Further characterization of repair of 8-methoxypsoralen crosslinks in UV-excision-defective Escherichia coli

recF and recR are required for the resumption of replication at DNA replication forks in Escherichia coli

Escherichia coli containing a mutation in recF are hypersensitive to UV. However, they exhibit normal levels of conjugational or transductional recombination unless the major pathway (recBC) is defective. This implies that the UV sensitivity of recF mutants is not due to a defect in recombination such as occurs during conjugation or transduction. Here, we show that when replication is disrupted, at least two genes in the recF pathway, recF and recR, are required for the resumption of replication at DNA replication forks, and that in their absence, localized degradation occurs at the replication forks. Our observations support a model in which recF and recR are required to reassemble a replication holoenzyme at the site of a DNA replication fork. These results, when taken together with previous literature, suggest that the UV hypersensitivity of recF cells is due to an inability to resume replication at disrupted replication forks rather than to a defect in recombination. Current biochemical and genetic data on the conditions under which recF-mediated recombination occurs suggest that the recombinational intermediate also may mimic the structure of a disrupted replication fork.

Nucleotide excision repair in Escherichia coli

One of the best-studied DNA repair pathways is nucleotide excision repair, a process consisting of DNA damage recognition, incision, excision, repair resynthesis, and DNA ligation. Escherichia coli has served as a model organism for the study of this process. Recently, many of the proteins that mediate E. coli nucleotide excision have been purified to homogeneity; this had led to a molecular description of this repair pathway. One of the key repair enzymes of this pathway is the UvrABC nuclease complex. The individual subunits of this enzyme cooperate in a complex series of partial reactions to bind to and incise the DNA near a damaged nucleotide. The UvrABC complex displays a remarkable substrate diversity. Defining the structural features of DNA lesions that provide the specificity for damage recognition by the UvrABC complex is of great importance, since it represents a unique form of protein-DNA interaction. Using a number of in vitro assays, researchers have been able to elucidate the action mechanism of the UvrABC nuclease complex. Current research is devoted to understanding how these complex events are mediated within the living cell.

Escherichia coli rep gene: sequence of the gene, the encoded helicase, and its homology with uvrD

The sequence of a 2.67-kilobase section of the Escherichia coli chromosome that contains the rep gene has been determined. This gene codes for a protein of predicted Mr 72,800, a DNA helicase, which is also a single-stranded DNA-dependent ATPase. The sequenced region contains an open reading frame of the correct length and orientation to encode the Rep protein. A secondary structure for the protein can be formulated from the amino acid sequence. We have compared both the primary and the secondary structures of Rep with other proteins and find the greatest homology between Rep and E. coli helicase II, the product of the uvrD gene.

Lethal and mutagenic effects of 8-methoxypsoralen-induced lesions on plasmid DNA

The genotoxic effect of 8-methoxypsoralen damages (monoadducts and crosslinks) on plasmid DNA was studied. pBR322 DNA was treated with several concentrations of 8-methoxypsoralen plus fixed UVA light irradiation. After transformation into E. coli cells with different repair capacities (uvrA, recA and wild-type), plasmid survival and mutagenesis in ampicillin- and tetracycline-resistant genes were analysed. Results showed that crosslinks were extremely lethal in all 3 strains; indeed, it seemed that they were not repaired even in proficient bacteria. Monoadducts were also found to be lethal although they were removed to some extent by the excision-repair pathway (uvrA-dependent). Damaged plasmid DNA appeared to induce mutagenic repair, but only in the wild-type strain. In order to study the influence of the SOS response on plasmid recovery, preirradiation of the host cells was also performed. Preirradiation of the uvrA or wild-type strains significantly increased plasmid recovery. Consistent with the expectations of SOS repair, no effect was observed in preirradiated recA cells. Plasmid recovery in the excision-deficient strain was mainly achieved by the mutagenic repair of some fraction of the lesions, probably monoadducts. The greatest increase in plasmid recovery was found in the wild-type strain. This likely involved the repair of monoadducts and some fraction of the crosslinks. We conclude that repair in preirradiated repair-proficient cells is carried out mainly by an error-free pathway, suggesting enhancement of the excision repair promoted by the induction of SOS functions.

Mutagenesis by 8-methoxypsoralen plus near-UV treatment: analysis of specificity in the lacI gene of Escherichia coli

We have studied the specificity of mutation induced by PUVA treatment in the lacI gene of E. coli. Cells were exposed to near UV (approximately 365 nm) in the presence of 8-methoxypsoralen under conditions yielding about 7% survival and a 10-fold increase in mutation frequency. The cloning and sequencing of 131 mutants recovered following PUVA treatment revealed that almost all classes of mutation including base substitutions, frameshifts and deletions were induced. The distribution of mutations was non-random and a region of the lacI gene was found to be virtually silent for all classes of mutation. Intriguingly, the broad spectrum of mutation is accompanied by the recovery of mutation at two spontaneous hotspots. We observed a 7-fold increase at a frameshift hotspot involving the gain or loss of a tetramer tandemly repeated 3 times at this site and a 23-fold increase at an A:T----G:C transition hotspot located at the +6 mutational spectrum recovered following PUVA treatment was unique and a detailed analysis of the different classes of mutations indicates a role for DNA repair of both monoadducts and cross-links in the production of mutation.

Psoralen photomutagenic specificity in Salmonella typhimurium

The cytotoxic and mutagenic specificity of two therapeutically employed psoralens was examined in several Ames Salmonella typhimurium strains with near ultraviolet light (UVA, 320-400 nm) activation. Photomutagenic activity of 8-methoxypsoralen (8MOP) and 4,5',8-trimethylpsoralen (TMP) was found to be sequence-specific, and additionally was dependent on the level of DNA-repair proficiency. Base-pair substitution photomutagenesis in hisG46 appeared to require plasmid pKM101-mediated "error-prone" repair. Frameshift photomutagenesis was observed in all hisC3076 strains but not in hisD3052 strains. Frameshift mutagenic activity in hisC3076 was enhanced in the absence of uvrB excision repair and increased further by plasmid pKM101. Phototoxicity was essentially identical in hisC3076, hisD3052 and hisG46 strains; uvrB- excision-repair-deficient bacteria were considerably more susceptible to lethal effects than wild-type parental strains, while the presence of pKM101 had no apparent effect on survival. Finally, the data show that psoralens are potent frameshift photomutagens in Salmonella hisC3076 strains and demonstrate the potential utility of these strains in evaluating photomutagenic and phototoxic activity of new furocoumarin derivatives.

Escherichia coli rep gene: identification of the promoter and N terminus of the rep protein

The functional Escherichia coli rep gene, which encodes the Mr 67,000 Rep helicase, has been localized within a 2.55-kilobase sequence. Its regulatory region has been characterized by the use of rep-lacZ fusions. The direction of transcription of the rep gene is clockwise on the E. coli chromosome, as are the nearby ilvC and rho genes. The sequence of the rep control region was determined, and putative regulatory sequences were identified; no evidence for autoregulation of expression was obtained. Transcription of the gene was not enhanced during the SOS response. The location of the promoter and the beginning of the protein were confirmed by S1 nuclease mapping of the 5' end of rep mRNA and determination of the NH2-terminal sequence of the rep protein.

Mutagenesis of the lac promoter region in M13 mp10 phage DNA by 4'-hydroxymethyl-4,5',8-trimethylpsoralen

Double-stranded M13 phage DNA (M13 mp10 replicative form) was photoreacted with 4'-hydroxymethyl-4,5',8-trimethylpsoralen, using light of wavelength greater than 320 nm or greater than 390 nm to generate predominantly crosslinks or monoadducts, respectively. The damaged DNAs were scored for inactivation and mutagenesis after transfection into Escherichia coli. The appearance of light-blue or colorless plaques on indicator medium showed that mutation had occurred in the lac insert of the viral DNA. A comparison of the consequences of the two phototreatments with psoralen supports the idea that crosslinks are both more lethal and more mutagenic than monoadducts. Numerous mutant clones partially or totally deficient in beta-galactosidase were plaque-purified and amplified. The viral DNA of each clone was sequenced by the dideoxy chain-terminating procedure. All of the observed base-pair changes were mapped to the lac promoter region and consisted of 3 transition, 14 transversion, and 6 single base-pair frame-shift mutations. The predominant mutation was a T.A----G.C transversion.

Uvr-independent repair of 8-methoxypsoralen crosslinks in Escherichia coli: evidence for a recombinational process

On the basis of survival data, repair of 8-methoxypsoralen DNA crosslinks in Escherichia coli strains lacking a functional uvrABC endonuclease, is shown to require the products of the recA, recB, recF and recN genes. Bacteria, grown under conditions where most cells contain only a single genome, show no evidence of crosslink repair. Similarly, bacteriophage lambda shows evidence of crosslink repair only in SOS-induced cells, and only at multiplicities of infection greater than 1. The requirement for rec+ genes may be partly ascribed to the need for a functional SOS response, but taken together, the results suggest a recombinational step involving a homologous region of DNA may occur during uvr-independent crosslink repair.

Paradoxical behaviour of pKM101; inhibition of uvr-independent crosslink repair in Escherichia coli by muc gene products

In strains of Escherichia coli deficient in excision repair (uvrA or uvrB), plasmid pKM101 muc+ but not pGW219 mucB::Tn5 enhanced resistance to angelicin monoadducts but reduced resistance to 8-methoxy-psoralen interstrand DNA crosslinks. Thermally induced recA-441 (= tif-1) bacteria showed an additional resistance to crosslinks that was blocked by pKM101. Plasmid-borne muc+ genes also conferred some additional sensitivity to gamma-radiation and it is suggested that a repair step susceptible to inhibition by muc+ gene products and possibly involving double-strand breaks may be involved after both ionizing radiation damage and psoralen crosslinks.