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

Analysis of the mutations induced in the E. coli lac Z gene by a psoralen analog

A psoralen in which intracyclic oxygen atoms were replaced by sulfur (7H-thieno [3,2-g]-[1]-[benzothiopyran-7-one) [PSO(S-S)]) was recently synthesized and its photobiological properties were investigated. M13mp19 DNA photosensitization mediated by PSO (S-S) followed by transfection into competent E. coli gave rise to a very low phage progeny showing the high aptitude of this compound to modify DNA. In order to characterize the role of oxidative damages in the photosensitized reaction mediated by PSO(S-S), plasmid bearing the gene encoding the formamidopyrimidine DNA glycosylase (Fpg) under the control of the inducible lac Z promoter was transfected in E. coli. Overexpression of Fpg was induced by addition of isopropyl-beta-D-thio-galactopyranoside (IPTG) to the cells and monitored by western blot analysis. Fpg overexpression did not influence the rate of M13mp19 DNA photoinactivation by PSO(S-S) neither the mutation frequency measured by the expression of beta-galactosidase encoded by the lac Z gene beared by M13mp19. Analysis of the mutation patterns recorded with or without Fpg overexpression showed that several G to T transversions due to oxidative damages were repaired by Fpg. These data show that oxidative DNA damages generated during PSO(S-S) photosensitization have only limited biological implications measured in terms of DNA photoinactivation.

Photoreaction of new psoralen analogs with DNA: sequence and mutation specificity in the Escherichia coli lacZ gene

New thio- and seleno-analogs of psoralen were synthesized and analyzed for their photoreactivity toward DNA. Using oligonucleotides of defined sequence, we first showed that these derivatives predominantly generated interstrand crosslinks at 5'-TpA sites. We also observed a surprisingly high reactivity of 7H-thiopyrano[3,2-f][1]benzofuran-7-one (PSO[O-S]) with the BamHI and PstI oligomers, giving rise to the formation of crosslinks at 5'-ApT sites and of the thymidine-psoralen-cytosine type. Next, the sequence specificity in the photochemical binding of all the compounds was investigated in two DNA fragments encompassing the lacZ gene of Escherichia coli, using the T4 DNA polymerase sequencing methodology. Resulting maps demonstrated that thio- and seleno-analogs of psoralen preferentially photoreacted with thymine and cytosine residues. The AT-rich sequences proved to be particularly reactive sites as did adjacent thymines, especially at C-surrounding residues. Likewise, photoaddition at cytosines in CA/AC context was observed. It was highly significant that all of the derivatives exhibited similar sequence specificities with only minor differences. However, PSO(O-S) differed from the other heteropsoralens. Photoadducts occurred with a higher frequency at AC and CA dinucleotides, and new sites were detected. A comparison with 8-methoxypsoralen photobinding is also reported. Finally, the mutagenic consequences of photoadducts induced in M13mp19 DNA by PSO(O-S) were determined in a forward system that detects all classes of mutagenic events. The high phototoxicity exhibited by PSO(O-S) could be attributed to crosslinks, and the comparison of the observed mutational specificity with the photoadduct distribution within the same gene showed that mutations were targeted at potential monoadduct sites where photolesions were detected in our footprinting experiments.

8-Methoxypsoralen photoinduced plasmid-chromosome recombination in Saccharomyces cerevisiae using a centromeric vector

The characterization of a new system to study the induction of plasmid-chromosome recombination is described. Single-stranded and double-stranded centromeric vectors bearing 8-methoxypsoralen photoinduced lesions were used to transform a wild-type yeast strain bearing the leu2-3,112 marker. Using the SSCP methodology and DNA sequencing, it was demonstrated that repair of the lesions in plasmid DNA was mainly due to conversion of the chromosomal allele to the plasmid DNA.

Analysis of mutations induced by 4'-hydroxymethyl-4,5',8-trimethylpsoralen and UVA in Escherichia coli lac Z gene and its regulatory region

The mutagenic consequences of covalent adducts induced in M13mp19 DNA by 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) and UVA have been determined in a forward mutational system capable of detecting all classes of mutagenic events. The photoreaction mediated by HMT has been carried out at a very low molar ratio of HMT to DNA which favours the induction of cross-links between high affinity reaction sites. When damaged M13mp19 DNA is used to transfect competent Escherichia coli K12 JM105 cells, a five-fold increase in mutation frequency is observed at 3.5% survivors when measured as a loss of beta-galactosidase alpha-complementation. The enhanced mutation frequency is largely due to base substitutions, frameshift events and large deletions. The single nucleotide substitutions occur both in the lac Z coding sequence and in its regulatory region. Transversion and transition have been detected with a predominant form consisting of A.T-to-G.C transversion at position +159. Frameshift mutations have been observed at five positions while three large deletions removing either part of the coding sequence or both the coding and the regulatory regions have been detected with a higher frequency. The spectrum of base substitutions detected between the M13 lac Z- phages surviving to the treatment is totally different from those appearing spontaneously whereas several frameshift events or deletions can already be detected between the spontaneous mutations. Despite the presence of these spontaneous hot spots, the spectrum of mutations recovered after HMT photoaddition appears to be unique and a detailed analysis of the different classes of mutations indicates an important role of cross-links in the production of mutations.

Molecular spectrum of mutations induced at the HPRT locus by a cross-linking agent in human cell lines with different repair capacities

Molecular characterization of mutations photoinduced by a cross-linking agent, 4,5',8-trimethylpsoralen (Me3Pso), in normal human lymphoblasts was conducted in parallel with lymphoblasts derived from Fanconi anemia patients. Such cells have been previously described to be impaired in repair of psoralen photolesions. The endogenous HPRT locus was used as a target gene. The treatment of cells with Me3Pso in combination with 365 nm irradiation leads to the formation of interstrand cross-links, and specific monoadducts. Our analysis revealed that the mutagenic processing of Me3Pso photoadducts in normal human cells results essentially in base substitutions (84%). These are localized to sequences shown previously to be favored for the formation of Me3Pso monoadducts. The mutagenic processing of the same lesions in Fanconi anemia cells results in fewer base substitutions (22%), with deletions (66%) being the predominant class of mutation. In contrast to prokaryotic systems, frameshifts are poorly represented among Me3Pso induced mutations in human cells. In spite of important differences between the kinds of mutations observed in the two cell lines, our analysis reveals similarities in the type of base substitutions and their sequence distribution. In both normal and Fanconi anemia cell lines mutations, mostly targeted on thymine residues, are preferentially located on the non-transcribed strand.

New aspects of the repair and genotoxicity of psoralen photoinduced lesions in DNA

Several approaches are described aiming at a better understanding of the genotoxicity of psoralen photoinduced lesions in DNA. Psoralens can photoinduce different types of photolesions including 3,4- and 4',5'-monoadducts and interstrand cross-links, oxidative damage (in the case of 3-carbethoxypsoralen (3-CPs)) and even pyrimidine dimers (in the case of 7-methylpyrido(3,4-c)psoralen (MePyPs)). The characterization and detection of different types of lesions has been essential for the analysis of their possible contributions to genotoxicity. For example, oxidative damage photoinduced by 3-CPs can be detected by the formamidopyrimidine glycosylase (FPG) protein. Furthermore, it is shown how the presence of MePyPs induced monoadducts may interfere with the photoreactivation of concomitantly induced pyrimidine dimers, how the ratio of monoadducts and interstrand cross-links (CL) affects the occurrence of double-strand breaks during the repair of photolesions and genotoxicity. In vitro treatment of yeast plasmids, followed by transformation, also indicates that the repair of photoadducts on exogenous DNA differs for 8-methoxy-psoralen (8-MOP) induced mono- and diadducts and for monoadducts alone. The recombinational rad52 dependent pathway is not needed for the repair of 8-MOP induced monoadducts. The results obtained suggest that the genotoxic effects of psoralens are conditioned by the nature, number, ratio and sequence distribution of the photolesions induced in DNA.

Molecular analysis of mutations induced by 4'-hydroxymethyl-4,5',8-trimethylpsoralen and UVA in the mouse HPRT gene

The effects of the reaction photosensitized by 4'-hydroxymethyl-4,5'-8-trimethylpsoralen (HMT) on a mouse lymphoma cell line have been examined. Using the hypoxanthine phosphoribosyltransferase (HPRT) locus as target gene, a mutagenic effect of the photoreaction can be detected concomitantly with a loss of cell viability. Isolation of HPRT deficient clones has permitted a molecular characterization of the mutational pattern induced by the photosensitization reaction mediated by HMT. Southern blotting analysis demonstrated that the HPRT deficiency could not be correlated with gene deletions larger than 300 bp. Using polymerase chain reaction on both DNA and cDNA, amplification products have been cloned into M13mp18 and sequenced. Base transversions targeted on thymine residues have been located in exon 2, 3, 8 and 9 together with spontaneous frameshift mutations occurring in a run of guanine residues in exon 3. HPRT deficiencies owing to mutations arising in the HPRT promoter region have also been observed. Dot and Northern blot analysis revealed that the photoreaction could lead to either a reduced level of gene transcription or to a complete absence of HPRT m-RNA. Using polymerase chain reaction (PCR) amplification and agarose gel electrophoresis, deletions in the HPRT promoter have been observed and correlated to deficient enzyme expression.

Involvement of RecB-mediated (but not RecF-mediated) repair of DNA double-strand breaks in the γ-radiation production of long deletions in Escherichia coli

Experiments were designed to determine the association between the repair of gamma-radiation-induced DNA double-strand breaks (DSB) and the induction of 700-1000 bp long deletions (Lac(-)----Lac+), base substitutions (leuB19----Leu+), and frameshifts (trpE9777----Trp+) in Escherichia coli K-12. Over the range of 2.5-20 krad, deletions were induced with linear kinetics, as has been shown for the induction of DSB, while the induction kinetics of base substitutions and frameshifts were curvilinear. Like the repair of DSB, deletion induction showed an absolute requirement for an intact recB gene as well as a dependency on the type of preirradiation growth medium; these requirements were not seen for base substitutions or frameshifts. In addition, about 80% of the spontaneous deletions were absent in the recB21 strain. A recC1001 mutation, which confers a 'hyper-Rec' phenotype, increased the rate of gamma-radiation-induced deletions as well as the low-dose production of base substitutions and frameshifts. A recF143 mutation increased the yield of gamma-radiation-induced deletions without increasing base substitutions or frameshifts. A mutS mutation markedly enhanced the gamma-radiation induction of frameshifts, and had a slight effect on base substitutions, but did not affect the induction of deletions. Resistance to gamma-irradiation and the capacity to repair DSB (albeit at about half the normal rate) were restored to the radiosensitive recB21 strain by the addition of the sbcB21 and sbcC201 mutations. However, the radioresistant recB sbcBC strain, which is recombination proficient via the RecF pathway, was still grossly deficient in the ability to produce deletions. A model for deletion induction as a by-product of the recB-dependent (Chi-dependent) repair of gamma-radiation-induced DSB is discussed, as is the inability to detect deletions in cells that use only the recF-dependent (Chi-independent) mechanism to repair DSB.

HPRT gene expression differs in mutants derived from normal and Fanconi anemia cells: analysis of spontaneous and psoralen-photoinduced mutants

Fanconi anemia (FA) is an autosomal recessive disorder characterized by chromosomal instability and abnormalities in the processing of DNA lesions induced by cross-linking agents. We previously reported that after photoaddition of psoralen derivatives the frequency of HPRT- mutants was significantly lower in FA than in normal human lymphoblasts. The hypomutability in FA cells was shown to be associated with an increased deletion frequency at the HPRT gene level. Further characterization of 70 unrearranged mutants (without detectable changes in restriction enzyme fragment length) according to the HPRT gene expression is reported here. Northern blot hybridization analysis demonstrates considerable differences in mRNA phenotyping between normal and FA cells. In normal cells, the minority of spontaneous (31%) and psoralen-induced mutants (0% and 14% according to treatment) arise from mutations that alter the HPRT gene transcription. In contrast to normal cells, in the majority of mutants isolated from FA cells, HPRT gene expression is found to be affected. Indeed a large proportion of either spontaneous (67%) or psoralen-induced (56% and 46%) mutants did not produce detectable amounts of mRNA. These results suggest that the mutagenic processing of spontaneous and psoralen-photoinduced lesions differs in normal and FA cells.

Damage distribution and mutation spectrum: the case of 8-methoxypsoralen plus UVA in mammalian cells

We determined the distribution of monoadducts and biadducts induced in the supF tRNA gene carried by the shuttle vector pZ189, after exposure to 8-methoxypsoralen (8-MOP) plus a double UVA (365 nm) irradiation. These data were compared to our previously published 8-MOP-photoinduced mutation spectrum obtained after propagation of the damaged shuttle vector in mammalian cells. One mutational hot spot in an ATAT/TATA sequence is targeted at a hot spot of biaddition. A second hot spot is not related to the presence of photoadducts either at or near the site. Moreover, it is located in a sequence which can be defined as 'mutation-prone'. Mutations occurring at GC base pairs are not targeted at sites of photoaddition, and may result from a decrease in fidelity of DNA polymerase when copying the damaged vector.

Hypomutability in Fanconi anemia cells is associated with increased deletion frequency at the HPRT locus

Fanconi anemia (FA) is an inherited human disorder associated with a predisposition to cancer and characterized by anomalies in the processing of DNA cross-links and certain monoadducts. We reported previously that the frequency of psoralen-photoinduced mutations at the HPRT locus is lower in FA cells than in normal cells. This hypomutability is shown here to be associated with an increased frequency of deletions in the HPRT gene when either a mixture of cross-links and monoadducts or monoadducts alone are induced. Molecular analysis of mutants in the HPRT gene was carried out. In normal cells the majority of spontaneous and induced mutants are point mutations whereas in FA deletion mutations predominate. In that case a majority of mutants were found to lack individual exons or small clusters of exons whereas in normal cells large (complete or major gene loss) and small deletions are almost equally represented. Thus we propose that the FA defect lies in a mutagenic pathway that, in normal cells, involves bypassing lesions and subsequent gap filling by a recombinational process during replication.

Photosensitization of DNA of defined sequence by furochromones, khellin and visnagin

The sequence specificity in the in vitro DNA photobinding of khellin and visnagin, two naturally occurring furochromones proposed for chemotherapy of vitiligo, was investigated by using DNA sequencing methodology. The 3'-5' exonuclease associated with the T4 DNA polymerase served as a tool for determining photoadducts distribution on DNA fragments of the lac I gene of Escherichia coli. The photoadduct distribution of psoralen is also studied for comparison. Upon UVA irradiation, visnagin mainly forms monoadducts with thymine and to a lower extent with cytosine. Alternating (A-T)n sequences are hot spots for visnagin photoaddition. This is a property shared with furocoumarins. TTT sites are also quite reactive to visnagin, as they are to methylated angelicins. In contrast, with psoralen derivatives, there is no preferential photobinding in 5'-TpA sites, and 5'-ApT sites react as well. Furthermore, many sites such as T in the GC context, and C in any context, react, although weakly. The visnagin photoadduct distribution resembles very much the photoadduct distribution of methylated angelicins as described by Miolo et al. The photoreaction of these two series of compounds is less sequence dependent than the photobinding of psoralen derivatives as described by Sage and Moustacchi and by Boyer et al. The sequence specificity in khellin-DNA photobinding is the same as for visnagin, even though it forms much fewer photoadducts. The absence of photo-oxidation of DNA after treatment with visnagin or khellin plus UVA suggests that furochromones do not present any photodynamic effect on DNA.

Analysis of spontaneous and psoralen-induced Salmonella typhimurium hisG46 revertants by oligodeoxyribonucleotide colony hybridization: use of psoralens to cross-link probes to target sequences

An improved DNA colony-hybridization method for the rapid characterization of Salmonella typhimurium hisG46 revertants is described. Oligodeoxyribonucleotides (15-mers) complementary to each of 6 possible transition or transversion mutations and an extragenic suppressor mutation, underlying the His+ phenotype, were prepared. Optimal sequence discrimination was achieved by hybridizing 15-mers at the apparent dissociation temperature (Td) for 2 h with chromosomal DNA of revertant colonies affixed to Whatman 541 filters. Subsequent exposure of filters to UVA radiation (320-400 nm) in the presence of 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) resulted in cross-linking of perfectly matched probes and target DNA sequences while sequences containing a single base-pair mismatch could be discriminated with a brief denaturing wash. No false negative results were obtained with the new procedure. An analysis of 204 spontaneous and 174 PUVA-induced TA100 revertants is presented.

Monofunctional angular furocoumarins: sequence specificity in DNA photobinding of 6,4,4'-trimethylangelicin and other angelicins

The sequence specificity in the photoreaction (365 nm) of 6,4,4'-trimethylangelicin (TMA) with DNA fragments of the lac I gene of Escherichia coli was studied by using DNA sequencing methodology. In order to map the sites of TMA photoaddition, we took advantage of the (3'-5') exonuclease activity associated with T4 DNA polymerase, which is blocked by bulky adducts, such as furocoumarin photoadducts. A quantitative analysis of the sites of photoaddition is reported. TMA was demonstrated to photoreact with thymine and, to a lower extent, to cytosine. AT-rich sequences and TTT sites in a GC context are the most reactive sites towards TMA whereas TA, AT, CA, AC sites are weaker sites with similar reactivity. Cytosines in alternated CG sequences are also targets of TMA photobinding. We observed a less pronounced sequence specificity of TMA than that of other psoralen derivatives already studied (Sage and Moustacchi, 1987; Boyer et al., 1988). A comparison with other furocoumarins 4,4'-dimethylangelicin (4,4'-DMA), 4'-methylangelicin (4'-MA), angelicin, 4,5',8-trimethylpsoralen (TMP) and 8-methoxypsoralen (8-MOP) is also reported. The role of flanking sequence and consequently of the local conformation at the various sites of photoaddition is discussed. A preferential orientation of the TMA molecule during the intercalation in the dark is suggested. Hot alkali treatment of TMA-modified DNA did not reveal any DNA strand breakage due to photooxidized bases.

Mutagenesis induced by site specifically placed 4'-hydroxymethyl-4,5',8-trimethylpsoralen adducts

Closed circular double stranded M13mp19 DNA containing a site-specifically placed HMT (4'-hydroxymethyl-4-5'-8-trimethylpsoralen) monoadduct or crosslink was synthesized in vitro. The damaged DNA were scored for loss of infectivity by transfection into repair proficient or deficient E. coli and into SOS induced E. coli. Mutant phages were detected by the loss of alpha-complementation between the viral and the host Lac Z genes or by the acquisition of resistance to kpn I digestion. Our results indicate that HMT mutagenesis is targeted and that deletion or transversion of the modified thymidine is the predominant sequence change elicited by a monoadduct or a crosslink. Transfection of the monoadducted DNA into a Uvr A deficient strain did not change the mutation pattern but did increase the respective mutation frequencies. Transfection of the crosslinked DNA into a SOS induced host resulted in the appearence of other types of mutations attributable to an increase in both targeted and untargeted mutations.

Missense mutation in the lacI gene of Escherichia coli. Inferences on the structure of the repressor protein

The lac repressor has been studied extensively but a precise three-dimensional structure remains unknown. Studies using mutational data can complement other information and provide insight into protein structure. We have been using the lacI gene-repressor protein system to study the mutational specificity of spontaneous and induced mutation. The sequencing of over 6000 lacI- mutations has revealed 193 missense mutations generating 189 amino acid replacements at 102 different sites within the lac repressor. Replacement sites are not distributed evenly throughout the protein, but are clustered in defined regions. Almost 40% of all sites and over one-half of all substitutions found occur within the amino-terminal 59 amino acid residues, which constitute the DNA-binding domain. The core domain (residues 60 to 360) is less sensitive to amino acid replacement. Here, substitution is found in regions involved in subunit aggregation and at sites surrounding residues that are implicated in sugar-binding. The distribution and nature of missense mutational sites directs attention to particular amino acid residues and residue stretches.

Suppressible base substitution mutations induced by angelicin (isopsoralen) in the Escherichia coli lacI gene: implications for the mechanism of SOS mutagenesis

Angelicin- plus near-UV-induced mutations were umuC dependent in Escherichia coli K-12. Angelicin, a monofunctional psoralen derivative, is believed to damage DNA almost exclusively at pyrimidine bases. To broaden our knowledge about the mutagenic specificity of SOS-dependent mutagens, we determined the mutational specificity of 233 suppressible lacI mutations induced by angelicin. More than 90% of the nonsense mutations arose via transversion substitutions. The three most frequently mutated sites were at A-T base pairs and accounted for more than one-third of all induced nonsense mutations. The two hottest sites were at the only occurrences of the 5'-TATA-3' tetranucleotide in lacI, a sequence expected to be a preferred binding site for a psoralen. Both A-T-to-T-A and A-T-to-C-G transversions were well induced by angelicin treatment, but the frequency of each transversion depended on the particular site. We also detected significant induction of transversion mutations at G-C sites. The induction of transversions by an SOS-dependent mutagen that generates lesions at pyrimidines supports the idea that DNA lesions influence the selection of bases that are incorporated via the process of SOS repair.

Defect in excision repair alters the mutational specificity of PUVA treatment in the lacI gene of Escherichia coli

The sequences of 152 lacI- mutations obtained following exposure of Escherichia coli UvrB- strain NR3951 to ultraviolet light in the presence of 8-methoxypsoralen (PUVA treatment) were compared to the spectrum of mutation induced by PUVA treatment in a Uvr+ strain, NR3835. Mutations recovered following PUVA treatment of the UvrB- strain were quite different from those recovered in the Uvr+ strain. In addition, they occurred at a restricted number of unique sites. For example, A.T----T.A base substitutions at position 141, minus G frameshifts at positions 586/587/588 and deletions of 15 base-pairs from position 78 to 92 accounted for 50% or more of mutations recovered in each of the above mutational classes. This altered mutational specificity was accompanied by a failure to recover mutations frequently identified following PUVA treatment of the Uvr+ strain. These mutations include spontaneous-hotspot frameshifts involving the gain or loss of a tetramer 5'-CTGG-3' repeated three times at position 620 to 631; and minus A.T base-pair frameshifts recovered at potential T-T crosslink sites. These results indicate that while crosslinks may play a substantial role in the induction of mutation in the Uvr+ strain, they do not contribute substantially to mutagenesis in the UvrB- strain. In addition, the data also suggest that excision repair may not always occur in an error-free manner.