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At least 595 records · Page 33Linked to original sources
PubMed2002

Stimulation of 3'-->5' exonuclease and 3'-phosphodiesterase activities of yeast apn2 by proliferating cell nuclear antigen.

The Apn2 protein of Saccharomyces cerevisiae contains 3'-->5' exonuclease and 3'-phosphodiesterase activities, and these activities function in the repair of DNA strand breaks that have 3'-damaged termini and which are formed in DNA by the action of oxygen-free radicals. Apn2 also has an AP endonuclease activity and functions in the removal of abasic sites from DNA. Here, we provide evidence for the physical and functional interaction of Apn2 with proliferating cell nuclear antigen (PCNA). As indicated by gel filtration and two-hybrid studies, Apn2 interacts with PCNA both in vitro and in vivo and mutations in the consensus PCNA-binding motif of Apn2 abolish this interaction. Importantly, PCNA stimulates the 3'-->5' exonuclease and 3'-phosphodiesterase activities of Apn2. We have examined the involvement of the interdomain connector loop (IDCL) and of the carboxy-terminal domain of PCNA in Apn2 binding and found that Apn2 binds PCNA via distinct domains dependent upon whether the binding is in the absence or presence of DNA. In the absence of DNA, Apn2 binds PCNA through its IDCL domain, whereas in the presence of DNA, when PCNA has been loaded onto the template-primer junction by replication factor C, the C-terminal domain of PCNA mediates the binding.

Amino Acid Motifs↗
PubMed2004

Gene-targeted mice lacking the Trex1 (DNase III) 3'-->5' DNA exonuclease develop inflammatory myocarditis.

TREX1, originally designated DNase III, was isolated as a major nuclear DNA-specific 3'-->5' exonuclease that is widely distributed in both proliferating and nonproliferating mammalian tissues. The cognate cDNA shows homology to the editing subunit of the Escherichia coli replicative DNA polymerase III holoenzyme and encodes an exonuclease which was able to serve a DNA-editing function in vitro, promoting rejoining of a 3' mismatched residue in a reconstituted DNA base excision repair system. Here we report the generation of gene-targeted Trex1(-/-) mice. The null mice are viable and do not show the increase in spontaneous mutation frequency or cancer incidence that would be predicted if Trex1 served an obligatory role of editing mismatched 3' termini generated during DNA repair or DNA replication in vivo. Unexpectedly, Trex1(-/-) mice exhibit a dramatically reduced survival and develop inflammatory myocarditis leading to progressive, often dilated, cardiomyopathy and circulatory failure.

Animals↗
PubMed1995

Difference in constitutive heterochromatin behaviour between human amniocytes and lymphocytes detected by a sequential in situ exonuclease III digestion-random primer extension procedure.

Fixed chromosomes from human amniotic fluid cells and peripheral blood lymphocytes were digested in situ with exonuclease III and the single stranded DNA obtained was used as template for an in situ random primer extension. Under these conditions an R banding pattern, more evident in lymphocytes than in amniocytes, was obtained. Nevertheless, constitutive heterochromatin of chromosomes 1, 16, Yq, and mainly the pericentromeric region of chromosome 9 was far more intensely labelled in amniocytes than in lymphocytes. Fluorescence in situ hybridisation with a specific classical satellite DNA probe, showed that this differential labelling was dependent on a greater sensitivity of chromosome 9 constitutive heterochromatin to exonuclease III digestion in amniocytes than in lymphocytes, thus indicating qualitative differences in this region between both human cellular materials.

Adolescent↗
PubMed1996

Differential sensitivity of some human alphoid and classical satellite DNA regions from lymphocyte chromosomes to in situ exonuclease III digestion.

Fluorescent in situ hybridization of alphoid and classical satellite III DNA sequences was performed on fixed chromosomes from human lymphocytes that were previously digested in situ with exonuclease III to produce single-stranded DNA motifs. Digital image analysis showed that while labeled alphoid satellite DNAs produced signals of similar strength to thermally denatured chromosomes, those of classical satellite III DNAs of chromosomes 9 and Yq were around 50% weaker. This result shows a differential sensitivity of these satellite DNA regions to in situ exonuclease III digestion and suggests structural differences in the higher-order organization of both subchromosomal constitutive heterochromatic regions.

Chromosomes, Human↗
PubMed2005

Degradation of human exonuclease 1b upon DNA synthesis inhibition.

In response to DNA damage, signaling pathways are triggered that either block the cell division cycle at defined transitions (G1-S and G2-M) or slow down progression through the S phase. Nucleases play important roles in DNA synthesis, recombination, repair, and apoptosis. In this study, we have examined the regulation of human exonuclease 1 (hEXO1b). The endogenous hEXO1b protein was only detected upon enrichment by immunoprecipitation. We found that hEXO1b was constantly expressed throughout the cell cycle. However, treatment of cells with agents that cause arrest of DNA replication led to rapid degradation of hEXO1b. This effect was fully reversed upon removal of the block. Analysis of synchronized cells showed that degradation of hEXO1b during the S phase was strictly dependent on DNA synthesis inhibition. DNA damage caused by UV-C radiation, ionizing radiation, cisplatin, or the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine did not affect hEXO1b stability. We show that hEXO1b was phosphorylated in response to inhibition of DNA synthesis and that phosphorylation coincided with rapid protein degradation through ubiquitin-proteasome pathways. Our data support the evidence that control of exonuclease 1 activity may be critical for the maintenance of stalled replication forks.

Antibodies↗
PubMedDate not supplied

[The correcting role of autonomous 3'-->5' exonucleases in mammalian multienzyme DNA polymerase complexes].

A study was made of the correcting role of autonomous 3'-->5' exonucleases (AE) contained in multienzyme DNA polymerase complexes of rat hepatocytes or calf thymocytes. DNA was synthesized on phage psi X174 amber3 or M13mp2 primer-templates, and used to transfect Escherichia coli spheroplasts. Frequencies were estimated for direct and reverse mutations resulting from mistakes made in the course of in vitro DNA synthesis. The mistake rate of the hepatocytic complex was estimated at 3 x 10(-6) with equimolar dNTP, and increased tenfold when proteins accounting for 70% of the total 3'-->5' exonuclease activity of the complex were removed. The fidelity of DNA synthesis was completely restored in the presence of exogenous AE (epsilon subunit of E. coli DNA polymerase III). Nuclear (Pol delta n) and cytosolic (Pol delta c) forms of DNA polymerase delta were isolated from calf thymocytes. The former was shown to contain an AE (TREX2) absent from the latter. As compared with Pol delta c, Pol delta n had a 20-fold higher exo/pol ratio and allowed 4-5 times higher fidelity of DNA synthesis. The mistake rate of DNA polymerase complexes changed when dNTP were used in nonequimolar amounts.

Animals↗
PubMed1991

Strand exchange protein 1 from Saccharomyces cerevisiae. A novel multifunctional protein that contains DNA strand exchange and exonuclease activities.

Strand exchange protein 1 (Sep1) from Saccharomyces cerevisiae catalyzes the formation of heteroduplex DNA molecules from single-stranded circles and homologous linear duplex DNA in vitro. Previously, Sep1 was purified as a 132,000-Da species; however, DNA sequence analysis indicates that the SEP1 gene is capable of encoding a 175,000-Da protein (Tishkoff, D.X., Johnson, A.W., and Kolodner, R.D. (1991) Mol. Cell. Biol. 11, 2593-2608). The SEP1 gene was cloned into a GAL10 expression vector and expressed in a protease-deficient yeast strain. Intact Sep1, which migrated as a Mr-160,000 polypeptide during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was purified to apparent homogeneity and shown to have activities similar to those of the originally purified Mr = 132,000 fragment. We report here that, in addition to strand exchange activity, Sep1 contains an intrinsic exonuclease that is active on single- and double-stranded DNA with a severalfold preference for single-stranded DNA. The nuclease was induced in crude extracts upon induction with galactose, it co-purified with the strand exchange activity of Sep1, and the nuclease and strand exchange activities of Sep1 showed the same kinetics of heat inactivation. Sep1 nuclease, which requires Mg2+, can be functionally separated from the strand exchange activity by the substitution of Ca2+ for Mg2+. Under these conditions, the nuclease is inactive, and strand exchange activity is dependent on prior resection of the DNA ends by an exogenous exonuclease. Thus, the nuclease is necessary for synapsis but not strand exchange. Electron microscopic analysis revealed that true strand exchange products, alpha molecules and nicked double-stranded circular molecules, were formed. In addition, strand transfer proceeded to similar extents on 5'-resected and 3'-resected DNA. This result suggests that the polarity of strand transfer by Sep1 is determined by the polarity of its intrinsic nuclease.

Amino Acid Sequence↗
PubMed1991

cDNA and deduced amino acid sequence of a mouse DNA repair enzyme (APEX nuclease) with significant homology to Escherichia coli exonuclease III.

We purified a mouse DNA repair enzyme having apurinic/apyrimidinic endonuclease, DNA 3'-phosphatase, 3'-5'-exonuclease and DNA 3' repair diesterase activities, and designated the enzyme as APEX nuclease. A cDNA clone for the enzyme was isolated from a mouse spleen cDNA library using probes of degenerate oligonucleotides deduced from the N-terminal amino acid sequence of the enzyme. The complete nucleotide sequence of the cDNA (1.3 kilobases) was determined. Northern hybridization using this cDNA showed that the size of its mRNA is about 1.5 kilobases. The complete amino acid sequence for the enzyme predicted from the nucleotide sequence of the cDNA (APEX nuclease cDNA) indicates that the enzyme consists of 316 amino acids with a calculated molecular weight of 35,400. The predicted sequence contains the partial amino acid sequences determined by a protein sequencer from the purified enzyme. The coding sequence of APEX nuclease was cloned into pUC18 SmaI and HindIII sites in the control frame of the lacZ promoter. The construct was introduced into BW2001 (xth-11, nfo-2) strain cells of Escherichia coli. The transformed cells expressed a 36.4-kDa polypeptide (the 316 amino acid sequence of APEX nuclease headed by the N-terminal decapeptide of beta-galactosidase) and were less sensitive to methyl methanesulfonate than the parent cells. The fusion product showed priming activity for DNA polymerase on bleomycin-damaged DNA and acid-depurinated DNA. The deduced amino acid sequence of mouse APEX nuclease exhibits a significant homology to those of exonuclease III of E. coli and ExoA protein of Streptococcus pneumoniae and an intensive homology with that of bovine AP endonuclease 1.

Amino Acid Sequence↗
PubMed1990

Biochemical and physical characterization of exonuclease V from Escherichia coli. Comparison of the catalytic activities of the RecBC and RecBCD enzymes.

Biochemical evidence is presented that confirms exonuclease V of Escherichia coli consists of three distinct subunits encoded by the recB, recC, and recD genes. The recD gene encodes a Mr 60,000 polypeptide and physically maps 3' to the recB structural gene. The role of the recD subunit in exonuclease V function has been examined by comparing the catalytic activities of the purified RecBCD enzyme with the RecBC enzyme. The RecBC enzyme retains significant levels of DNA-dependent ATPase activity and DNA helicase activity. Endonucleolytic activity on single-stranded covalently closed DNA becomes ATP-dependent. Exonucleolytic activity on either single- and double-stranded DNA was not detected. Taken together with the phenotypic properties of recD null mutants, it appears that the exonucleolytic activities of the RecBCD enzyme are not required for genetic recombination and the repair of either UV-induced photoproducts or mitomycin C-generated DNA cross-links, but are essential for the repair of methyl methanesulfonate-induced methylation.

Adenosine Triphosphatases↗
PubMed1987

[Determination of inhibition sites during hydrolysis of polydeoxyribonucleotides by exonucleases III from Bacillus amyloliquefaciens and Escherichia coli].

The influence of the primary structure of polydeoxyribonucleotides on the rate of hydrolysis with exonuclease III from Bacillus amyloliquefaciens and Escherichia coli was investigated. The substrates used were synthetic oligodeoxyribonucleotides and pBR 322 DNA fragments labeled with 32P at the 5'-termini of one of the chains. According to the data from polyacrylamide gel electrophoresis performed under denaturing conditions, the hydrolysis of these substrates by unsaturating concentrations of B. amyloliquefaciens and E. coli exonuclease III proceeds with several reproducible "stops". The decrease of the reaction rate was shown to take place just before the pyrimidine blocks in the digested DNA chain.

Bacillus↗
PubMed1986

Bacteriophage N4-coded 5'----3' exonuclease. Purification and characterization.

Bacteriophage N4 DNA replication requires the activity of a phage-induced exonuclease. We show here that the activity is phage coded. We have purified this enzyme to apparent homogeneity. It has a denatured molecular weight of 45,000 and exists in solution as a dimer. Duplex DNA is the preferred substrate which it degrades in a 5'----3' direction to 5' mononucleotides by a distributive mechanism. The enzyme does not act at a nick or a gap; indeed, it requires an end for activity. A possible role for this exonuclease in N4 replication is discussed.

Coliphages↗
PubMed1987

Determination of the nucleotide sequence for the exonuclease I structural gene (sbcB) of Escherichia coli K12.

The complete nucleotide sequence of the structural gene for Escherichia coli exonuclease I has been determined. The coding region corresponds to a 465-amino acid protein with molecular weight of 53,174. The partial amino acid sequence of purified exonuclease I agrees with that predicted by the DNA sequence. Two putative weak promoters have been localized by S1 nuclease analysis. The sbcB coding sequence contains many non-optimal codons, characteristic of many poorly expressed E. coli genes.

Amino Acid Sequence↗
PubMed1994

Psoralen--lexitropsin hybrids: DNA sequence selectivity of photoinduced cross-linking from MPE footprinting and exonuclease III stop assay, and mode of binding from electric linear dichroism.

The properties of certain hybrids 3 and 5 bearing a photoactivatable psoralen group attached to DNA sequence recognizing lexitropsin carriers have been examined. The hybrids bind to poly(dA-dT) with Kapp of 2.8 and 0.9 x 10(7) M-1, i.e. greater than or equal to that of netropsin (Kapp = 1.0 x 10(7) M-1), indicating that the psoralen moiety may contribute to binding in the case of 5. Photoinduced cross-linking of DNA by 3 and 5, while efficient, is less so than that of individual psoralens and reaches a maximum at a ligand to DNA base pair ratio (r) of 0.2. Complementary strand methidium-propyl-EDTA (MPE).Fe(II) footprinting demonstrated that, in the dark, the sequence preferential recognition of hybrids 3 and 5 is dominated by the lexitropsin moiety. Examination of 360 nm photoinduced DNA cross-linking by the hybrids 3 and 5 was carried out using an exonuclease III stop assay. This revealed that > 95% of the DNA remained double stranded, indicating that 3 and 5 generate primarily biadducts at AT-rich sequences. This assay also located individual monoadduct sites, some of which are remote from the dominant cross-linked sites. When the samples were exposed to 254 nm UV light before loading onto the gel to reverse the photoproducts, the pattern of the exonuclease III stop bands was not altered significantly compared with the experiment without 254 nm irradiation. It is concluded that these termination sites include both mono- and biadducts. Electric linear dichroism examination of the DNA complexes of hybrids 3 and 5 (without light activation) provides evidence that the lexitropsin portion binds in the minor groove, while the psoralen portion intercalates in a suitably located site for subsequent photoinduced cross-linking.

Antineoplastic Agents↗
PubMed1994

Isolation, characterization, and kinetic properties of truncated forms of T4 DNA polymerase that exhibit 3'-5' exonuclease activity.

Limited proteolysis of T4 DNA polymerase generated a 45-kDa and 35-kDa protein complex, which had 3'-5' exonucleolytic activity but lacked polymerase activity. After partial chymotryptic digestion of the cloned and expressed 45-kDa protein derived from T4 DNA polymerase, we isolated a 27-kDa fragment (residues 96-331) that still had 3'-5' exonuclease activity, thus demonstrating that the amino acid residues required for catalysis are included within this fragment. We also show that the apparent Km values for the 3'-5' exonuclease activity exhibited by the 27-kDa fragment are considerably greater than the apparent Km values determined for the intact DNA polymerase on deoxyoligonucleotide substrates having more than 3 bases. In contrast, the kcat values for phosphodiester bond hydrolysis of 3'-terminal nucleotides are not very different when comparing intact T4 DNA polymerase with the 27-kDa fragment derived from it. Thus, participation of residues distal to 331 are not required for catalysis, but only for binding, and, based on the similarity of kcat values, the geometry of the residues responsible for catalysis are preserved even in the absence of the carboxyl-terminal 567 residues.

Bacteriophage T4↗
PubMed1994

Spatial relationship between polymerase and exonuclease active sites of phage T4 DNA polymerase enzyme.

The spatial relationship between the polymerase and exonuclease active sites of bacteriophage T4 DNA polymerase enzyme has been examined using a bulky biotin-streptavidin block at a specified position in an oligonucleotide (Fig. 1). The idea was to monitor the closest distance of approach of the T4 enzyme before being blocked by the bulky biotin-streptavidin complex while performing either of its activities. The results indicated a distance of 4-5 nucleotides between the biotin-streptavidin probe and the exonuclease site and a distance requirement of at least 7 nucleotides between the bulky probe and the 3'-primer terminus for efficient polymerization by the T4 enzyme. The difference in the two distances suggested a separation of 2-3 nucleotides between the two active sites of the T4 enzyme.

Bacterial Proteins↗
PubMed1997

[Phenotypic characterization of Bacillus subtilis mutants with decreased exonuclease I activity].

A Bacillus subtilis strain containing a mutation decreasing exonuclease I activity by up to 25% as compared to normal cells of the original BD46 strain was developed. A decrease in B. subtilis exonuclease I activity increased the sensitivity of mutant cells to UV irradiation and mitomycin C, decreased the frequency of recombination during chromosomal transduction and transformation, decreased the frequency of transposon Tn917 translocation from plasmid to the bacterial chromosome, and did not affect the frequency of plasmid transformation. The corresponding mutation was mapped.

Bacillus subtilis↗
PubMed1998

Stimulation of murine B lymphocytes induces a DNA exonuclease whose activity on switch-mu DNA is specifically inhibited by other germ-line switch region RNAs.

The Ig heavy chain class switch in B lymphocytes involves a unique genetic recombination that fuses specific regions within the Ig locus and deletes intervening sequences. Here we describe a novel exonuclease activity in nuclear lysates of B cells in an in vitro assay. This activity was induced in B lymphocytes after treatment with either LPSs or CD40 ligand/anti-delta-dextran, both of which induce switch recombination, and considerably less activity was detected in untreated or anti-delta-dextran-treated B cells, Con A-stimulated spleen cells, liver cells, or a number of cell lines. The exonuclease activity was dependent on divalent cations, and both 3' and 5' labels were efficiently removed from DNA substrates. The presence of RNase A, but not RNase H, inhibited exonucleolytic digestion, suggesting that a ribonucleoprotein is responsible for the exonucleolysis. The DNA digestion appears to be nonspecific, since DNA substrates with either switch-mu or unrelated sequence were hydrolyzed with comparable efficiency. Germ-line switch region transcripts (Ig gamma1, Ig gamma3, and Ig alpha) strongly inhibited the exonucleolysis of switch-mu DNA but not that of unrelated control DNA, while switch antisense RNA or tRNA were much less effective inhibitors.

Animals↗
PubMed1998

Human exonuclease I interacts with the mismatch repair protein hMSH2.

DNA mismatch repair (MMR) plays a vital role in the faithful replication of DNA, and its inactivation leads to a mutator phenotype that has been associated with the common cancer susceptibility syndrome Hereditary Non-Polyposis Colorectal Cancer (HNPCC). Here, we report on a novel human exonuclease (hExoI) that is related to the yeast exonuclease 1. The hExoI cDNA comprises 2541 bp, which code for a Mr 94,000 protein that appears to be highly expressed in testis tissue and at very low levels in other tissues. The hExoI gene has 14 exons and is located on chromosome 1q43, as determined by fluorescence in situ hybridization and radiation hybrid mapping. hExoI was found to interact strongly with the human MMR protein hMSH2, suggesting its involvement in the MMR process and/or DNA recombination.

Amino Acid Sequence↗