Repair replication in Escherichia coli as measured by the photolysis of bromodeoxyuridine

Shedding light on proteins, nucleic acids, cells, humans and fish

I was trained as a physicist in graduate school. Hence, when I decided to go into the field of biophysics, it was natural that I concentrated on the effects of light on relatively simple biological systems, such as proteins. The wavelengths absorbed by the amino acid subunits of proteins are in the ultraviolet (UV). The wavelengths that affect the biological activities, the action spectra, also are in the UV, but are not necessarily parallel to the absorption spectra. Understanding these differences led me to investigate the action spectra for affecting nucleic acids, and the effects of UV on viruses and cells. The latter studies led me to the discovery of the important molecular nature of the damages affecting DNA (cyclobutane pyrimidine dimers) and to the discovery of nucleotide excision repair. Individuals with the genetic disease xeroderma pigmentosum (XP) are extraordinarily sensitive to sunlight-induced skin cancer. The finding, by James Cleaver, that their skin cells were defective in DNA repair strongly suggested that DNA damage was a key step in carcinogenesis. Such information was important for estimating the wavelengths in sunlight responsible for human skin cancer and for predicting the effects of ozone depletion on the incidence of non-melanoma skin cancer. It took experiments with backcross hybrid fish to call attention to the probable role of the longer UV wavelengths not absorbed by DNA in the induction of melanoma. These reflections trace the biophysicist's path from molecules to melanoma.

The repair patch of E. coli (A)BC excinuclease

The size of repair patch made by E. coli DNA polymerase I (Poll) following the removal of a thymine-psoralen monoadduct by E. coli (A)BC excinuclease was determined by using an M13mp19 DNA with a single psoralen monoadduct at the polylinker region. Incubation of this substrate with (A)BC excinuclease, Poll and a combination of 3 dnTP plus 1 dNTP(alpha S) for each nucleotide, and DNA ligase resulted in a repair patch with phosphorothioate linkages. The preferential hydrolysis of phosphorothioate bonds by heating in iodoethanol revealed a patch size--with minimal nick translation--equal in length to the 12 nucleotide gap generated by this excision nuclease.

A novel repair enzyme: UVRABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region

The uvrA, uvrB, and uvrC proteins of Escherichia coli were purified from strains that greatly overproduce these proteins. Using the purified proteins, the UVRABC nuclease was reconstituted in vitro. The reconstituted enzyme acted specifically on DNA damaged with UV, cis-platinum, and psoralen plus near UV. When UV-irradiated DNA was used as substrate, the enzyme made two cuts on the damaged DNA strand, one on each side of the damaged region. The enzyme hydrolyzed the eighth phosphodiester bond on the 5' side of pyrimidine dimers. On the 3' side of pyrimidine dimers, the UVRABC nuclease cut the fourth or the fifth phosphodiester bond 3' to pyrimidine dimers. The oligonucleotide with the damaged bases that is generated by these two cuts was released during treatment with the enzyme. We have also obtained evidence suggesting that the enzyme acts by the same mechanism on PydC photoproducts which are thought to be of primary importance in UV-induced mutagenesis.

The effect of mutations in the uvrD cistron of Escherichia coli on repair resynthesis

The resynthesis step of the excision repair pathway has been examined in Escherichia coli K12 strains isogenic except for mutations in the uvrD cistron. Strains mutant at the uvrD3, uvrD101, uvrE156, and recL152 loci exhibited slight but distinct differences in their response to ultraviolet radiation. The repair capacity of the uvrD101 mutant was given special attention. Repair resynthesis in this mutant was saturated at fluences greater than about 20 J/m2. Isopycnic analysis of repaired deoxyribonucleic acid from this strain revealed a two-fold increase over its wild-type counterpart in the amount of repair replication performed after a dose of 15 J/m2. Sedimentation velocity analysis of DNA after selective photolysis of bromouracil-containing repaired regions showed that the uvrD101 mutation exerted its primary effect on the long-patch component of excision repair. The uvrD101 mutant performed long-patch repair at a larger number of sites than the number repaired by this mode in the wild-type strain; these patches were more extensive in length than the long-patch component in wild-type.

Cysteamine protection of SCEs induced by UV and fluorescent light

CHO cells were grown for 36 h in the presence of BUDR. 12 h before harvesting, the cells were irradiated with UV or with fluorescent (FL) light. Part of the cultures were treated with cysteamine (Cys) during irradiation. Metaphase spreads were stained by the Hoechst-plus-Giemsa method, and the frequency of SCEs per chromosome was determined in second-mitosis cells. The basal frequency of SCEs (1.07 +/- 0.073) was not increased by Cys treatment (1.15 +/- 0.048). On the other hand, UV and FL induced a 3-4-fold increase in the frequency of exchanges (4.18 +/- 0.2 and 3.32 +/- 0.12 resp.). Cys, when present during irradiation, markedly reduced the frequency of UV- and FL-induced SCEs (2.7 +/- 0.14 and 2.29 +/- 0.11 resp.). It is assumed that Cys prevents the formation of radiation-induced breakages in the BUDR-substituted DNA. The residual increase over the basal levels of SCEs which remains after the treatment with Cys may be due to the persistence of some open breaks, to the presence of protein-DNA crosslinking, or to the combined action of both types of lesion.

Excision repair and patch size in UV-irradiated bacteriophage T4

We determined the average size of excision repair patches in repair of UV lesions in bacteriophage T4 by measuring the photolysis of bromodeoxyuridine incorporated during repair. The average patch was small, approximately four nucleotides long. In control experiments with the denV1 excision-deficient mutant, we encountered an artifact, a protein(s) which remained bound to phenol-extracted DNA and prevented nicking by the UV-specific endonucleases of Micrococcus luteus and bacteriophage T4.

Analysis of resynthesis tracts in repaired Escherichia coli deoxyribonucleic acid

Excision repair of ultraviolet radiation-induced damage in a wild-type strain of Escherichia coli has been examined, using two methods for characterizing the resynthesis step of the repair process. Comparison of data obtained after both isopycnic analysis of repaired deoxyribonucleic acid and sedimentation velocity analysis of deoxyribonucleic acid after selective photolysis of bromouracil-containing repaired regions has shown that the repaired deoxyribonucleic acid molecules contain a semicontinuous distribution of sizes of repair tracts. Further analysis of our data suggests two major classes of repair patches, one abut 20 to 40 nucleotides in length, and the other containing 1,600 to 2,000 nucleotides. Under the conditions employed, approximately 2 to 10% of the fully repaired regions are long repair patches.

Short deoxyribonucleic acid repair patch length in Escherichia coli is determined by the processive mechanism of deoxyribonucleic acid polymerase I

The lengths of ultraviolet irradiation-induced repair resynthesis patches were measured in repair-competent extracts of Escherichia coli. Extracts containing wild-type deoxyribonucleic acid (DNA) polymerase I introduced a patch 15 to 20 nucleotides in length during repair of ColE1 plasmid DNA; extracts containing the polA5 mutant form of DNA polymerase I introduced a patch only about 5 nucleotides in length in a similar reaction. The repair patch length in the presence of either DNA polymerase corresponded to the processivity of that polymerase (the average number of nucleotides added per enzyme-DNA binding event) as determined with purified enzymes and DNA treated with a nonspecific endonuclease. The base composition of the repair patch inserted by the wild-type DNA polymerase was similar to that of the bacterial genome, whereas the patch inserted by the mutant enzyme was skewed toward greater pyrimidine incorporation. This skewing is expected, considering the predominance of pyrimidine incorporation occurring at the ultraviolet lesion and the short patch made by the mutant enzyme. Since the defect in the polA5 DNA polymerase which causes premature dissociation from DNA is reflected exactly in the repair patch length, the processive mechanism of the polymerase must be a central determinant of patch length.

Dimer excision and repair replication patch size in recL152 mutant of Escherichia coli K-12

Dimers are excised slowly in a recL152 mutant. This observation is not an artifact of altered DNA degradation because degradation is the same in recL+ and recL strains. The repair patch size was measured by the bromodeoxyuridine-313 nm radiation photolysis technique. In the recL+ strain, the average patch size was found to be about 30 nucleotides in length, but in the recL mutant, it was about 360.

The measurement of chemically-induced DNA repair synthesis in human cells by BND-cellulose chromatography

Repair synthesis in human cells in tissue culture can be readily separated from semi-conservative DNA synthesis with the aid of a benzoylated naphthoylated DEAE cellulose (BND-cellulose) column. Cells are incubated with a radioactive DNA precursor during treatment with a repair-inducing agent. An inhibitor of semi-conservative DNA synthesis (hydroxyurea) is added to slow the progression of the DNA growing point. The cells are lysed and after treatment with ribonuclease and pronase the lysates are sheared and passed through a BND-cellulose column. Native DNA is eluted with I M NaCl. Any increase in radioactivity in the native DNA is due to repair synthesis and the specific repair activity (nucleotides inserted per mug of DNA) can be determined from radioactivity and absorbancy measurements. Repair can also be measured in the region of the DNA growing point by fractionation of the material eluted from BND-cellulose with 50% formamide. Repair was not detected in N-acetoxy-2-acetylaminofluorene (AAAF)-treated lymphoblasts derived from an individual with xeroderma pigmentosum although methyl methanesulfonate (MMS)-induced repair was observed in these cells.

Selective excision of gamma ray damaged thymine from the DNA of cultured mammalian cells

Three mammalian cell lines (WI-38, SV40-transformed WI-38 and Chinese hamster ovary) were exposed to high doses of 137-Cs gamma rays and their DNA analysed, following various periods of postirradiation incubation, for products of the 5,6-dihydroxy-dihydrothymine type. Within fifteen minutes of incubation at 37 degrees C 70 to 90 percent of these radiation products were removed from acid-precipitable material in all three cell lines. The amount of DNA degradation induced by radiation varied from approximately one percent in WI-38 cells to 15 percent in SV40-transformed WI-38 cells. Comparison of DNA degradation with the amount of thymine radiation product removed indicates that a selective gamma ray-induced excision repair capability exists in mammalian cells. Because of its more rapid kinetics, gamma ray excision repair is probably a distinct process as compared with ultraviolet-induced pyrimidine dimer excision.

Ultraviolet-light-induced incorporation of bromodeoxyuridine into parental DNA of an excision-defective mutant of Escherichia coli

Bromodeoxyuridine-containing regions approximately 1.5 X 10(4) Nucleotides in length, and at intervals equivalent to the pyrimidine dimer content of the DNA, have been observed in the parental DNA of an excision-defective strain of Escherichia coli exposed to 10 ergs mm-2 at 254 nm followed by prolonged incubation in the presence of bromodeoxyuridine.

Ultraviolet mutagenesis and its repair in an Escherichia coli strain containing a nonsense codon

Ultraviolet mutagenesis and its repair were studied mainly in WU36-10-89, a uvr(-) strain of Escherichia coli containing a UAG mutation in a gene for leucine biosynthesis. Following ultraviolet (UV) irradiation revertants appearing with or without direct photoreactivation (PR) were classified according to the presence and type of suppressor they contained. We find UV mutation production to be quite specific. An analysis of revertants produced by UV indicates they are formed mainly from GC --> AT and that the miscoding is due to a cytosine residue at the site of mutation in a cytosine-thymine (CT) dimer. We propose that the dimer serves as template during some aspects of repair replication and at the time of replication the C in the dimer directs the insertion of A in the complementary strand. We also note that C --> A and T -->G changes caused by a CT dimer occur much less frequently.

Interrelationship of repair mechanisms in ultraviolet-irradiated Escherichia coli

Investigation of the effect of photoreactivation, excision, and recombination repair, individually and in combination, on the survival of ultraviolet-irradiated Escherichia coli K-12 mutants has led to a possible explanation of the loss of photoreactivability and of the complex changes in viability observed during liquid-holding. It is suggested that at higher ultraviolet light doses the excision repair mechanism becomes saturated due to overlapping of excised regions on opposite strands of the deoxyribonucleic acid helix. The results also provide support for the existing hypothesis that states that the shape of shouldered survival curves of ultraviolet-irradiated bacteria can be described in terms of the probability of occurrance of overlapping excised regions. Using the data obtained with repair-deficient mutants with closely related genetic makeup, we present a mathematical model that accurately predicts the shape of the observed survival curves and provides an estimate of the number of nucleotides in each fragment of deoxyribonucleic acid removed by the excision repair mechanism.

Repair of DNA containing interstrand crosslinks in Escherichia coli: sequential excision and recombination

The repair of DNA containing interstrand crosslinks induced by psoralen-plus-light in E. coli cells has been investigated. During a 30-minute incubation after psoralen-plus-light treatment, crosslinks were excised and the cellular DNA was cut into discrete pieces. The molecular weight of these pieces corresponds to about twice the single-strand distance between crosslinks, as measured by sedimentation velocity in alkaline sucrose. During further incubation, these DNA fragments were covalently joined into high molecular weight DNA. This joining did not occur in cells carrying a mutation at recA; in these strains the DNA was further degraded to smaller polynucleotides and acid-soluble material. The possibility that repair of crosslinked DNA involves strand exchanges between homologous duplexes was investigated. Cells were grown in (13)C,(15)N-containing medium for several generations, then switched to medium of normal density that also contained [(3)H]thymidine for about 0.5 generation. After the crosslinking treatment, the cells were incubated in medium of normal density in order for repair to occur. The DNA was extracted and centrifuged in alkaline CsCl density gradients, where the light and heavy strands were separated. Molecules of intermediate density that contained (3)H accumulated during repair in wild-type cells, but not in control cells or treated recA(-) cells. After molecular weight reduction of the intermediate-density DNA, the (3)H could be separated from the heavy strands, demonstrating that covalent joining between heavy and light strands of homologous duplexes accompanies repair. A mechanism involving sequential excision and genetic recombination is proposed for the repair of DNA containing interstrand crosslinks.

Breakage of parental DNA strands in Haemophilus influenzae by 313 nm radiation after replication in the presence of 5-bromodeoxyuridine

Haemophilus influenzae was labeled with thymidine-(3)H (dThd), then grown in the presence of 5-bromodeoxyuridine (BrdUrd), and then irradiated with 313 nm light (a wavelength that selectively photolyzes DNA containing 5-bromouracil [BrUra]). Irradiation with 313 nm light induced breaks in the (3)H-labeled strands in cells grown with BrdUrd at a much higher frequency than in (14)C-labeled DNA of cells not exposed to BrdUrd. Breakage of the (3)H-labeled strands was about 0.6% as efficient as that of fully BrUra-substituted DNA. During growth in the presence of BrdUrd, susceptibility to 313 nm-induced breakage of the (3)H-labeled DNA strands increased, reaching a maximum in about one generation, and it decreased to zero during subsequent growth for one generation in medium containing dThd instead of BrdUrd. Heat denaturation of DNA extracted from dThd-(3)H-labeled cells grown in the presence of BrdUrd eliminated 313 nm-induced breakage of the (3)H-labeled strands. It is concluded that breakage of the (3)H-labeled DNA strands resulted from reaction with photoproducts in the base-paired, BrUra-containing strands, rather than from photolysis of BrdUrd incorporated into parental strands. It may be possible to utilize the phenomenon of interstrand breakage in physical studies of DNA replication.