Ultraviolet light induces different spectra of lacI sequence changes in vegetative and conjugating cells of Escherichia coli

Following the RAD6 pathway

Errol Friedberg suggested that I write a biographical account of the work carried out in my lab for the Historical Reflections section of the DNA Repair. Although I started out studying meiotic recombination, I have spent much of the last four and a half decades focused on trying to understand the mechanism underlying induced mutagenesis, which led me into what was eventually called DNA damage tolerance, the process that facilitates the resumption of replication when replicases are stalled at sites of DNA template damage. The following account highlights some of our work that contributed to an understanding of the mechanisms underlying these activities, carried out by the RAD6 pathway, my main preoccupation over this period.

Cellular determinants of the mutational specificity of 1-nitroso-6-nitropyrene and 1-nitroso-8-nitropyrene in the lacI gene of Escherichia coli

We have characterized 202 lacI(-) mutations, and 158 dominant lacI(-d) mutations following treatment of Escherichia coli strains NR6112 and EE125 with 1-nitroso-6-nitropyrene (1,6-NONP), an activated metabolite of the carcinogen 1,6-dinitropyrene. In all, 91% of the induced point mutations occurred at G:C residues. The -(G:C) frameshifts were the dominant mutational class in the lacI(-) collections of both NR6112 and EE125, and in the lacI(-d) collection of NR6112. Frameshift mutations occurred preferentially in runs of guanine residues, and their frequency increased with the length of the reiterated sequence. In strain EE125, which contained the plasmid pKM101, there was a marked stimulation in the frequency of base substitution mutations that was particularly apparent in the lacI(-d) collection. This study completes a comprehensive analysis of 1194 lacI(-) and 348 lacI(-d) mutations induced by either 1,6-NONP or its positional isomer 1-nitroso-8-nitropyrene (1,8-NONP) in strains of E. coli that differ with regard to their ability to carry out nucleotide excision repair and/or their ability to express the translesion synthesis DNA polymerase RI (MucAB) encoded by plasmid pKM101. Among the mutations are 763 frameshift mutations, 367 base substitutions and 47 deletions; these mutations have been characterized at more than 300 distinct sites in the lacI gene. Our studies provide detailed insight into the DNA sequence alterations and mutational mechanisms associated with dinitropyrene mutagenesis. We review the mutational spectra, and discuss cellular lesion repair or tolerance mechanisms that modulate the observed mutational specificity.

Involvement of 5-methylcytosine in sunlight-induced mutagenesis

In human skin cancers, more than 30 % of all mutations in the p53 gene are transitions at dipyrimidines within the sequence context CpG, i.e. 5'-TCG and 5'-CCG, found at several mutational hotspots. Since CpGs are methylated along the p53 gene, these mutations may be derived from solar UV-induced pyrimidine dimers forming at sequences that contain 5-methylcytosine. In Xorder to define the contribution of 5-methylcytosine to sunlight-induced mutations, we have used mouse fibroblasts containing the CpG-methylated lacI transgene as a mutational target. We sequenced 182 UVC (254 nm UV)-induced mutations and 170 mutations induced by a solar UV simulator, along with 75 mutations in untreated cells. Only a few of the mutations in untreated cells were transitions at dipyrimidines, but more than 95% of the UVC and solar irradiation-induced mutations were targeted to dipyrimidine sites, the majority being transitions. After UVC irradiation, 6% of the base substitutions were at dipyrimidines containing 5-methylcytosine and only 2.2% of all mutations were transitions within this sequence context. However, 24% of the solar light-induced mutations were at dipyrimidines that contain 5-methylcytosine and most of them were transitions. Two sunlight-induced mutational hotspots at methylated CpGs correlated with sequences that form the highest levels of cyclobutane pyrimidine dimers after irradiation with sunlight but not with UVC. The data indicate that dipyrimidines that contain 5-methylcytosine are preferential targets for sunlight-induced mutagenesis in cultured mammalian cells, thus explaining the large proportion of p53 mutations at such sites in skin tumors in vivo.

The Big Blue(R) transgenic mouse mutation detection assay: the mutation pattern of sectored mutant plaques

There are mutational artifacts in the Big Blue(R) assay and it is important to characterize the source and nature of these mutations. Differences were reported in the mutation patterns of a small sample of 23 sectored and 91 circular mutant plaques derived from skin using the Big Blue(R) transgenic mouse mutation detection system [G. R. Stuart, N.J. Gorelick, J.L. Andrews, J.G. de Boer, B.W. Glickman, The genetic analysis of lacI mutations in sectored plaques from Big Blue transgenic mice, Environ. Mol. Mutagen 28 (1996) 385-392.]. We have extended these observations by analyzing 46 sectored and 224 circular mutant plaques derived from seven tissues. The frequency of sectored mutant plaques is estimated to be 16% with no significant variation with tissue type. However, the patterns of mutation for sectored mutants and mouse-derived mutations differed significantly (p=0.04). Base substitutions in sectored mutant plaques do not show the asymmetries found in circular mutants consistent with integration of a GC rich transgene into the AT rich mammalian genome. Sectored mutants have mutation patterns consistent with a mixture of mouse, in vitro and Escherichia coli-derived mutations. Data on the relative frequencies of different mutant plaque morphologies suggests that overlapped plaques are substantially contaminated by sectored plaques at recommended plating densities.

The lacI gene as a target for mutation in transgenic rodents and Escherichia coli

The lacI gene has been used extensively for the recovery and analysis of mutations in bacteria with various DNA repair backgrounds and after exposure to a wide variety of mutagens. This has resulted in a large database of information on mutational mechanisms and specificity of many mutagens, as well as the effect of DNA repair background on mutagenicity. Most importantly, knowledge about the mutational sensitivity of the lacI gene is now available, yielding information about mutable nucleotides. This popularity and available knowledge resulted in the use of the lacI gene in transgenic rodents for the study of mutagenesis in mammals, where it resides in approximately 40 repeated copies. As the number of sequenced mutations recovered from these animals increases, we are able to analyze the sites at which mutations have been recovered in great detail and to compare the recovered sites between bacteria and transgenic animals. The nucleotides that code for the DNA-binding domain are nearly saturated with base substitutions. Even after determining the sequences of approximately 10,000 mutations recovered from the animals, however, new sites and new changes are still being recovered. In addition, we compare the nature of deletion mutations between bacteria and animals. Based on the nature of deletions in the animals, we conclude that each deletion occurs in a single copy of the gene.

Lactose repressor protein: functional properties and structure

The lactose repressor protein (LacI), the prototype for genetic regulatory proteins, controls expression of lactose metabolic genes by binding to its cognate operator sequences in E. coli DNA. Inducer binding elicits a conformational change that diminishes affinity for operator sequences with no effect on nonspecific binding. The release of operator is followed by synthesis of mRNA encoding the enzymes for lactose utilization. Genetic, chemical and physical studies provided detailed insight into the function of this protein prior to the recent completion of X-ray crystallographic structures. The structural information can now be correlated with the phenotypic data for numerous mutants. These structures also provide the opportunity for physical and chemical studies on mutants designed to examine various aspects of lac repressor structure and function. In addition to providing insight into protein structure-function correlations, LacI has been utilized in a wide variety of applications both in prokaryotic gene expression and in eukaryotic gene regulation and studies of mutagenesis.

Mutagenic properties of the T-C cyclobutane dimer

G x C-->A x T transitions within T-C or C-C bipyrimidine sequences are by far the most frequent class of mutation induced by 254-nm UV irradiation in most genes and species investigated, but the reason for the high degree of mutability and specificity at these sites is uncertain. Some data implicate the deamination of cytosine to uracil as a possible cause, but other results appear to indicate that the rate of deamination is too low for this to be significant in Escherichia coli. If deamination is not the cause, the high degree of mutability must presumably reflect the inherent properties of T-C and C-C dimers. We investigated this question by transfecting excision-deficient and excision-proficient strains of E. coli with single-stranded vectors that carried a site-specific cis-syn T-C cyclobutane dimer and by analyzing the nucleotide sequences of replicated vector products. We found that replication past the T-C dimer, like replication past its T-T and U-U counterparts, is in fact >95% accurate and that the frequencies of bypass are also very similar for these photoproducts. Since the T-C dimer appears to be only weakly mutagenic, the high frequency of UV-induced mutations at T-C sites presumably depends on some other process, such as deamination, although the mechanism remains to be established.

Towards validation of the Big Blue transgenic mouse mutagenesis assay: the mutational spectrum of ex vivo pinpoint mutant plaques

To explore further the origin of spontaneous mutations recovered with the Big Blue transgenic mouse mutagenesis assay, the spectrum of ex vivo mutations from pinpoint mutant plaques was determined and compared with the spectrum of putatively mouse-derived mutations from circular, mutant plaques. The entire lacI gene and lacZ operator region from 62 pinpoint blue plaques was sequenced. The observed mutational spectrum of pinpoint mutants differed significantly from that seen in circular mutants (p < 0.0001). Only four percent of the mutations were transitions at CpG sites whereas this type of mutation was the most common (35%) in circular mutants. Microdeletions/microinsertions were seen more frequently in pinpoint mutants relative to circular mutants. Four base pair deletion/insertion events at the E. coli hotspot tandem repeats were seen in 10 of 62 (16%) pinpoint mutants and minor hotspots of mutation were observed at bp 141 and 1110. The mutational spectrum of pinpoint mutants provides further evidence that most circular mutants originate in mouse.

Spontaneous mutation in Big Blue transgenic mice: analysis of age, gender, and tissue type

A lacI-containing transgenic mouse mutation detection system (Big Blue) was used to determine the frequency and spectrum of spontaneous mutation in two rapidly dividing tissues (male germ cells and thymus) and one slowly dividing tissue (brain) at 3 and 10 months of age. By screening 9.4 million lambda plaques, a total of 343 circular mutant plaques were recovered from the three tissues. The mutation frequencies and spectra were determined by sequencing the lacI gene and associated lacZ operator in all samples and correcting for "jackpot" mutations. The mutation frequencies and spectra were similar in all three tissues and there were no age-dependent or gender-dependent changes. When the mutation spectrum in each tissue was compared by utilizing large numbers of independent mutations (average: 75 per tissue), there was evidence for small tissue-specific differences. The spectrum of "jackpot" mutations, which clearly represents in vivo mouse-derived mutations, was similar to that of nonjackpot mutations, providing additional evidence that observed mutations occur in mouse. In the aggregate, the results suggest that there is: (i) a core mutation frequency and spectrum that is modified weakly by tissue-specific metabolism, and (ii) a steady-state level of spontaneous mutation in adult mice reflecting the balance between the accumulation of new mutations and the elimination of mutated cells by either selection against suboptimal cellular function or apoptosis triggered by accumulated DNA damage.

Software package for the management of sequencing projects using lacI transgenic animals

The bacterial lacI gene has been used for many years as a mutational target for the study of the mechanisms of mutation. A wealth of information has been collected for many mutagenic treatments and in strains with diverse DNA repair backgrounds. Recently this gene has been used in the construction of a transgenic mouse, named Big Blue, and a transgenic rat, as well as a rat cell line. The lacI gene in these animals and cells can conveniently be recovered and analyzed in bacteria. This makes it possible to study mutagenic potential of chemical compounds in vivo using a mammal. Tissue, strain, and gender specificity can be addressed. In addition, mutations recovered from tumour tissues or from animals with specific genetic backgrounds can be analyzed conveniently. The mammalian systems can produce large numbers of mutants that require computer assistance to manage the samples and the resulting DNA sequence data. Accordingly, a computer software system was developed. The system maintains an inventory of bacteriophage lambda lacI mutants and allows entry of mutant sequences while performing accuracy checks on the data. The software features several options for displaying lists of mutants. The system can perform several analyses, including mutant class compilations, mutational spectra comparisons, and clonal expansions analysis. An extensive database obtained from the bacterial lacI system is included with the software and can be analyzed along with mutants derived from transgenic animals.

The rex genes of lambda prophage modify ultraviolet light and N-methyl-N-nitrosourea-induced responses to DNA damage in Escherichia coli

Inactivation and mutagenesis of Escherichia coli by ultraviolet light and N-methyl-N-nitrosourea (MNU) were examined in isogenic strains that were (i) free of lambda phage, (ii) lysogenic for lambda or (iii) contained the lambda rexAB operon on a plasmid (prex20). Inactivation was enhanced when rex genes were present and this enhancement was greater for MNU than for UV. Mutagenesis was not greatly affected by the presence of the rex genes with one exception; UV-induced glnU degrees suppressor mutations were reduced in the strain harboring prex20. Control experiments using a strain containing only plasmid pACYC184 showed no effect on inactivation. A small depression in UV-induced mutagenesis was observed, however. These data suggest that the lambda RexAB proteins interfere with processes necessary for recovery from DNA damage and for fixation of one example of UV-induced mutation. This and other recent observations of effects by rex genes are discussed.

U-U and T-T cyclobutane dimers have different mutational properties

We have examined the mutagenic properties in E. coli of single stranded vectors containing a uniquely placed cis-syn or trans-syn uracil-uracil cyclobutane dimer in the sequence 5' GCAAGUUGGAG 3', and compared these with the properties of the corresponding T-T dimers in the same sequence context. The frequencies with which U-U and T-T photoproducts were bypassed were similar in SOS induced cells, and each induced similar frequencies of mutations. However, although both U-U and T-T cis-syn dimers showed a preference for misincorporation in about 5-7% of the replication products, with T or G being incorporated in place of A, the ratios of these events differed, being > 4:1 for T-T cis-syn, but only 2:1 for U-U cis-syn. A shift towards G insertion opposite dimerized uracil was also found with the trans-syn dimers, but the difference was greater; T and G were misincorporated opposite the U-U trans-syn dimer in a ratio of 1:2, compared with 4:1 for its T-T counterpart. In addition, the U-U dimer induced only nucleotide substitutions, unlike the T-T photoproduct which induced single nucleotide deletions as well as substitutions. We conclude that even relatively minor differences in photoproduct structure, such as the presence of a methyl group at C-5, can alter mutational properties, and that such properties cannot depend only on the attributes of the DNA polymerase. Neither the efficiency of bypass, the error frequency nor the mutation spectrum of either U-U isomer is influenced by DNA uracil glycosylase. In vitro, the U-U cis-syn dimer is a substrate for DNA photolyase, but not for the glycosylase.

Mutagenesis induced by single UV photoproducts in E. coli and yeast

Data from experiments with single-stranded vectors that carry a site-specific cyclobutane dimer, pyrimidine (6-4) pyrimidone adduct, or abasic lesion, replicated in either E. coli or, in some cases, bakers' yeast, Saccharomyces cerevisiae, are used to examine two questions: (i) what factors are responsible for the lesion's mutagenicity? and (ii) what are the relative contributions of different photoproducts to the spectrum of UV-induced mutations? With respect to the first question, we suggest that the structure of the mutagen-modified template itself largely determines the kinds of mutations induced, but the relative frequencies of these mutations, the error frequency, and the bypass frequency are strongly dependent on the particular organism studied. With respect to the second question, we suggest that cyclobutane dimers may be responsible for most of the mutations in slowly replicating genomes because of the deamination of cytosine, and that the T-T, and to a lesser extent the T-C, (6-4) adducts play a greater role in the UV mutagenesis of quickly replicating viruses, such as M13 and lambda phage.

Replication of damaged DNA and the molecular mechanism of ultraviolet light mutagenesis

On UV irradiation of Escherichia coli cells, DNA replication is transiently arrested to allow removal of DNA damage by DNA repair mechanisms. This is followed by a resumption of DNA replication, a major recovery function whose mechanism is poorly understood. During the post-UV irradiation period the SOS stress response is induced, giving rise to a multiplicity of phenomena, including UV mutagenesis. The prevailing model is that UV mutagenesis occurs by the filling in of single-stranded DNA gaps present opposite UV lesions in the irradiated chromosome. These gaps can be formed by the activity of DNA replication or repair on the damaged DNA. The gap filling involves polymerization through UV lesions (also termed bypass synthesis or error-prone repair) by DNA polymerase III. The primary source of mutations is the incorporation of incorrect nucleotides opposite lesions. UV mutagenesis is a genetically regulated process, and it requires the SOS-inducible proteins RecA, UmuD, and UmuC. It may represent a minor repair pathway or a genetic program to accelerate evolution of cells under environmental stress conditions.

Transcription-repair coupling determines the strandedness of ultraviolet mutagenesis in Escherichia coli

We have analyzed the spectra of UV-induced mutations in the lacI gene of a wild-type and an mfd strain of Escherichia coli. mfd strains have been recently proposed to be deficient in a factor coupling DNA repair and transcription. Analysis of UV-induced mutations occurring at adjacent pyrimidines showed that mutations in the wild-type strain arose largely from the nontranscribed strand but arose predominantly from the transcribed strand in the mfd strain. The overall strand switch was 14-fold. One mutation, G.C-->A.T in the lacI initiation codon, showed a > 300-fold shift. No effect was observed for mutations at non-pyrimidine-pyrimidine sequences. These results provide in vivo evidence for a key role of the mfd gene in controlling the strandedness of mutagenesis and support the proposed role of the mfd gene product in directing DNA excision repair to the transcribed strand of a damaged gene.

The distribution of UV damage in the lacI gene of Escherichia coli: correlation with mutation spectrum

We have determined the UV (254 nm) damage distribution in the transcribed and non-transcribed strands of the i-d region of the Escherichia coli lacI gene. The locations of replication blocking lesions were revealed as termination sites of T7 DNA polymerase and/or T4 DNA polymerase 3'-5' exonuclease. Termination products, i.e. both cyclobutane pyrimidine dimers and 6-4 photoproducts, were resolved and analysed on an automated DNA sequencer. These two major photoproducts are not randomly distributed along the gene, but occur in clusters, in longer runs of pyrimidines. We also have compared the UV damage distribution with the previously reported UV-induced base substitutions in the same region. Mutational hotspots, in both repair-deficient and repair-proficient strains of E. coli, are all located in stretches of pyrimidines, and thus correlate well with the distribution of photolesions. One mutational hotspot in the wild-type strain may reflect the high frequency of closely opposed lesions. To explain the other mutational hotspots, we propose that the repair of UV lesions is impaired due to the local conformation of the DNA, which might deviate from the B-form. This hypothesis is supported by the excess of mutational hotspots in pyrimidine runs in the Uvr+ strain compared to Uvr-. Runs of pyrimidines thus represent both damage- and mutation-prone sequences following UV treatment.

A temperature-sensitive calmodulin mutant loses viability during mitosis

Although rare, a recessive temperature-sensitive calmodulin mutant has been isolated in Saccharomyces cerevisiae. The mutant carries two mutations in CMD1, isoleucine 100 is changed to asparagine and glutamic acid 104 is changed to valine. Neither mutation alone conferred temperature sensitivity. A single mutation that allowed production of an intact but defective protein was not identified. At the nonpermissive temperature, the temperature-sensitive mutant displayed multiple defects. Bud formation and growth was delayed, but this defect was not responsible for the temperature-sensitive lethality. Cells synchronized in G1 progressed through the cell cycle and retained viability until the movement of the nucleus to the neck between the mother cell and the large bud. After nuclear movement, less than 5% of the cells survived the first mitosis and could form colonies when returned to permissive conditions. The duplicated DNA was dispersed along the spindle, extending from mother to daughter cell. Cells synchronized in G2/M lost viability immediately upon the shift to the nonpermissive temperature. At a semipermissive temperature, the mutant showed approximately a 10-fold increase in the rate of chromosome loss compared to a wild-type strain. The mitotic phenotype is very similar to yeast mutants that are defective in chromosome disjunction. The mutant also showed defects in cytokinesis.

The thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct is highly mutagenic and specifically induces 3' thymine-to-cytosine transitions in Escherichia coli

We have constructed single-stranded, M13-based vectors that contain a specifically located thymine-thymine pyrimidine-pyrimidone(6-4) UV photoproduct and have used these to estimate the frequency and accuracy of DNA replication past this adduct in uvrA6 cells of Escherichia coli. Both the normal and the Dewar valence photoisomer of the (6-4) adduct were studied. In the absence of SOS induction, vectors carrying the photoproducts were rarely replicated; relative to the lesion-free control, 1.9% of vectors carrying the normal (6-4) isomer produced plaques, and with the Dewar valence isomer the proportion was 0.4%. In SOS-induced cells, these frequencies rose to 22.1% and 12.3%, respectively. The error frequency of replication past the normal isomer in SOS-induced cells was high; in a random sample of 185 progeny phage analyzed, 169 (91%) contained mutations, all of which were targeted. Equally striking, a high proportion of the mutations (158/169; 93%) were of only one type, namely 3' T----C transitions. Both the error frequency and the specificity were much reduced with the Dewar valence isomer; overall, 74/140 (53%) of the phage analyzed were mutant, and of these only 34 (46%) entailed the 3' T----C transition. We speculate that the high error frequency and specificity arise from the formation of a stable T-G base pair, involving hydrogen bonds at O-2 and N-3 in the pyrimidone ring. Potential hydrogen bonds at these sites are coplanar in the normal but not in the Dewar isomer, perhaps explaining the reduced specificity of mutagenesis with the latter adduct.

DNA sequence changes in mutations induced by ultraviolet light in the gpt gene on the chromosome of Escherichia coli uvr+ and urvA cells

Sequence changes in mutations induced by ultraviolet light are reported for the chromosomal Escherichia coli gpt gene in almost isogenic E. coli uvr+ and excision-deficient uvrA cells. Differences between the mutagenic spectra are ascribed to preferential removal of photoproducts in the transcribed strand by excision repair in uvr+ cells. This conclusion is confirmed by analysis of published results for genes in both uvr+ and uvr- cells, showing a similar selective removal of mutagenic products from the transcribed strand of the E. coli lacI gene and of the lambda phage cI repressor gene. Comparison of these data with published results for ultraviolet mutagenesis of gpt on a chromosome in Chinese hamster ovary cells showed that a mutagenic hot spot in mammalian cells is not present in E. coli; the possibility is suggested that the hot spot might arise from localized lack of excision repair. Otherwise, mutagenesis in hamster cells appeared similar to that in E. coli uvr+ cells, except there appears to be a smaller fraction of single-base additions and deletions (frameshifts) in mammalian than in bacterial cells. Phenotypes of 6-thioguanine-resistant E. coli showed there is a gene (or genes) other than gpt involved in the utilization of thioguanine by bacteria.

Specificity of spontaneous mutation in the lacI gene cloned into bacteriophage M13

We have studied the specificity of spontaneous mutation in the lacI gene of Escherichia coli cloned into bacteriophage M13. The comparison of the spectrum of 85 spontaneous mutations with that of the lacI gene carried on an E. coli F' episone revealed the following characteristics: (i) base substitution was predominant, accounting for 80% of spontaneous events compared with only 11% on the F' episome; (ii) among the base substitutions, the majority were G:C----A:T transitions (86%); (iii) not one mutation recovered on M13 corresponded to a mutation at the spontaneous hotspots seen in the F' spectrum (i.e., neither the addition or deletion of the tetramer 5'-CTGG-3' at position 620-631 nor the A:T----G:C transition at position +6 of lacO were recovered). The enhanced rate of cytosine deamination in single-stranded DNA, the unique replication mechanism and the refractory nature of single-stranded DNA to excision-repair processes present likely explanations for the observed mutational spectrum.

UmuC function is not essential for the production of all targeted lacI mutations induced by ultraviolet light

Up to a quarter or more of the normal yield of lacI- mutations could be induced by ultraviolet light in a uvrA6 umuC122:: Tn5 strain if they were detected by plating on 5-bromo-4-chloro-3-indolyl-beta-D-galactoside medium, where all surviving cells can form colonies. Using phenyl beta-D-galactoside selection, which curtails post-irradiation growth, only low yields of mutations were induced. Nucleotide sequence analysis of 134 spontaneous and 145 ultraviolet light-induced mutations shows that broadly similar kinds of mutations were induced in the umuC mutant and its uvrA6 umuC+ counterpart. In particular, these data offer no reason for believing that most of the mutations induced in the umuC mutant were other than normal, targeted events. We conclude that UmuC function, rather than being essential, facilitates recovery and specifically, following the model of Bridges & Woodgate, that it facilitates the prompt resumption of chain elongation.