Structural homology of DNA polymerase beta from various mammalian cells

Rho-kinase phosphorylates COOH-terminal threonines of ezrin/radixin/moesin (ERM) proteins and regulates their head-to-tail association

The ezrin/radixin/moesin (ERM) proteins are involved in actin filament/plasma membrane interaction that is regulated by Rho. We examined whether ERM proteins are directly phosphorylated by Rho-associated kinase (Rho-kinase), a direct target of Rho. Recombinant full-length and COOH-terminal half radixin were incubated with constitutively active catalytic domain of Rho-kinase, and approximately 30 and approximately 100% of these molecules, respectively, were phosphorylated mainly at the COOH-terminal threonine (T564). Next, to detect Rho-kinase-dependent phosphorylation of ERM proteins in vivo, we raised a mAb that recognized the T564-phosphorylated radixin as well as ezrin and moesin phosphorylated at the corresponding threonine residue (T567 and T558, respectively). Immunoblotting of serum-starved Swiss 3T3 cells with this mAb revealed that after LPA stimulation ERM proteins were rapidly phosphorylated at T567 (ezrin), T564 (radixin), and T558 (moesin) in a Rho-dependent manner and then dephosphorylated within 2 min. Furthermore, the T564 phosphorylation of recombinant COOH-terminal half radixin did not affect its ability to bind to actin filaments in vitro but significantly suppressed its direct interaction with the NH2-terminal half of radixin. These observations indicate that the Rho-kinase-dependent phosphorylation interferes with the intramolecular and/ or intermolecular head-to-tail association of ERM proteins, which is an important mechanism of regulation of their activity as actin filament/plasma membrane cross-linkers.

DNA polymerase beta gene mutations in human bladder cancer

We examined 24 human bladder cancer tissues for possible mutations in the entire coding region of the human DNA polymerase beta gene using polymerase chain reaction analysis, single-strand conformational polymorphism analysis of RNA, and sequence analysis. DNA polymerase beta gene mutations were observed in four of the 24 cases (16.7%) and included three missense point mutations and a single base insertion. The single base insertion was also observed in our previous study of human prostate cancer, suggesting that this region may be a hot spot for mutation of the DNA polymerase beta gene. No clinical or pathological association was found among the four cases that contained the mutation. Three of the four cases with DNA polymerase beta gene mutation had mutations of the p16 or RB genes or loss of heterozygosity of the p53 and APC gene loci. The results of the study presented here suggest that DNA polymerase beta gene mutations, in combination with mutations of tumor suppressor genes, may be involved in certain cases of human bladder cancer.

Purification and characterization of a beta-like DNA polymerase from Trypanosoma cruzi

A DNA polymerase was purified to near homogeneity from Trypanosoma cruzi epimastigotes. This preparation had a major polypeptide of 50 kDa and a minor band of 45 kDa. SDS-PAGE studies and a novel colorimetric activity gel technique demonstrated that the 50-kDa polypeptide chain is the catalytic subunit of this T. cruzi DNA polymerase. Western blot analysis of different purification stage fractions strongly suggests that this 50-kDa protein is the intact catalytic subunit and does not correspond to a degradation product from a larger one. This T. cruzi DNA polymerase is insensitive to aphidicolin, butylphenyldeoxyguanosine triphosphate, berenil, ethidium bromide and N-ethylmaleimide, but is markedly inhibited by the dideoxythymidine triphosphate analogue. Studies with different DNA templates showed that the DNA polymerase prefers activated DNA as substrate and that it cannot elongate oligoriboadenylate primers. The data presented in this paper are consistent with the hypothesis that this enzyme corresponds to a beta-like DNA polymerase present in the parasitic protozoon T. cruzi.

Rapid phosphorylation of 28-kDa heat-shock protein by treatment with okadaic acid and phorbol ester of BALB/MK-2 mouse keratinocytes

Protein phosphorylation by okadaic acid and 12-O-tetradecanoylphorbol-13-acetate (TPA) was examined using quiescent cultures of BALB/MK-2, a cell line derived from mouse epidermal keratinocytes. Treatment with okadaic acid caused rapid phosphorylation of five proteins with molecular masses of 65, 55, 50, 28 and 15 kDa (p65, p55, p50, p28, p15, respectively) while TPA caused rapid phosphorylation of five proteins with molecular masses of 80, 70, 40, 34 and 28 kDa (p80, p70, p40, p34, p28, respectively). In the present study, we examined p28, a common target protein of okadaic acid and TPA. The phosphorylation of p28 increased depending on time of exposure and doses of okadaic acid and TPA. Combined treatment with okadaic acid and TPA resulted in an additive effect. Its position on two-dimensional gel electrophoresis suggested that p28 is the 28-kDa heat-shock protein (HSP28). This possibility was confirmed by migration of p28 with HSP28 and comparative peptide mapping of the two proteins. The phosphoamino-acid residue of phosphorylated HSP28 was serine. In two-dimensional tryptic peptide maps, the same peptides were phosphorylated after treatment with both okadaic acid and TPA.

Structure-function analysis of DNA polymerase-beta using monoclonal antibodies: identification of a putative nucleotide binding domain

DNA polymerase-beta was purified from Novikoff hepatoma and used as an antigen in an in vitro immunization system to produce monoclonal antibodies. These reagents surprisingly showed cross-reactivity to a number of proteins, including several DNA polymerases. Nearly all of these proteins possess nucleotide binding sites, which suggested the potential value of using the monoclonals to elucidate structure-function relationships within polymerase-beta. Furthermore, these antibodies were able to partially neutralize (40-50%) polymerase-beta activity, and this effect could be blocked by dNTP1 but not by dNMP or rNTP. The limited neutralization phenomenon is at least partially explained by the weak binding affinity of these antibodies. Scatchard analysis of immunoprecipitation data predicted a Kd of 1.8 x 10(-8) M. Epitope mapping studies showed that the region of polymerase-beta recognized by one of the monoclonal antibodies is within residues 235-335, and sequence homology studies indicated that the epitope is probably located in the region of amino acids 283-320. At least a portion of this area, namely residues 301-308 and 311-315, appears to be part of a nucleotide binding domain which has sequence homology with a portion of the highly conserved ATP binding site in adenylate kinase.

A novel testis-specific 105-kDa protein related to the 90-kDa heat-shock protein

Brain 90- and 100-kDa heat-shock proteins (HSP90 and HSP100) were purified and antibodies against them prepared. The two antibodies were very specific and did not cross-react with each other. In rat, immunoblotting with the anti-HSP90 antibody showed the most abundant presence of HSP90 in testis as well as brain, compared with lung, liver, spleen, kidney, cardiac muscle, ovarium and uterus. The anti-HSP90 antibody showed the presence of a new 105-kDa protein in rat testis. This novel 105-kDa protein was also detected in brain at a very low concentration but not in HeLa cells or other organs including the uterus and ovarium. The testis 105-kDa protein was purified from rat testis; although it was clearly separable from HSP90 by two-dimensional gel electrophoresis, Q-Sepharose and hydroxyapatite column chromatographies, the properties of this protein were very similar to HSP90. The similarity was higher than 60% on peptide mapping with trypsin digestion, the 105-kDa protein cross-reacted with anti-HSP90 antibody, both were bound similarly to heparin-Sepharose gel and both are located in the cytosol fraction. When the 105-kDa protein was fractionated by HPLC, a molecular mass of 195 kDa was calculated, indicating that it is composed of two identical subunits, similarly to HSP90. The 105-kDa protein did not react with the anti-HSP100 antibody. There was a slight similarity between the 105-kDa protein and HSP100 on the peptide mapping. HSP100 was present in the microsomal fraction as well as in the cytosol. It is concluded that the 105-kDa protein is a testis-specific and HSP90-related protein.

Difference in the expression level of DNA polymerase beta among mouse tissues: high expression in the pachytene spermatocyte

The expression level of DNA polymerase beta was determined in various mouse tissues. Northern blot hybridization analysis using rat cDNA as a probe revealed that the mRNA of about 1.5 kb for this enzyme is present in all kinds of tissues examined, but its content widely varies among tissues; the most abundant DNA polymerase beta mRNA was present in the testis, which was followed by brain, thymus, and spleen. The mRNA content was low in heart, kidney, and liver. In testis and brain, two minor species of transcripts of 3.3 and 6.2 kb were detected in addition to that of 1.5 kb. DNA polymerase beta activities in these tissues were closely correlated with the mRNA content, indicating that the expression of this enzyme is mainly regulated by the level of the mRNA. A survey of DNA polymerase beta mRNA levels in the testes at successive postnatal developmental stages and in isolated spermatogenic cells indicated that DNA polymerase beta mRNA was most abundant in spermatocytes at early pachytene. Since meiotic recombination occurs in this period, DNA polymerase beta may be involved in the repair-type DNA synthesis associated with the recombination process.

Studies on myosin light chain phosphorylation in intact platelets, utilizing a cell-penetrating thiol protease inhibitor

By employing a cell penetrating thiol protease inhibitor, EST: ethyl(+)-(2S,3S)-3-[(S)-3-methyl-1-(3-methylbutylcarbamoyl)buty lcarbamoyl]- 2-oxiranecarboxylate, the role of calpain, a major thiol protease in platelets, on 20K protein (myosin light chain) phosphorylation was examined in intact human platelets. EST dose-dependently inhibited 20K phosphorylation in platelets stimulated by thrombin, ionomycin or collagen. Phosphopeptides mapping revealed the phosphorylation by these agonists was rendered only by the action of myosin light chain kinase (MLCK). However, in TPA (12-O-tetradecanoylphorbol-13-acetate) stimulated platelets, EST did not inhibit 20K phosphorylation which was mediated by the action of C-kinase. [Ca2+]i determined by the use of quin-2 was elevated after the stimulation of thrombin, ionomycin or collagen but not TPA. Thus, it was suggested that calpain enhances MLCK activity on 20K phosphorylation in intact platelets following the stimulation by the agonist which elevates [Ca2+]i.

Genetic relatedness of human DNA polymerase beta and terminal deoxynucleotidyltransferase

The Protein Identification Resource (PIR) protein sequence data bank was searched for sequence similarity between known proteins and human DNA polymerase beta (Pol beta) or human terminal deoxynucleotidyltransferase (TdT). Pol beta and TdT were found to exhibit amino acid sequence similarity only with each other and not with any other of the 4750 entries in release 12.0 of the PIR data bank. Optimal amino acid sequence alignment of the entire 39-kDa Pol beta polypeptide with the C-terminal two thirds of TdT revealed 24% identical aa residues and 21% conservative aa substitutions. The Monte Carlo score of 12.6 for the entire aligned sequences indicates highly significant aa sequence homology. The hydropathicity profiles of the aligned aa sequences were remarkably similar throughout, suggesting structural similarity of the polypeptides. The most significant regions of homology are aa residues 39-224 and 311-333 of Pol beta vs. aa residues 191-374 and 484-506 of TdT. In addition, weaker homology was seen between a large portion of the 'nonessential' N-terminal end of TdT (aa residues 33-130) and the first region of strong homology between the two proteins (aa residues 31-128 of Pol beta and aa residues 183-280 of TdT), suggestive of genetic duplication within the ancestral gene. On the basis of nucleotide differences between conserved regions of Pol beta and TdT genes (aligned according to optimally aligned aa sequences) it was estimated that Pol beta and TdT diverged on the order of 250 million years ago, corresponding roughly to a time before radiation of mammals and birds.

Synthesis of the nuclear protein cyclin (PCNA) and its relationship with DNA replication

Synthesis of the nuclear protein cyclin (MW 36 000) and DNA in quiescent mouse fibroblasts is coordinately induced by serum and purified growth factors. Inhibition of DNA synthesis by hydroxyurea or aphidicolin in serum-stimulated quiescent cells does not affect the induction of cyclin. The levels of cyclin synthesis decrease rapidly at the end of the S phase. Immunofluorescence studies reveal that there are dramatic changes in the nuclear distribution of cyclin during S phase and that these depend on DNA synthesis or events during S phase. These observations strengthen the notion that cyclin is an important component of the events leading to DNA replication.

Mutational specificity of animal cell DNA polymerases

Since DNA polymerases are involved in DNA replication, recombination, and repair, the frequency with which these enzymes commit errors during synthesis is likely to be an important factor in controlling mutation rates in cells. The fidelity of DNA polymerases was originally studied by following misincorporation using synthetic nucleic acid templates containing only one or two bases. Later, by assaying for reversion of an amber codon after copying phi X174 single-stranded DNA molecules, the base substitution accuracy of in vitro DNA synthesis on natural DNA was determined. Most recently, a forward mutation assay has been developed that uses gap-filling synthesis on an M13mp2 DNA template, thus permitting the detection of a variety of different errors during DNA synthesis on natural DNA templates. Detailed mutational spectra for animal cell polymerases-alpha, beta, and gamma have been determined and demonstrate that a variety of errors can be generated by these purified enzymes. The frequencies of base mispairs, base additions, and deletion errors by DNA polymerases vary widely and depend on both the DNA sequence and the enzyme used. An understanding of the mechanisms by which DNA polymerases avoid or generate various mutations depends on the definition of the parameters that influence the frequency and specificity of particular errors. Future experiments will combine the use of the methods available to measure fidelity with advances in DNA replication enzymology and should lead to exciting new insights into the mechanisms of spontaneous mutagenesis.

Localization of 350K molecular weight and related proteins in both the cytoskeleton and nuclear flecks that increase during G1 phase

Monoclonal and polyclonal antibodies were raised against the highest molecular weight microtubule-associated protein (MAP-1) isolated from brain. Immunoblotting with the antibodies revealed the presence of cross-reactive protein of 350K or less on whole cells, isolated nuclei and cellular microtubules. Two-dimensional peptide maps showed substantial homology of immunoprecipitated cellular proteins of 350K, 80K and 51K with a 25K fragment of brain MAP-1. On antibody staining, immunofluorescence was seen on a cytoplasmic network, the mitotic spindle, the centrosome, and intranuclear flecks. The antibody causing immunofluorescence in all these sites was absorbed most effectively with slices of blotted membrane which contained the 350K protein. These results suggest that the cross-reactive molecules in diverse sites belong to the family of the 350K protein. The number of nuclear flecks and the amount of bound radioactivity of 125I-antibody almost doubled during G1 phase.

Synthesis of catalytically active polymerase alpha by in vitro translation of calf RNA

The cell-free synthesis of DNA polymerase in translation mixtures containing calf thymus total and poly (A+) RNA was examined using activity gel analysis and immunobinding with a monoclonal antibody to calf thymus alpha-polymerase. Activity gel analysis indicated that functional DNA polymerase catalytic polypeptides of Mr = 110,000 to 120,000 and Mr approximately 68,000 were synthesized. Sucrose density gradient centrifugation of total RNA resulted in resolution and partial purification of the mRNAs encoding these two DNA polymerase polypeptides. Immunobinding experiments with the monoclonal antibody to calf alpha-polymerase confirmed that an immunoreactive polypeptide of 110 to 120 kilo-daltons had been formed in vitro. This polypeptide and the 68,000-Mr polypeptide correspond in size to alpha-polymerase catalytic polypeptides observed in crude extracts of calf cells and in purified calf alpha-polymerase.

Structural polymorphism of mouse complement C2 detected by microscale peptide mapping: linkage to H-2

Complement C2 was isolated from 17 mouse strains by immunoprecipitation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis and examined for structural polymorphism by using micro-peptide mapping. By comparing the peptide maps of tryptic digest of C2 from various strains, two allotypic variations were detected. B10 and 14 other mouse strains demonstrated C2.1 type, while a wild mouse line (M.Mol-Ohm) and one B10 congenic strain, B10.MOL.OHM, which carries the H-2 derived from M.Mol-Ohm, demonstrated C2.2 type. (B10 X B10.MOL.OHM)F1 demonstrated codominantly expressed C2 type (C2.1.2). Desialation of mouse C2 did not abolish the observed variation of mouse C2. It is concluded that an H-2-linked codominant locus controls the structure of mouse complement C2, further confirming the extensive homology of the major histocompatibility complex among higher vertebrate species.

Improved conditions for activity gel analysis of DNA polymerase catalytic polypeptides

In a study of mouse DNA polymerase catalytic polypeptides using activity gel analysis, it was found that the sensitivity of detection of purified enzymes is markedly increased by addition of a heterogeneous mixture of proteins to the enzyme sample prior to electrophoresis (Karawya E., and Wilson, S.H. (1982) J. Biol. Chem. 257, 13,129-13,134). This modification and the use of a micromolar level of [32P]dNTP substrate are the basis of an improved activity gel assay for DNA polymerase catalytic polypeptides. This modified assay is several orders of magnitude more sensitive than the original procedure (Spanos, A., Sedgwick, S.G., Yarranton, G.T., Hubscher, U., and Banks, G.R. (1981) Nucl. Acids Res. 9, 1825-1839), and it enables measurement of two reference enzymes, calf beta-polymerase and Escherichia coli DNA polymerase I large fragment, in the picogram range. Further, it was found that it is essential to survey different lots of sodium dodecyl sulfate to identify those which enable high enzyme activity signals after renaturation.

Characterization of messenger RNA for chick-embryo DNA polymerase beta and its translation product in vitro

A specific immunoprecipitation method, using rabbit anti-(chick DNA polymerase beta) IgG was applied to detect the polypeptide of DNA polymerase beta among translation products obtained in vitro with mRNA extracted from chick embryos. A polypeptide of Mr = 40 000 was specifically immunoprecipitated from [35S]methionine-labeled translation products and was competitive with the purified DNA polymerase beta for the antibody. Furthermore, the 40 000-Mr translation product obtained in vitro had DNA polymerase activity, which was detected by assay in situ after electrophoresis in a polyacrylamide gel containing DNA. The mRNA for DNA polymerase beta was polyadenylated and its content was estimated as the range of 0.001% of total poly(A)-rich RNA on the basis of [35S]methionine incorporation in the translation in vitro. The size of this mRNA was determined to be about 1800 nucleotides by zone sedimentation and agarose gel electrophoresis under denaturating conditions.