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E C Friedberg

Publications and source records attributed to E C Friedberg.

At least 163 records · Page 9Linked to original sources
PubMed1985

The RAD2 gene of Saccharomyces cerevisiae: nucleotide sequence and transcript mapping.

We have determined the nucleotide (nt) sequence of a segment of the yeast chromosome carrying the RAD2 gene. The coding region consists of 2925 bp and could encode a protein of 975 amino acids with a calculated Mr of 111 100. A major transcriptional start point was mapped to a position of approx. 22 bp upstream from the first ATG codon. A number of minor transcriptional start points were also identified in this region, all of them 5' to the putative translational start codon. We noted a number of consensus nt sequences in the 5' and 3' non-coding regions of the RAD2, RAD1 and RAD3 genes of Saccharomyces cerevisiae. In addition, three regions of amino acid sequence homology in the putative RAD1 and RAD2 polypeptides were observed.

Amino Acid Sequence↗
PubMed1985

RAD3 gene of Saccharomyces cerevisiae: nucleotide sequence of wild-type and mutant alleles, transcript mapping, and aspects of gene regulation.

We determined the complete nucleotide sequence of the RAD3 gene of Saccharomyces cerevisiae. The coding region of the gene contained 2,334 base pairs that could encode a protein with a calculated molecular weight of 89,796. Analysis of RAD3 mRNA by Northern blots and by S1 nuclease mapping indicated that the transcript was approximately 2.5 kilobases and did not contain intervening sequences. Fusions between the RAD3 gene and the lac'Z gene of Escherichia coli were constructed and used to demonstrate that the RAD3 gene was not inducible by DNA damage caused by UV radiation or 4-nitroquinoline-1-oxide. Two UV-sensitive chromosomal mutant alleles of RAD3, rad3-1 and rad3-2, were rescued by gap repair of a centromeric plasmid, and their sequences were determined. The rad3-1 mutation changed a glutamic acid to lysine, and the rad3-2 mutation changed a glycine to arginine. Previous studies have shown that disruption of the RAD3 gene results in loss of an essential function and is associated with inviability of haploid cells. In the present experiments, plasmids carrying the rad3-1 and rad3-2 mutations were introduced into haploid cells containing a disrupted RAD3 gene. These plasmids expressed the essential function of RAD3 but not its DNA repair function. A 74-base-pair deletion at the 3' end of the RAD3 coding region or a fusion of this deletion to the E. coli lac'Z gene did not affect either function of RAD3.

Alleles↗
PubMed1985

Nucleotide excision repair of DNA in eukaryotes: comparisons between human cells and yeast.

Little is known about the molecular mechanism of nucleotide excision repair in eukaryotes. Studies on human cells have been stimulated by the availability of excision repair-defective cell lines from patients suffering from the autosomal recessive disease xeroderma pigmentosum. Such studies have contributed appreciably to an understanding of the genetic complexity of excision repair in human cells. However, to date no human excision repair genes or gene products known to complement the repair defect in xeroderma pigmentosum cells have been isolated. The yeast Saccharomyces cerevisiae is an interesting model for exploring the molecular mechanism of nucleotide excision repair in eukaryotic cells. As is true in human cells, multiple yeast genes are involved in this phenomenon and at least five genes are required for the specific incision of ultraviolet-irradiated DNA in vivo. These five genes have been isolated by molecular cloning and the nucleotide sequences of four of them have been determined. Each of these cloned genes will be used for overexpression of protein and it is anticipated that the purification and characterization of these proteins will provide insight into the biochemistry of nucleotide excision repair in eukaryotes.

Base Sequence↗
PubMed1984

Physical mapping and complete nucleotide sequence of the denV gene of bacteriophage T4.

Phage T4 deletion mutants that are folate analog resistant (far) and contain deletions in the region of the T4 genome near denV have been isolated previously. We showed that one of these mutants (T4farP12) expressed normal denV gene activity, whereas another mutant (T4farP13) was defective in the denV gene. The rII-distal (right) physical endpoints of these deletions defined the limits of the interval in which the rII-proximal (left) endpoint of the denV gene should be located. The deletion endpoints were identified by restriction and Southern hybridization analyses of phage derivatives containing deoxycytidine instead of hydroxymethyldeoxycytidine in their DNAs. The results of these analyses localized the rII-proximal (left) end of the denV gene to a region between 62.4 and 64.3 kilobases on the T4 physical map. denV+ phage resulted from marker rescue with two of five denV- alleles tested, using plasmids containing a 1.8-kilobase fragment from this region or a 179-base-pair terminal fragment derived from it. Sequencing of the 179-base-pair fragment from wild-type DNA showed a 130-base-pair open reading frame with its termination codon at the rII-proximal end. Confirmation that this open reading frame is part of the denV coding sequence was obtained by identifying a TAG amber codon in the homologous DNA derived from a denV amber mutant strain. This mutant strain rescued the denV+ allele from plasmids containing the wild-type sequence. An adjacent overlapping restriction fragment was also cloned, permitting determination of the remaining denV gene sequence. Based on these results, the 3' end of the coding region of the denV locus was mapped to kilobase position 64.07 on the T4 physical map, and the 5' end was mapped to position 64.48.

Base Sequence↗
PubMed1984

Molecular cloning and nucleotide sequence analysis of the Saccharomyces cerevisiae RAD1 gene.

We have screened a yeast genomic library for complementation of the UV sensitivity of mutants defective in the RAD1 gene and isolated a plasmid designated pNF1000 with an 8.9-kilobase insert. This multicopy plasmid quantitatively complemented the UV sensitivity of two rad1 mutants tested but did not affect the UV resistance of other rad mutants. The location of the UV resistance function in pNF1000 was determined by deletion analysis, and an internal fragment of the putative RAD1 gene was integrated into the genome of a RAD1 strain. Genetic analysis of several integrants showed that integration occurred at the chromosomal RAD1 site, demonstrating that the internal fragment was derived from the RAD1 gene. A 3.88-kilobase region of pNF1000 was sequenced and showed the presence of a small open reading frame 243 nucleotides long that is apparently unrelated to RAD1, as well as a 2,916-nucleotide larger open reading frame presumed to encode RAD1 protein. Depending on which of two possible ATG codons initiates translation, the size of the RAD1 protein is calculated at 110 or 97 kilodaltons.

Amino Acid Sequence↗
PubMed1984

Saccharomyces cerevisiae RAD2 gene: isolation, subcloning, and partial characterization.

A plasmid (pNF2000) containing a 9.7-kilobase pair DNA insert that complements the UV sensitivity of rad2-1, rad2-2, and rad2-4 mutants of Saccharomyces cerevisiae has been isolated from a yeast genomic library. Genetic analysis of strains derived by transformation of rad2 mutants with an integrating plasmid containing a 9.3-kilobase pair fragment from pNF2000 shows that the fragment integrates exclusively at the chromosomal rad2 gene. We therefore conclude that this plasmid contains the RAD2 gene. The 9.3-kilobase pair fragment was partially digested with Sau3A and cloned into a multicopy yeast vector designed for easy retrieval of Sau3A inserts. The smallest subclone that retains the RAD2 gene is 4.5 kilobase pairs. This fragment was partially digested with Sau3A and cloned into an integrating plasmid. These plasmids were isolated and integrated into a heterozygous rad2/RAD2 strain. Plasmids containing internal fragments of the RAD2 gene were identified because they yielded UV-sensitive transformants due to disruption of the RAD2 gene. Sporulation of diploids transformed with integrating plasmids containing internal fragments of RAD2 gave rise to four viable haploids per tetrad, indicating that unlike the RAD3 gene of S. cerevisiae, the RAD2 gene is not essential for the viability of haploid cells under normal growth conditions. Measurements of the RNA transcript by RNA-DNA hybridization with the internal fragment as the probe indicate a size of approximately 3.2 kilobases.

Cloning, Molecular↗
PubMed1984

Use of plasmid-mediated resistance to the antibiotic G418 for the rapid screening of a yeast mutant library.

Both haploid and diploid yeast cells are sensitive to the antibiotic G418. The former develop spontaneous resistance to G418 at a frequency of approximately 2 X 10(-6), however, the frequency of resistance in diploids is less than 1 X 10(-9) and was undetectable in these experiments. Mating of spontaneously resistant haploid cells to G418-sensitive strains yields sensitive diploids, indicating that spontaneous resistance to the antibiotic is a recessive trait. Both haploid and diploid cells can be efficiently transformed to G418 resistance by a plasmid carrying the Escherichia coli kanamycin resistance (kanr) marker. The ability to select for cells transformed with plasmids containing the kanr gene has facilitated the screening of a large series of temperature sensitive yeast mutants to determine whether any of them are allelic to RAD3.

Anti-Bacterial Agents↗
PubMed1983

A DNA repair gene required for the incision of damaged DNA is essential for viability in Saccharomyces cerevisiae.

A diploid strain (RAD3/RAD3) of Saccharomyces cerevisiae was transformed with an integration plasmid containing an internal fragment of the cloned yeast RAD3 gene. Integration by homologous recombination inactivated one of the diploid RAD3 genes, creating a recessive mutation. This mutation is inferred to be lethal in haploid cells since sporulation of diploid transformants segregated two viable and two inviable spores per tetrad, while integration of plasmids containing one or the other end of the RAD3 gene resulted in diploid transformants that segregated normally--i.e., four viable spores in each tetrad. Evidence that integration of the internal fragment occurred specifically at one of the RAD3 genes in the diploid is provided by DNA . DNA hybridizations. In addition, transformation of a diploid strain heterozygous for the RAD3 gene (RAD3/rad3-2) (carrying a rad3 mutation that does not affect the viability of haploid cells) results in the rad- phenotype in half of the transformants, indicating that the RAD3 gene was inactivated in these cells.

Base Sequence↗
PubMed1983

Use of an Escherichia coli mutant strain permits measurement of single-stranded apurinic-apyrimidinic endonuclease in crude extracts: studies with untransformed cells and cells transformed with plasmids containing the uvrC gene.

We have constructed a strain of Escherichia coli that is defective in exonuclease VII and uracil-DNA glycosylase activities. This strain (xse ung) facilitates the quantitation of single-stranded apurinic-apyrimidinic endonuclease activity in crude extracts. Quantitative comparisons of single-stranded apurinic-apyrimidinic endonuclease activity under conditions in which uvrC protein is overexpressed showed no differences, suggesting that single-stranded apurinic-apyrimidinic endonuclease and uvrC protein are probably distinct.

Bacterial Proteins↗
PubMed1983

Measurement of repair patch size by quantitation of nucleotides excised during DNA repair in vivo.

Escherichia coli uvr- cells, prelabeled in their DNA, were infected with phage T4 denV+ or T4 denV- under conditions that preclude phage-mediated degradation of the bacterial chromosome. Measurement of the distribution of acid-soluble radioactivity between pyrimidine dimers and nondimer nucleotides in cell extracts yielded calculated estimates of the average size of excision repair tracts that are in good agreement with the size of repair patches determined by others using direct measurement of repair synthesis.

DNA Repair↗
PubMed1982

Use of high-performance liquid chromatography to quantitate thymine-containing pyrimidine dimers in DNA.

We have developed two high-performance liquid chromatographic systems for the measurement of pyrimidine dimers in hydrolysates of DNA. Normal-phase chromatography on an NH2 column in methanol-ethyl acetate (3.97) at an elution rate of 2.0 ml/min allowed quantitation of thymine-containing (thymine-thymine plus thymine-uracil) pyrimidine dimers at levels as low as 0.1% of the total radioactivity as thymine in DNA. This system was unaffected by the presence of up to 1 mg of contaminating protein (bovine serum albumin) or 40 micrograms of DNA in hydrolysates prepared for chromatography. Reversed-phase chromatography on a muBondapak C18 column allowed measurement of thymine-thymine dimers at concentrations as low as 0.02% of the total radioactivity. With 0.1% tetrahydrofuran in water as the solvent at a flow-rate of up to 0.6 ml/min, thymine-thymine, thymine-uracil, and uracil-uracil dimers were completely resolved. We were not able to quantitate the latter two dimeric forms, however, owing to the presence of other radioactive components of undefined origin that eluted concomitantly with the uracil-containing dimers.

Chromatography, High Pressure Liquid↗
PubMed1982

An enzyme activity from Escherichia coli that attacks single-stranded deoxyribopolymers and single-stranded deoxyribonucleic acid containing apyrimidinic sites.

We have isolated an enzyme activity from extracts of Escherichia coli that catalyzes the hydrolysis of phosphodiester bonds in the single-stranded deoxyribopolymer (dU.[3H]dT)(2000) containing depyrimidinated sites created by enzymatic removal of uracil with uracil-DNA glycosylase. Nondepyrimidinated polymer is not degraded by the enzyme, nor is the depyrimidinated polymer degraded after reduction of apyrimidinic sites with sodium borohydride. The enzyme also degrades circular M13 DNA containing uracil or denatured phage PBS2 DNA (which naturally contains uracil) only after the removal of uracil from these substrates by uracil-DNA glycosylase. Undamaged or depurinated duplex PM2 or ColE1 DNA and undamaged M13 single-stranded DNA are not attacked by the enzyme. The activity sediments in glycerol gradients with a relative s value of 4.2 S and has a Stokes radius of 31 A, yielding a calculated Mr approximately 56,000. The fractional ratio (f/f0) is calculated at 1.25. The enzyme has no requirement for any known cofactors and is insensitive to inhibition by p-(chloromercuri)benzoate. Activity is inhibited in the presence of adenosine 5'0-triphosphate (ATP), tRNA or high ionic strength and is slightly stimulated by MnCl2 or CaCl2.

DNA Repair↗
PubMed1982

Molecular cloning of eucaryotic genes required for excision repair of UV-irradiated DNA: isolation and partial characterization of the RAD3 gene of Saccharomyces cerevisiae.

We describe the molecular cloning of a 6-kilobase (kb) fragment of yeast chromosomal DNA containing the RAD3 gene of Saccharomyces cerevisiae. When present in the autonomously replicating yeast cloning vector YEp24, this fragment transformed two different UV-sensitive, excision repair-defective rad3 mutants of S. cerevisiae to UV resistance. The same result was obtained with a variety of other plasmids containing a 4.5-kb subclone of the 6-kb fragment. The UV sensitivity of mutants defective in the RAD1, RAD2, RAD4, and RAD14 loci was not affected by transformation with these plasmids. The 4.5-kb fragment was subcloned into the integrating yeast vector YIp5, and the resultant plasmid was used to transform the rad3-1 mutant to UV resistance. Both genetic and physical studies showed that this plasmid integrated by homologous recombination into the rad3 site uniquely. We conclude from these studies that the cloned DNA that transforms the rad3-1 mutant to UV resistance contains the yeast chromosomal RAD3 gene. The 4.5-kb fragment was mapped by restriction analysis, and studies on some of the subclones generated from this fragment indicate that the RAD3 gene is at least 1.5 kb in size.

Cloning, Molecular↗
PubMed1982

Demonstration of pyrimidine dimer-DNA glycosylase activity in vivo: bacteriophage T4-infected Escherichia coli as a model system.

An approach to the detection of pyrimidine dimer-DNA glycosylase activity in living cells is presented. Mutants of Escherichia coli defective in uvr functions required for incision of UV-irradiated DNA were infected with phage T4 denV+ or denV- (defective in the T4 pyrimidine dimer-DNA glycosylase activity). In the former case the denV gene product catalyzed the incision of UV-irradiated host DNA, facilitating the subsequent excision of thymine-containing pyrimidine dimers. Isolation of these dimers from the acid-soluble fraction of infected cells was achieved by a multistep thin-layer chromatographic system. Exposure of the dimers to irradiation that monomerizes pyrimidine dimers (direct photoreversal) resulted in the stoichiometric formation of free thymine. Thus, in vivo incision of UV-irradiated DNA dependent on a pyrimidine dimer-DNA glycosylase can be demonstrated.

Cell-Free System↗
PubMed1981

Specificity of the bacteriophage PBS2 induced inhibitor of uracil-DNA glycosylase.

The purified PBS2 phage-coded inhibitor of uracil-DNA glycosylase (Ura-DNA glycosylase) from Bacillus subtilis has been tested for its ability to inhibit this enzyme isolated from other prokaryotic and from eukaryotic sources. In addition, the inhibitor has been assayed for its effect on DNA glycosylases specific for other base residues in DNA. The data indicate that Ura-DNA glycosylases from a variety of sources are equally sensitive to inhibition by the inhibitor. DNA glycosylases specific for base residues in DNA other than uracil are not inhibited by the PBS2-coded inhibitor.

Bacillus subtilis↗
PubMed1981

The repair of DNA damage: recent developments and new insights.

This brief review presents the salient features of new developments in the enzymatic repair of base damage to DNA. DNA glycosylases and apurinic/apyrimidinic (AP) endonucleases are reviewed and evidence is presented that in at least two prokaryote systems incision of UV-irradiated DNA occurs by the sequential action of these two classes of enzymes. In contradistinction, the uvrA, uvrB, and uvrC gene products of E coli appear to function as a multi-protein complex that catalyzes hydrolysis of phosphodiester bonds in damaged DNA directly. The inducible rapid repair of O6-methylguanine in E coli is also reviewed.

DNA↗