Bacterial mutagenesis: review of new insights

History of environmental and molecular mutagenesis

Environmental and Molecular Mutagenesis, the journal of the Environmental Mutagen Society (EMS), marks its 25th anniversary in 2004. The journal, originally called Environmental Mutagenesis, was established in 1979 with Seymour Abrahamson as its first editor. The development of the journal is closely linked to the evolution of the fields of mutation research and genetic toxicology. This perspective traces the founding of the journal and discusses its editorial history, growth, content, style, administration, and relationship to the EMS.

Quantum yield for preferential photodimerization in long pyrimidine tracts

The quantum yield for cyclobutyl-pyrimidine dimerization in DNA has been observed to increase approximately linearly with increasing pyrimidine tract length. A model without adjustable parameters for this yield is proposed based on energy delocalization, vibronic symmetry switching, and saturation statistics that describe the average number of (base pairwise) breathing modes in a given tract of pyrimidines. This average number of modes is an approximately linear function of the tract length. Monte Carlo techniques are used to simulate base sequences and photochemical events, and indicate that this model is consistent with experiment for Tetrahymena pyriformis 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.

The development of ideas about the effect of DNA repair on the induction of gene mutations and chromosomal aberrations by radiation and by chemicals

An historical overview is given of the development of ideas about chromosomal and DNA repair as they relate to the induction of mutations, chromosomal aberrations, and sister-chromatid exchanges by radiations and chemicals. The genetic and molecular bases of the various repair pathways are reviewed whenever possible. Work on both prokaryotes and eukaryotes is included. Mention is made, when deemed appropriate, of major developments in other areas that served as essential background for the repair work, but no attempt is made to cover these background developments in any detail. Near the end, a brief review is given of factors affecting polymerase fidelity. The history is subdivided into approximately 10-year intervals. For the most part, references are to reviews and symposia in which the ideas of the time were brought together. The implications of these findings for some practical problems in genetic toxicology and for our understanding of the maintenance of the genome are discussed at the end.

The molecular basis of the evolution of sex

Traditionally, sexual reproduction has been explained as an adaptation for producing genetic variation through allelic recombination. Serious difficulties with this explanation have led many workers to conclude that the benefit of sex is a major unsolved problem in evolutionary biology. A recent informational approach to this problem has led to the view that the two fundamental aspects of sex, recombination and outcrossing, are adaptive responses to the two major sources of noise in transmitting genetic information, DNA damage and replication errors. We refer to this view as the repair hypothesis, to distinguish it from the traditional variation hypothesis. On the repair hypothesis, recombination is a process for repairing damaged DNA. In dealing with damage, recombination produces a form of informational noise, allelic recombination, as a by-product. Recombinational repair is the only repair process known which can overcome double-strand damages in DNA, and such damages are common in nature. Recombinational repair is prevalent from the simplest to the most complex organisms. It is effective against many different types of DNA-damaging agents, and, in particular, is highly efficient in overcoming double-strand damages. Current understanding of the mechanisms of recombination during meiosis suggests that meiosis is designed for repairing DNA. These considerations form the basis for the first part of the repair hypothesis, that recombination is an adaptation for dealing with DNA damage. The evolution of sex can be viewed as a continuum on the repair hypothesis. Sex is presumed to have arisen in primitive RNA-containing protocells whose sexual process was similar to that of recombinational repair in extent segmented, single-stranded RNA viruses, which are among the simplest known organisms. Although this early form of repair occurred by nonenzymatic reassortment of replicas of undamaged RNA segments, it evolved into enzyme-mediated breakage and exchange between long DNA molecules. As some lines of descent became more complex, their genome information increased, leading to increased vulnerability to mutation. The diploid stage of the sexual cycle, which was at first transient, became the predominant stage in some lines of descent because it allowed complementation, the masking of deleterious recessive mutations. Out-crossing, the second fundamental aspect of sex, is also maintained by the advantage of masking mutations. However, outcrossing can be abandoned in favor of parthenogenesis or selfing under conditions in which the costs of mating are very high.(ABSTRACT TRUNCATED AT 400 WORDS)

Absence of deoxyuridine and 5-hydroxymethyldeoxyuridine in the DNA from three tissues of mice of various ages

Mutational damage to DNA may modulate the aging process as well as contribute to the high incidence of cancer in older animals. Uracil (Ura) is the deamination product of cytosine and hydroxymethyluracil (HMU) is an oxidation product of thymine. Ura, when generated from cytosine, induces mutations by mispairing with adenine. Both HMU and Ura are known to be excised from DNA by glycosylases that cleave the respective N-glycosidic bonds. This hydrolysis leaves apyrimidinic sites which are subsequently repaired by excision repair. In this report a sensitive method to detect these altered bases of HPLC separation of the components of DNA hydrolysates is described. Neither deoxyuridine (dU) nor 5-hydroxymethyldeoxyuridine (dHMU) were found in hydrolysates of DNA samples from brain, liver or small intestinal mucosa of mice of different ages.

Background levels of DNA damage in the population

In addition to the dangers of man-made mutagenic substances, there exist a variety of naturally-occurring agents and processes than can cause DNA damage in man. These include exogenous agents, such as sunlight and dietary mutagens, as well as endogenous agents, such as reactive oxygen species which are formed within the cell via normal metabolism. These processes can lead to at least six major types of DNA damage: base loss, base deamination, base alkylation, base dimerization, base oxidation, and single-strand breakage. Based upon in vitro measurements in cell-free model systems or cultured cells, estimates of the rates of production of these lesions have been made for the average human cell: about 26,000 base losses per day, primarily purines lost because of spontaneous hydrolysis of the glycosyl bond; about 350 cytosine deaminations per day; tens of thousands of base alkylations per day, primarily methylations of guanine caused by S-adenosylmethionine; up to 50,000 pyrimidine dimerizations per day, dependent upon exposure to sunlight; and about 100,000 single-strand breaks per day. Based upon measurements of DNA oxidation products in human urine, we estimate that the total rate of formation of all oxidative DNA damage products in man is on the order of a few thousand events per cell per day. In addition, base mispairing can take place in the absence of DNA damage because of tautomeric shifts, base ionization, or base rotation.(ABSTRACT TRUNCATED AT 250 WORDS)

Isolation and characterization of Escherichia coli antimutators. A new strategy to study the nature and origin of spontaneous mutations

To identify the nature and origin of spontaneous mutability we developed a screening procedure suitable to isolate antimutators showing a lower error rate than 10(-10) per base per replication. Among about 500,000 mutagenized colonies we found 20 mutants showing a reduced spontaneous mutability. These antimutators can be subdivided into three groups: (i) Mutants in which the level of spontaneous mutability is reduced due to an increase in efficiency of the error correcting mechanism (amu4). (ii) Mutants which are deficient in several pathways of DNA repair. This finding supports the hypothesis that much spontaneous mutability is due to error-prone repair (amu59, amu47, amu50, amu62, amu43, amu38). (iii) Mutants in which the antimutator effect seems to be the result of an auxotrophy such as Pur- (amu17), Thr- (amu1, amu28) and Ser- (amu31). This finding might support the hypothesis that metabolically induced lesions are important in spontaneous mutagenesis. Eleven of these antimutators were mapped at ten bacterial loci in the following positions: amu31 (2 min); amu4 (4 min); amu62 (82 min); amu47 (85 min); amu59 (86 min); amu17 (89 min); amu50 (95 min); amu1/amu28 (100 min); amu38 (23-27 min) and amu43 (74-81 min).

Genotoxic classification of anticancer drugs

The effects of bacterial DNA excision repair on the mutagenic and lethal actions of 17 injectable anticancer drugs have been used to classify them into three levels of potential risk to medical personnel who are involved in their preparation and administration.

Mutagenicity of ozone in different repair-deficient strains of Escherichia coli

The mutagenic activity of ozone was investigated by the isolation of streptomycin-resistant mutants (Smr) in different strains of Escherichia coli. RecA, lexA, polA and parental strains were ozonated and streptomycin-resistant mutants were scored after a short or long phenotypic delay. Our results suggest that ozone is an active mutagen for forward mutation and that this oxidizing agent could be able to induce mutations via two mechanisms: directly and indirectly by the rec-lex error-prone repair system.

Liquid-holding experiments with human peripheral lymphocytes. II. Experiments with trenimon and 1-beta-D-arabinosylcytosine

Liquid holding of trenimon-treated human peripheral lymphocytes in the G0 stage of the cell cycle leads to an elevation in the frequencies of chromosome aberrations and a decrease in the frequencies of chromatid aberrations. The frequencies of aberrant metaphases are not influenced significantly under these experimental conditions. Storage of trenimon-treated cells in the presence of 1-beta-D-arabinosylcytosine (araC) leads to an additional increase in the frequencies of chromosome-type aberrations, with an increase in the frequencies of aberrant metaphases as well. These findings are interpreted as DNA double-strand breaks being formed during the repair of damaged DNA, and that araC exaggerates this effect by inhibiting repair. AraC does not influence the frequencies of SCEs significantly, which indicates that either the lesions or the repair pathways leading to chromosome aberrations are different from those leading to SCEs.

Methodologies for the determination of various genetic effects in permeable strains of E. coli K-12 differing in DNA repair capacity. Quantification of DNA adduct formation, experiments with organ homogenates and hepatocytes, and animal-mediated assays

Derivatives of E. coli K-12 strain 343/113 differing in DNA repair capacity, in permeability to large molecules, and in some metabolizing activities (nitroreductase, glutathione), were constructed for the quantitative determination of the induction of various genetic effects, such as forward and back mutations, lysogenic induction of prophage lambda, and repairable DNA damage. These E. coli strains can be used in assay procedures which allow variation and control over several experimental conditions, such as oxygen tension, time, pH, temperature of incubation and growth phase of the indicator cells. Methods are described for the simultaneous determination of genetic effects and of DNA-adduct formation during mutagen treatment, i.e. by using radio-labeled compounds or by means of an enzyme-linked immunosorbent assay (ELISA). Mammalian biotransformation of xenobiotics can be investigated by including various fractions of mammalian organs in the system. Examples of the relative effectiveness of the activating potential of S9, S100 and isolated hepatocytes for dialkylnitrosamines and other carcinogens are presented. Host-mediated assays, finally, are described which, in addition to gene mutations, can also be used for the determination of repairable DNA damage in bacteria present in different organs, including the liver, spleen, lungs, kidneys, pancreas, and the blood stream of chemically treated mice. It is concluded that quantitative tests in vitro for assessment of induced mutagenic spectrum and genotoxic potency, combined with the host-mediated assay as a monitor, in vivo, of genotoxic factors present in various organs of animals, may become useful in the assessment of genotoxic (and possibly tumor-initiating) properties of chemicals for which long-term in-vivo mutagenicity and/or carcinogenicity data are not yet available.

A differential DNA-repair test using mixtures of E. coli K12 strains in liquid suspension and animal-mediated assays

The feasibility of performing tests for repairable DNA damage in animal assay procedures was investigated by using repair-proficient and repair-deficient derivatives of E. coli K12 strain 343/113, including mutations in the uvrB, recA, polA and dam genes. To avoid variations in the relative recovery of viable cells from different samples, the strains were further marked with auxotrophic growth requirements, so that mixtures could be treated and the survival of each strain determined individually on media containing the corresponding growth factors. Spot tests were performed with the various strains to re-assess the necessity of using a combination of repair deficiencies, when genotoxic agents of differing mode of action are to be detected. Liquid suspension tests on mixtures of the different strains, furthermore, confirmed that the survival of the individual strains can be determined separately on selective media after treatment with methyl methanesulfonate (MMS) and methyl nitrosourea (MNU). These tests were also used to demonstrate that dimethyl nitrosamine (DMNA) is activated by Aroclor-1254-induced rat-liver S9 fractions to genotoxic products, as measured by the low survival of a recA derivative compared with the repair-proficient wild-type strain. Intrasanguineous host-mediated assays using the present derivatives of E. coli K12/343/113 showed that the various strains, injected simultaneously into mice, could be recovered in amounts sufficient for the individual determination of the relative survival in liver, spleen, lungs, kidneys, pancreas and the blood stream of the host animals. Using a mixture of the repair-proficient parent and the recA derivative inoculated into mice that were subsequently treated with MMS, NMU or DMNA, we found that these chemicals induce a larger decrease in survival in the recA strain as compared with the wild-type in cells recovered from the liver and the spleen. The order of genotoxic potency so determined was DMNA greater than MNU greater than MMS; this is similar to the ranking of the carcinogenicity of these compounds in rodents and probably also reflects the various degrees of DNA alkylation in cells of the livers of the treated animals. The general usefulness of the host-mediated differential DNA repair assay for detecting genotoxic factors in various organs of animals remains to be assessed by using chemical mutagens of different modes of action.

The effects of excision repair and the plasmid pKM101 on the induction of his+ revertants by chemical agents in Salmonella typhimurium

Expansion of the Ames Salmonella/microsome mutagenesis test to include plasmid pKM101-bearing, excision repair-proficient derivatives permits 1) the identification of mutagens that require both factors for activity; 2) the identification of genotoxins through the enhancement of survival by excision repair; and 3) the classification of substances according to the effects of excision repair on their mutagenesis. Class I includes substances that require excision repair to effect mutagenesis. Class II contains substances whose mutagenesis is not affected by excision repair. Class III mutagens cause premutational lesions in DNA which are readily removed by excision repair. This classification scheme is suggested as a preliminary step in making a risk estimation for a mutagen.

Mutagen sensitivity of Drosophila melanogaster. V. Identification of second chromosomal mutagen sensitive strains

Six recessive second chromosomal mutants of Drosophila melanogaster exhibiting larval hypersensitivity to methyl methanesulfonate have been identified and assigned to six complementation groups. The strains have been analyzed for their sensitivities to UV, X-ray, nitrogen mustard and formaldehyde. Two classes of mutants not previously observed in Drosophila have been identified. The mus 204A1 and mus 205A1 mutants exhibit sensitivity to MMS and UV but not X-ray or nitrogen mustard, while the mus 206A1 and mus 207A1 mutants display sensitivity to MMS, UV, and nitrogen mustard. Four of the seven strains exhibit poor female fertility and two of these are shown to have a weak meiotic disjunctional defect. Biochemical studies of the mus 205A1 mutant suggest a defect in DNA synthetic ability associated with excision and postreplication repair performed on UV and alkylation-damaged templates (Boyd and Harris 1981; Brown and Boyd 1981 b; R.L. Dusenbery, manuscript in preparation).

Comparative mutability of the Ames tester strains of Salmonella typhimurium by ultraviolet radiation and by 4-nitroquinoline 1-oxide

A standard method for determining mutant frequencies per survivor was used to study the detailed kinetics of reverse mutations of Ames tester strains of Salmonella typhimurium induced by UV and by 4NQO. After UV irradiation, strain TA1538 was non-mutable, but its plasmid-containing derivative TA98 was mutable, whereas TA1535 was mutable and its plasmid-bearing derivative TA100 was about 10-fold more mutable. After treatment with 4NQO, TA98 was less mutable than TA1538, whereas TA100 was more mutable than TA1535 by a factor of 10-50. TA1537 was slightly less mutable than TA1535 by either UV or 4NQO. The differential mutabilities of these strains are briefly discussed in relation to the "hot spot" base sequences for reversion and the nature of DNA damage caused by UV and 4NQO.

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.