'-exonuclease degradation. Steady-state kinetic studies point to an ordered bibi mechanism for the polymerization reaction. Metal activation, which is required for polymerization, did not alter the Km for either the dNTP or the template--primer.     

DNA repair synthesis in mouse spermatogenesis involves DNA polymerase beta activity

The role of DNA polymerase alpha-DNA primase complex and DNA polymerase beta in DNA replication and ultraviolet-induced DNA repair synthesis has been analyzed in mouse spermatogenesis. Autoradiographic experiments with germ cells in culture, indicating an involvement of DNA polymerase alpha and/or delta in DNA replication, and of DNA polymerase beta in DNA repair synthesis, have been confirmed by studying partially purified enzymes. These findings support the idea that, different from other biological systems, in meiotic and post meiotic male mouse germ cells DNA polymerase beta is the main DNA polymerase form needed for DNA repair.     

Mapping of the gene for DNA polymerase beta to mouse chromosome 8

We conducted Southern blot analysis of DNAs from mouse x hamster somatic cell hybrids and progeny of an interspecies backcross to localize the mouse gene for DNA polymerase beta (Polb) to the centromeric end of Chromosome 8. These results provide additional support for the regional localization of polymerase beta on the short arm of human chromosome 8 or the very proximal end of the long arm.     

DNA polymerase beta mRNA and protein expression in Xiphophorus fish

Herein we report Xiphophorus DNA polymerase beta (XiphPolbeta) mRNA and protein expression levels in brain, liver, gill, and testes tissues from Xiphophorus maculatus, Xiphophorus helleri, and Xiphophorus couchianus parental line fish and two different tumor-bearing Xiphophorus interspecies hybrids. Polymerase beta protein levels in the Xiphophorus tissues were measured by Western blot, and mRNA was measured with a quantitative real time RT-PCR method which employed cRNA construction to produce accurate calibration curves. We found significant differences in both mRNA and protein levels between the tumor-bearing hybrid animals and the three parental species. However, there were no significant differences in either mRNA levels or protein expression observed between the parental species. Thus, interspecies hybridization results in dysregulation of Polbeta expression and this may manifest a modulation in DNA repair capability and susceptibility to latent tumorigenesis.     

Structural design of a eukaryotic DNA repair polymerase: DNA polymerase beta

DNA polymerase beta, the smallest eukaryotic DNA polymerase, is designed to synthesize DNA in short DNA gaps during DNA repair. It is composed of two specialized domains that contribute essential enzymatic activities to base excision repair (BER). Its amino-terminal domain possesses a lyase activity necessary to remove the 5'-deoxyribose phosphate (dRP) intermediate generated during BER. Removal of the dRP moiety is often the rate-limiting step during BER. Failure to remove this group may initiate alternate BER pathways. The larger polymerase domain has nucleotidyl transferase activity. This domain has a modular organization with sub-domains that bind duplex DNA, catalytic metals, and the correct nucleoside triphosphate in a template-dependent manner. X-ray crystal structures of DNA polymerase beta, with and without bound substrates, has inferred that domain, sub-domain, and substrate conformational changes occur upon ligand binding. Many of these conformational changes are distinct from those observed in structures of other DNA polymerases. This review will examine the structural aspects of DNA polymerase beta that facilitate its role in BER.     

A novel testis-specific RAG2-like protein,Peas: its expression in pachytene spermatocyte cytoplasm and meiotic chromatin

We report a novel gene Peas that constitutes an overlapping gene complex in mammalian genome. We have cloned human and mouse Peas cDNAs (hPEAS/mPeas) and analyzed their tissue and stage-specific expressions. Peas protein contains six repeated kelch motifs, structurally similar to RAG2, a V(D)J recombination activator, and is evolutionarily conserved among mammals, birds, insects, and nematodes. Northern, RNA in situ hybridization and immunohistochemical analyses showed that mPeas is specifically transcribed in testis, particularly in pachytene spermatocytes in which it is localized to the cytoplasm and meiotic chromatin. It is suggested that Peas may be involved in meiotic recombination process.     

DNA synthesis at selective sites during pachytene in mouse spermatocytes

DNA repair replication has been previously demonstrated to occur in mouse spermatocytes during the pachytene stage. The results reported in this study provide a more detailed characterization of pachytene repair by focusing upon specific properties of the sites of replication. Our data demonstrate that single-strand breaks persist within replicated sequences throughout a period which corresponds to a defined interval of the pachytene stage. A large fraction of the sites may be nicked more than once within the same DNA strand, allowing the selective release of replicated DNA sequences from gently denatured spermatocyte DNA. DNA fragments thus prepared from pachytene spermatocytes are not of random sequence composition, but are derived from a specific subset of the mouse genome. Sites of replication are also associated with chromatin of distinctive structure in pachytene spermatocytes, as evidenced by the sensitivity of replicated chromatin to DNase II, and its solubility in the presence of Mg²⁺. In each of these respects, sequences replicated in pachytene spermatocytes closely resemble their counterparts in the LiHum genome.     

RNA aptamers selected against DNA polymerase beta inhibit the polymerase activities of DNA polymerases beta and kappa

DNA polymerase β (polβ), a member of the X family of DNA polymerases, is the major polymerase in the base excision repair pathway. Using in vitro selection, we obtained RNA aptamers for polβ from a variable pool of 8 × 10¹² individual RNA sequences containing 30 random nucleotides. A total of 60 individual clones selected after seven rounds were screened for the ability to inhibit polβ activity. All of the inhibitory aptamers analyzed have a predicted tri-lobed structure. Gel mobility shift assays demonstrate that the aptamers can displace the DNA substrate from the polβ active site. Inhibition by the aptamers is not polymerase specific; inhibitors of polβ also inhibited DNA polymerase κ, a Y-family DNA polymerase. However, the RNA aptamers did not inhibit the Klenow fragment of DNA polymerase I and only had a minor effect on RB69 DNA polymerase activity. Polβ and κ, despite sharing little sequence similarity and belonging to different DNA polymerase families, have similarly open active sites and relatively few interactions with their DNA substrates. This may allow the aptamers to bind and inhibit polymerase activity. RNA aptamers with inhibitory properties may be useful in modulating DNA polymerase actvity in cells.     

The chromomere map of the pachytene spermatocyte of the Turkish hamster (Mesocricetus brandti).

The chromomere map of the early to mid pachytene spermatocyte of the Turkish hamster (Mesocricetus brandti) is described. Each autosomal bivalent was identified and a total of 304 chromomeres was found. A sex bivalent with a despiralized Xq protruding from the sex vesicle and a small number of the polymorphic 16q bivalents were observed.     

DNA polymerase beta can substitute for DNA polymerase I in the initiation of plasmid DNA replication.

We previously demonstrated that mammalian DNA polymerase beta can substitute for DNA polymerase I of Escherichia coli in DNA replication and in base excision repair. We have now obtained genetic evidence suggesting that DNA polymerase beta can substitute for E. coli DNA polymerase I in the initiation of replication of a plasmid containing a pMB1 origin of DNA replication. Specifically, we demonstrate that a plasmid with a pMB1 origin of replication can be maintained in an E. coli polA mutant in the presence of mammalian DNA polymerase beta. Our results suggest that mammalian DNA polymerase beta can substitute for E. coli DNA polymerase I by initiating DNA replication of this plasmid from the 3' OH terminus of the RNA-DNA hybrid at the origin of replication.     

Inhibitors of DNA polymerase beta: activity and mechanism

Bioassay-guided fractionation of extracts prepared from Couepia polyandra and Edgeworthia gardneri resulted in the isolation of the DNA polymerase beta (pol beta) inhibitors oleanolic acid (1), edgeworin (2), betulinic acid (3), and stigmasterol (4). Study of these pol beta inhibitors revealed that three of them inhibited both the lyase and polymerase activities of DNA polymerase beta, while stigmasterol inhibited only the lyase activity. Further investigation indicated that the four inhibitors had substantially different effects on the DNA-pol beta binary complex that is believed to be an obligatory intermediate in the lyase reaction. It was found that the inhibitors potentiated the inhibitory action of the anticancer drug bleomycin in cultured A549 cells, without any influence on the expression of pol beta in the cells. The results of the unscheduled DNA synthesis assay support the thesis that the potentiation of bleomycin cytotoxicity by DNA pol beta inhibitors was a result of an inhibition of DNA repair synthesis.     

Evidence of finely tuned expression of DNA polymerase beta in vivo using transgenic mice

DNA polymerase (Pol) is an error-prone repair DNA polymerase that has been shown to create genetic instability and tumorigenesis when overexpressed by only 2-fold in cells, suggesting that a rigorous regulation of its expression may be essential in vivo. To address this question, we have generated mice which express a transgene (Tg) bearing the Pol cDNA under the control of the ubiquitous promoter of the mouse H-2K gene from the major histocompatibility complex. These mice express the Tg only in thymus, an organ which normally contains the most abundant endogenous Pol mRNA and protein, supporting the idea of a tight regulation of Pol in vivo. Furthermore, we found no tumor incidence, suggesting that the single Pol overexpression event is not sufficient to initiate tumorigenesis in vivo.     

Mechanism of nucleotide incorporation in DNA polymerase beta

DNA polymerases play a central role in the mechanisms of DNA replication and repair. Here, we report mechanisms of the beta-polymerase catalyzed phosphoryl transfer reactions corresponding to correct and incorrect nucleotide incorporations in the DNA. Based on energy minimizations, molecular dynamics simulations, and free energy calculations of solvated ternary complexes of pol beta and by employing a mixed quantum mechanics molecular mechanics Hamiltonian, we have uncovered the identities of transient intermediates in the phosphoryl transfer pathways. Our study has revealed that an intriguing Grotthuss hopping mechanism of proton transfer involving water and three conserved aspartate residues in pol beta's active site mediates the phosphoryl transfer in the correct as well as misincorporation of nucleotides. The significance of this catalytic step in serving as a kinetic check point of polymerase fidelity may be unique to DNA polymerase beta, and is discussed in relation to other known mechanisms of DNA polymerases.