Complex frameshift mutations mediated by plasmid pKM101: mutational mechanisms deduced from 4-aminobiphenyl-induced mutation spectra in Salmonella

Small Indels in the Androgen Receptor Gene: Phenotype Implications and Mechanisms of Mutagenesis

CONTEXT

Despite high abundance of small indels in human genomes, their precise roles and underlying mechanisms of mutagenesis in Mendelian disorders require further investigation.

OBJECTIVE

To profile the distribution, functional implications, and mechanisms of small indels in the androgen receptor (AR) gene in individuals with androgen insensitivity syndrome (AIS).

METHODS

We conducted a systematic review of previously reported indels within the coding region of the AR gene, including 3 novel indels. Distribution throughout the AR coding region was examined and compared with genomic population data. Additionally, we assessed their impact on the AIS phenotype and investigated potential mechanisms driving their occurrence.

RESULTS

A total of 82 indels in AIS were included. Notably, all frameshift indels exhibited complete AIS. The distribution of indels across the AR gene showed a predominance in the N-terminal domain, most leading to frameshift mutations. Small deletions accounted for 59.7%. Most indels occurred in nonrepetitive sequences, with 15.8% situated within triplet regions. Gene burden analysis demonstrated significant enrichment of frameshift indels in AIS compared with controls (P < .00001), and deletions were overrepresented in AIS (P < .00001).

CONCLUSION

Our findings underscore a robust genotype-phenotype relationship regarding small indels in the AR gene in AIS, with a vast majority presenting complete AIS. Triplet regions and homopolymeric runs emerged as prone loci for small indels within the AR. Most were frameshift indels, with polymerase slippage potentially explaining half of AR indel occurrences. Complex frameshift indels exhibited association with palindromic runs. These discoveries advance understanding of the genetic basis of AIS and shed light on potential mechanisms underlying pathogenic small indel events.

Analysis of chemical structures and mutations detected by Salmonella TA98 and TA100

As part of an analysis performed under the auspices of the International Workshop on Genotoxicity Testing (IWGT) in 2017, we and others showed that Salmonella frameshift strain TA98 and base-substitution strain TA100 together + /- S9 detected 93% of the mutagens detected by all the bacterial strains recommended by OECD TG471 (Williams et al., Mutation Res. 848:503081, 2019). We have extended this analysis by identifying the numbers and chemical classes of chemicals detected by these two strains either alone or in combination, including the role of S9. Using the Leadscope 2021 SAR Genetox database containing > 21,900 compounds, our dataset containing 7170 compounds tested in both TA98 and TA100. Together, TA98 and TA100 detected 94% (3733/3981) of the mutagens detected using all the TG471-recommended bacterial strains; 39% were mutagenic in one or both strains. TA100 detected 77% of all of these mutagens and TA98 70%. Considering the overlap of detection by both strains, 12% of these mutagens were detected only by TA98 and 19% only by TA100. In the absence of S9, sensitivity dropped by 31% for TA98 and 29% for TA100. Overall, 32% of the mutagens required S9 for detection by either strain; 9% were detected only without S9. Using the 2021 Leadscope Genetox Expert Alerts, TA100 detected 18 mutagenic alerting chemical classes with better sensitivity than TA98, whereas TA98 detected 10 classes better than TA100. TA100 detected more chemical classes than did TA98, especially hydrazines, azides, various di- and tri-halides, various nitrosamines, epoxides, aziridines, difurans, and half-mustards; TA98 especially detected polycyclic primary amines, various aromatic amines, polycyclic aromatic hydrocarbons, triazines, and dibenzo-furans. Model compounds with these structures induce primarily G to T mutations in TA100 and/or a hotspot GC deletion in TA98. Both TA98 and TA100 + /- S9 are needed for adequate mutagenicity screening with the Salmonella (Ames) assay.

Mutagenicity and carcinogenicity of combustion emissions are impacted more by combustor technology than by fuel composition: A brief review

Studies during the past 50 years have characterized the carcinogenicity and mutagenicity of extractable organic material (EOM) of particulate matter (PM) in ambient air and from combustion emissions. We have summarized conclusions from these studies and present data supporting those conclusions for 50 combustion emissions, including carcinogenic potencies on mouse skin (papillomas/mouse/mg EOM), mutagenic potencies (revertants/μg EOM) in the Salmonella (Ames) mutagenicity assay, and mutagenicity emission factors (revertants/kg fuel or revertants/MJthermal ) in Salmonella. Mutagenic potencies of EOM from PM in ambient air and combustion emissions span 1-2 orders of magnitude, respectively. In contrast, the revertants/m3 span >5 orders of magnitude due to variable PM concentrations in ambient air. Carcinogenic potencies of EOM from combustion emissions on mouse skin and EOM-associated human lung cancer risk from those emissions both span ~3 orders of magnitude and are highly associated. The ubiquitous presence of polycyclic aromatic hydrocarbons (PAHs), nitroarenes, and aromatic amines results in mutagenic and carcinogenic potencies of PM that span only 1-3 orders of magnitude; most PM induces primarily G to T mutations. Mutagenicity emission factors of combustion emissions span 3-5 orders of magnitude and correlate with PAH emission factors (r > 0.9). Mutagenicity emission factors were largely a function of how material was burned (highly efficient modern combustors versus open burning) rather than what materials were burned. Combustion systems that minimize kinetic and mass-transfer limitations and promote complete oxidation also minimize the mutagenicity of their emissions. This fundamental engineering principle can inform environmental and public health assessments of combustion emissions.

Clusters of Multiple Mutations: Incidence and Molecular Mechanisms

It has been long understood that mutation distribution is not completely random across genomic space and in time. Indeed, recent surprising discoveries identified multiple simultaneous mutations occurring in tiny regions within chromosomes while the rest of the genome remains relatively mutation-free. Mechanistic elucidation of these phenomena, called mutation showers, mutation clusters, or kataegis, in parallel with findings of abundant clustered mutagenesis in cancer genomes, is ongoing. So far, the combination of factors most important for clustered mutagenesis is the induction of DNA lesions within unusually long and persistent single-strand DNA intermediates. In addition to being a fascinating phenomenon, clustered mutagenesis also became an indispensable tool for identifying a previously unrecognized major source of mutation in cancer, APOBEC cytidine deaminases. Future research on clustered mutagenesis may shed light onto important mechanistic details of genome maintenance, with potentially profound implications for human health.

Reinventing the ames test as a quantitative lab that connects classical and molecular genetics

While many institutions use a version of the Ames test in the undergraduate genetics laboratory, students typically are not exposed to techniques or procedures beyond qualitative analysis of phenotypic reversion, thereby seriously limiting the scope of learning. We have extended the Ames test to include both quantitative analysis of reversion frequency and molecular analysis of revertant gene sequences. By giving students a role in designing their quantitative methods and analyses, students practice and apply quantitative skills. To help students connect classical and molecular genetic concepts and techniques, we report here procedures for characterizing the molecular lesions that confer a revertant phenotype. We suggest undertaking reversion of both missense and frameshift mutants to allow a more sophisticated molecular genetic analysis. These modifications and additions broaden the educational content of the traditional Ames test teaching laboratory, while simultaneously enhancing students' skills in experimental design, quantitative analysis, and data interpretation.

Genetic analysis of ionizing radiation-induced mutagenesis in Saccharomyces cerevisiae reveals TransLesion Synthesis (TLS) independent of PCNA K164 SUMOylation and ubiquitination

Ionizing radiation-induced mutagenesis (IR-IM) underlies a basis for radiation associated carcinogenesis as well as resistance to radiation therapy. This process was examined in Saccharomyces cerevisiae using an array of isogenic DNA repair deficient mutants. Mutations inactivating homologous recombination (rad51, 52, 54) or nucleotide excision repair (rad1, rad10, rad4) caused elevated IR-IM whereas inactivation of TransLesion Synthesis (TLS: rad6) caused severely defective IR-IM. Of the mutations inactivating TLS polymerases, rev3 and rev1 caused equally severe defects in IR-IM whereas rad30 did not significantly affect the process. The effects of the rev3, rev1, and rad6 mutations on IR-IM were epistatic, suggesting the requirement of both polymerase zeta and Rev1p in IR-IM related TLS. Although PCNA K164 SUMOylation/ubiquitination is a proposed prerequisite for TLS, the IR-IM defect of a rev3 or a rad6 mutant was worse than and epistatic to the pol30K164R mutant, a mutant in which the PCNA had been mutated to abolish such modifications. These results suggested that IR-IM related TLS occurs in the absence of PCNA K164 modification. Further analysis of a mutant simultaneously defective in SUMOylation and mono-ubiquitination (rad18 siz1) revealed that these modifications redundantly affected TLS as well as NHEJ. A genetic model based on these observations is proposed.

Rapid selection of nonhotspot mutants among hisD+ revertants of Salmonella typhimurium TA98 in Ames test by peptide nucleic acid (PNA)-mediated PCR clamping

Ames test is the most popular method of assessing mutagenicity using Salmonella typhimurium as an indicator. Recently, sequence analyses have been introduced for the investigation of mutation mechanisms. Most revertants (>70%) carry 2-bp deletion within an 8-bp CG repeat in hisD (hotspot mutation) in the Ames test using S. typhimurium TA98. We developed a new specific amplification method for nonhotspot mutants by peptide nucleic acid (PNA)-mediated PCR clamping. It markedly reduces the labor and cost of this kind of studies.

4-Aminobiphenyl induces liver DNA adducts in both neonatal and adult mice but induces liver mutations only in neonatal mice

The mechanisms underlying the susceptibility of neonatal mice to genotoxic carcinogens were investigated by analyzing the DNA adducts and mutations induced in the livers of neonatal and adult Big Blue transgenic mice by 4-aminobiphenyl (4-ABP), a potent human and rodent carcinogen. Neonatal and adult mice were treated with a regimen of 4-ABP known to induce tumors in neonatal mice. Animals were sacrificed 1 day after the last treatment for DNA adduct analysis and 8 weeks after the last treatment for analysis of lacI and cII mutant frequency (MF). N-(Deoxyguanosin-8-yl)-4-ABP was the major DNA adduct identified in the livers of the 4-ABP-treated mice and levels of this adduct were significantly higher in treated animals than in the controls for both the neonates and adults. Adduct levels for adult females (44.0 +/- 4.8 adducts/10(6) nucleotides) were higher than in neonatal females (25.9 +/- 2.2 adducts/10(6) nucleotides), while adduct levels in adult males (13.5 +/- 2.0 adducts/10(6) nucleotides) were lower than in neonatal males (33.8 +/- 4.1 adducts/10(6) nucleotides). 4-ABP treatment significantly increased the liver cII MFs in both sexes of neonatal mice but not in adult mice. Sequence analysis of cII mutant DNA revealed that 4-ABP induced a unique spectrum of mutations in neonatal mice, characterized by a high frequency of G:C-->T:A transversion, while the mutation spectrum in 4-ABP-treated adults was similar to that of control mice. Our results indicate that DNA adduct formation by 4-ABP depends as much on sex as it does on age, whereas the conversion of DNA adducts into mutations differed with animal age. These observations suggest that neonates are more sensitive than adults to genotoxic carcinogens because the relatively high levels of cell division in the developing animal facilitate the conversion of DNA damage into mutation. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat/index.html

Mutant spectra analysis at hisG46 in Salmonella typhimurium strain YG1029 induced by mammalian S9- and plant-activated aromatic amines

Mutant spectra analysis was conducted with spontaneous hisG46 revertants of Salmonella typhimurium strain YG1029 and revertants induced by the plant- and mammalian S9-activation of benzidine and 4-aminobiphenyl (4-ABP). Under preincubation conditions, YG1029 cells were exposed to benizidine or 4-ABP with mammalian S9 activation or to a high molecular weight fraction that contained the plant-activated products. The induced revertants were isolated at mutagen concentrations that caused an increased mutant frequency of approximately 4- to 10-fold above background. Genomic DNA from each revertant was isolated and the hisG region was amplified using polymerase chain reaction (PCR). Using a series of specific probes and a modified version of the ECL3's-oligolabelling and detection system, each of the six possible base-pair substitution mutations at hisG46 that leads to a reversion event was determined. Of the YG1029 spontaneous revertants, transition mutations were 31.8% and transversion mutations were 68.2%. The YG1029 spontaneous mutant spectrum differed significantly from the spontaneous spectrum of TA1535 but did not significantly differ from the spontaneous TA100 mutant spectrum. The differences of the spontaneous mutant spectra among these highly related strains illustrate that the introduction of the plasmid pKM101 into S. typhimurium increased the frequency of transversions (CCC-->ACC; CCC-->CAC) and reduced site 2 (CCC-->CTC) transitions. With plant-activated benzidine, 21.1% of recovered revertants resulted from transitions and 78.9% from transversions while S9 activated-benzidine induced revertants were recovered as 14.2% from transition and 85.8% from transversion mutations. Plant-activated 4-ABP recovered 20.0% transitions and 80.0% transversions. S9-activated 4-ABP-induced 21.4% transitions and 78.6% transversions. Chi-square analysis of mutant spectra indicated that the DNA lesions that resulted in reversion at the hisG46 allele induced by plant-activated benzidine or 4-ABP were different from those generated after mammalian S9 activation of these promutagens. The plant-activated benzidine and 4-ABP induced statistically identical mutant spectra. Also, the mammalian-activated benzidine and 4-ABP induced statistically similar mutant spectra. These data show that the plant-activated and mammalian-activated aromatic amine products inflicted different types or distributions of DNA lesions that were reflected in the resulting induced mutant spectra.

Origins of spontaneous mutations: specificity and directionality of base-substitution, frameshift, and sequence-substitution mutageneses

Spontaneous mutations are derived from various sources, including errors made during replication of undamaged template DNA, mutagenic nucleotide substrates, and endogenous DNA lesions. These sources vary in their frequencies and resultant mutations, and are differently affected by the DNA sequence, DNA transactions, and cellular metabolism. Organisms possess a variety of cellular functions to suppress spontaneous mutagenesis, and the specificity and effectiveness of each function strongly affect the pattern of spontaneous mutations. Base substitutions and single-base frameshifts, two major classes of spontaneous mutations, occur non-randomly throughout the genome. Within target DNA sequences there are hotspots for particular types of spontaneous mutations; outside of the hotspots, spontaneous mutations occur more randomly and much less frequently. Hotspot mutations are attributable more to endogenous DNA lesions than to replication errors. Recently, a novel class of mutagenic pathway that depends on short inverted repeats was identified as another important source of hotspot mutagenesis.

Spontaneous hotspot mutations resistant to mismatch correction in Escherichia coli: transcription-dependent mutagenesis involving template-switching mechanisms

The generation and stabilization of spontaneous mutations are affected by many factors, including the accuracy of DNA replication, the generation of spontaneous DNA lesions, and the capacity of mutation-avoidance systems. However, little is known about the causes of spontaneous mutations in cells with fully active mutation-avoidance systems. Using the rpsL forward mutation assay, we previously found that the directionality of replication fork movement significantly affects spontaneous mutagenesis in Escherichia coli. In particular, sequence substitutions and a hotspot type of single-base frameshift, both of which are caused by quasipalindrome-directed mutagenesis, appeared to depend on the directionality of the replication fork. These mutations are also resistant to post-replicative mismatch correction. Here, we show that the level of transcription of the rpsL gene strongly affects spontaneous mutagenesis at two mutational hotspot sites in the target sequence, one for a T-->G base substitution and the other for a+1 single-base frameshift. Mutation frequencies at the hotspot sites were below a detectable level when the transcription of the target sequence was tightly suppressed, but were dramatically increased when the target sequence was highly transcribed. Both of the hotspot mutations were also dependent on the directionality of the replication fork and were caused by quasipalindrome-directed mutagenesis. The frequencies of the hotspot mutations were unchanged in a mismatch-repair deficient strain, indicating that the hotspot mutations are resistant to the mismatch correction. Based on these findings, we propose a novel mutagenic process for these hotspot mutations that depends on transcription and involves template-switching mechanisms induced by spontaneous DNA lesions.

Using base-specific Salmonella tester strains to characterize the types of mutation induced by benzidine and benzidine congeners after reductive metabolism

Although benzidine (Bz), 4-aminobiphenyl (ABP), 3,3'-dichlorobenzidine HCl (DCBz), 3,3'-dimethylbenzidine (DMBz), 3,3'-dimethoxybenzidine (DMOBz) and the benzidine congener-based dye trypan blue (TB) produce primarily frameshift mutations in Salmonella typhimurium, the base-substitution strain TA100 also responds to these compounds when S9 is present. Performing DNA sequence analysis, other investigators have shown that ABP induces frameshift, base-pair and complex mutations. Also, it was found that an uninduced hamster liver S9 preparation with glucose-6-phosphate dehydrogenase, FMN, NADH and four times glucose 6-phosphate gave a stronger mutagenic response than the conventional plate incorporation with rat S9 activation mixture for all the compounds tested. Using the base-specific tester strains of S. typhimurium (TA7001-TA7006) with the above reductive metabolic activation system, we surveyed these compounds for the ability to produce specific base-pair substitutions after reductive metabolism. Bz was weakly mutagenic in TA7005 (0.04 revertants/microg). ABP was mutagenic in TA7002 (1.4 revertants/microg), TA7004 (0.6 revertants/microg), TA7005 (2.98 revertants/microg) and TA7006 (0.4 revertants/microg). DCBz was weakly mutagenic in TA7004 (0.01 revertants/microg). It was concluded that benzidine induced some CG->AT transversions in addition to frameshift mutations. ABP induced TA->AT, CG->AT, and CG->GC transversions as well as GC->AT transitions. DCBz induced only GC->AT transitions. Because DMBz, DMOBz and TB were not mutagenic in this base-substitution mutagen detection system, their mutagenic activity was attributed strictly to frameshift mechanisms.

DNA polymerase zeta introduces multiple mutations when bypassing spontaneous DNA damage in Saccharomyces cerevisiae

Spontaneous DNA damage can be dealt with by multiple repair/bypass pathways that have overlapping specificities. We have used a frameshift reversion assay to examine spontaneous mutations that accumulate in yeast strains defective for the high-fidelity nucleotide excision repair or recombination pathways. In contrast to the simple frameshift mutations that occur in wild-type strains, the reversion events in mutant strains are often complex in nature, with the selected frameshift mutation being accompanied by one or more base substitutions. Genetic analyses demonstrate that the complex events are dependent on the Pol zeta translesion polymerase, thus implicating the DNA damage bypass activity of low-fidelity translesion polymerases in hypermutation phenomena.

The Escherichia coli lacZ reversion mutagenicity assay

The Escherichia coli lacZ reversion assay, based on the set of episomal lacZ alleles engineered by Miller et al., provides an attractive system for studies of mutagenesis and mutational specificity. Each strain in the lacZ set reverts by a specific base substitution or frameshift event. Revertants are selected by growth on lactose minimal medium. In this review, I describe the development of the assay and its subsequent modifications and improvements. Examples of its application are presented and detailed protocols for the implementation of the assay are given.

Mutation spectra in Salmonella of analogues of MX: implications of chemical structure for mutational mechanisms

We determined the mutation spectra in Salmonella of four chlorinated butenoic acid analogues (BA-1 through BA-4) of the drinking water mutagen 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX) and compared the results with those generated previously by us for MX and a related compound, MCF. We then considered relationships between the properties of mutagenic potency and mutational specificity for these six chlorinated butenoic acid analogues. In TA98, the three most potent mutagens, BA-3, BA-4, MX, and the organic extract, all induced large percentages of complex frameshifts (33-67%), which distinguish these agents from any other class of compound studied previously. In TA100, which has only GC sites for mutation recovery, >71% of the mutations induced by all of the agents were GC-->TA transversions. The availability of both GC and TA sites for mutation in TA104 resulted in greater distinctions in mutational specificity than in TA100. MX targeted GC sites almost exclusively (98%); the structurally similar BA-4 and BA-2 produced mutations at similar frequencies at both GC and AT sites; and the structurally similar BA-3 and BA-1 induced most mutations at AT sites (69%). Thus, large variations in structural properties influencing relative mutagenic potency appeared to be distinct from the more localized similar structural features influencing mutagenic specificity in TA104. Among a set of physicochemical properties examined for the six butenoic acids, a significant correlation was found between pK(a) and mutagenic potency in TA100, even when the unionized fraction of the activity dose was considered. In addition, a correlation in CLOGP for BA-1 to BA-4 suggested a role for bioavailability in determining mutagenic potency. These results illustrate the potential value of structural analyses for exploring the relationship between chemical structure and mutational mechanisms. To our knowledge, this is the first study in which such analyses have been applied to structural analogues for which both mutagenic potency and mutation spectra date were available.

Influence of DNA repair on mutation spectra in Salmonella

This paper reviews the influence of DNA repair on spontaneous and mutagen-induced mutation spectra at the base-substitution (hisG46) and -1 frameshift (hisD3052) alleles present in strains of the Salmonella (Ames) mutagenicity assay. At the frameshift allele (mostly a CGCGCGCG target), DeltauvrB influences the frequency of spontaneous hotspot mutations (-CG), duplications, and deletions, and it also shifts the sites of deletions and duplications. Cells with pKM101+DeltauvrB spontaneously produce complex frameshifts (frameshifts with an adjacent base substitution). The spontaneous frequency of 1-base insertions or concerted (templated) mutations is unaffected by DNA repair, and neither mutation is inducible by mutagens. Glu-P-1, 1-nitropyrene (1NP), and 2-acetylaminofluorene (2AAF) induce only hotspot mutations and are unaffected by pKM101, whereas benzo(a)pyrene and 4-aminobiphenyl induce only hotspot in pKM101(-), and hotspot plus complex in pKM101(+). At the base-substitution allele (mostly a CC/GG target), the DeltauvrB allele increases spontaneous transitions in the absence of pKM101 and increases transversions in its presence. The frequency of suppressor mutations is decreased 4x by DeltauvrB, but increased 7. 5x by pKM101. Both repair factors cause a shift in the proportion of mutations to the second position of the CC/GG target. With UV light and gamma-rays, the DeltauvrB allele increases the proportion of transitions relative to transversions. pKM101 is required for mutagenesis by Glu-P-1 and 4-AB, and the types and positions of the substitutions are not altered by the addition of the DeltauvrB allele. Changes in DNA repair appear to cause more changes in spontaneous than in mutagen-induced mutation spectra at both alleles. There is a high correlation (r(2)=0.8) between a mutagen's ability to induce complex frameshifts and its relative base-substitution/frameshift mutagenic potency. A mutagen induces the same primary class of base substitution in TA100 (DeltauvrB, pKM101) as it does in Escherichia coli, mammalian cells, or rodents as well as in the p53 gene of human tumors associated with exposure to that mutagen. Thus, a mutagen induces the same primary class of base substitution in most organisms, reflecting the conserved nature of DNA replication and repair processes.

Comparison of SYBR Green I nucleic acid gel stain mutagenicity and ethidium bromide mutagenicity in the Salmonella/mammalian microsome reverse mutation assay (Ames test)

SYBR Green I nucleic acid gel stain is an unsymmetrical cyanine dye developed for sensitive detection of nucleic acids in electrophoretic gels. Its mechanism of nucleic acid binding is not known, whereas the most commonly used nucleic acid gel stain, ethidium bromide, is a well-characterized intercalator. We compared the mutagenicity of SYBR Green I stain with that of ethidium bromide in Salmonella/mammalian microsome reverse mutation assays (Ames tests). As expected [J. McCann, E. Choi, E. Yamasaki, B.N. Ames, Proc. Natl. Acad. Sci. USA, 72 (1975) 5135-5139], ethidium bromide showed high revertant frequencies in several frameshift indicator strains (averaging 68-fold higher than vehicle controls in TA98, 80-fold higher in TA1538, 15-fold higher in TA1537, and 4.4-fold higher in TA97a), only in the presence of rat liver extracts (S9). Small increases in revertant frequencies were observed for ethidium bromide in the base-substitution indicator strain TA102 both in the presence and absence of S9 (averaging 2.0- and 1.8-fold higher than vehicle controls, respectively) and in base-substitution indicator strain TA100 in the presence of S9 (averaging 1.6-fold higher than vehicle controls). A small mutagenic effect was detected for SYBR Green I stain in frameshift indicator strain TA98 (averaging 2. 2-fold higher than vehicle controls) only in the absence of S9 and in base-substitution indicator strain TA102, both in the presence and absence of S9 (averaging 2.2- and 2.7-fold higher than vehicle controls, respectively). Thus, SYBR Green I stain is a weak mutagen and appears to be much less mutagenic than ethidium bromide. These results suggest that SYBR Green I stain may not intercalate, and if it does, that its presence does not give rise to point mutations at a high frequency.

Mutation spectrum in Salmonella induced by environmental tobacco smoke

Environmental tobacco smoke (ETS) is a major source of indoor air pollution. Extractable-respirable particulate (ERP) from the ETS-contaminated indoor air (ERP-ETS) was collected from six passenger train cars and one control room. The mutagenicity of ERP-ETS was tested in the Ames/Salmonella test in the presence of male rat liver microsomal fraction S9. The mutation spectrum of ERP-ETS was determined by colony probe hybridization and polymerase chain reaction/DNA sequence analysis in approximately 2,370 His+ revertants. The results indicate that the majority of ERP-ETS-induced mutations were a two-base deletion of GC or CG within the hotspot sequence of CGCGCGCG at the frameshift hisD3052 allele in strain TA98. The ERP-ETS from the control room induced approximately 94.3% such deletions, while the ERP-ETS collected from the passenger cars induced approximately 89.6% such deletions. The ERP-ETS either from the control room or from the passenger cars induced approximately 74% C/G --> A/T transversions, and approximately 23% C/G --> T/A transitions within the primary target CCC at the hisG46 allele in strain TA100.

Spectra of spontaneous frameshift mutations at the hisD3052 allele of Salmonella typhimurium in four DNA repair backgrounds

To characterize the hisD3052 -1 frameshift allele of Salmonella typhimurium, we analyzed approximately 6000 spontaneous revertants (rev) for a 2-base deletion hotspot within the sequence (CG)4, and we sequenced approximately 500 nonhotspot rev. The reversion target is a minimum of 76 bases (nucleotides 843-918) that code for amino acids within a nonconserved region of the histidinol dehydrogenase protein. Only 0.4-3.9% were true rev. Of the following classes, 182 unique second-site mutations were identified: hotspot, complex frameshifts requiring DeltauvrB + pKM101 (TA98-specific) or not (concerted), 1-base insertions, duplications, and nonhotspot deletions. The percentages of hotspot mutations were 13.8% in TA1978 (wild type), 24.5% in UTH8413 (pKM101), 31.6% in TA1538 (DeltauvrB), and 41.0% in TA98 (DeltauvrB, pKM101). The DeltauvrB allele decreased by three times the mutant frequency (MF, rev/10(8) survivors) of duplications and increased by about two times the MF of deletions. Separately, the DeltauvrB allele or pKM101 plasmid increased by two to three times the MF of hotspot mutations; combined, they increased this MF by five times. The percentage of 1-base insertions was not influenced by either DeltauvrB or pKM101. Hotspot deletions and TA98-specific complex frameshifts are inducible by some mutagens; concerted complex frameshifts and 1-base insertions are not; and there is little evidence for mutagen-induced duplications and nonhotspot deletions. Except for the base substitutions in TA98-specific complex frameshifts, all spontaneous mutations of the hisD3052 allele are likely templated. The mechanisms may involve (1) the potential of direct and inverted repeats to undergo slippage and misalignment and to form quasi-palindromes and (2) the interaction of these sequences with DNA replication and repair proteins.

Spectrum of spontaneous and 2,4,6-trinitrotoluene (TNT)-induced mutations in Salmonella typhimurium strains with different nitroreductase and O-acetyltransferase activities

Spontaneous and 2,4,6-trinitrotoluene (TNT)-induced mutation spectra were determined at the hisD3052 allele of Salmonella typhimurium strains TA98, YG1021 (nitroreductase-overproducing) and YG1024 (O-acetyltransferase-overproducing). In TA98, 55% (11/20) of the spontaneous reversions and 95% (19/20) of reversions in TNT-treated plates were deletions of two bases at the same site (-2 hotspot deletions), whereas the respective figures were 65% (13/20) and 80% (16/20) in YG1021, and 75% (15/20) and 95% (19/20) in YG1024. Other mutations observed in the TNT treatment were complex frameshifts consisting of either a -2 hotspot deletion and a base substitution, or a +1 addition and base substitution at the stop codon. In addition, different kinds of deletions were recovered in the spontaneous spectra. The elevated enzymatic activities of strains, YG1021 and YG1024, resulting in enhanced mutagenicity of TNT, did not seem to have an effect on the spectrum of TNT-induced mutations. However, the YG strains, which also have a higher spontaneous revertant yield than the parental strain TA98, seemed to differ from TA98 in their spontaneous spectra. The increase consisted of revertants containing the -2 hotspot deletion, possibly indicating elevated activation of exogenous or endogenous premutagens by the higher enzyme activities of the YG strains.

Urinary promutagens of smokers: comparison of concentration methods and relation to cigarette consumption

Different extraction techniques can be used to concentrate the promutagens of cigarette smokers' urine before evaluation of their mutagenic potency by Ames test. In this study, three solid adsorbents, C18, XAD2 and CN were compared for their ability to concentrate the promutagens of smokers' urine prior to acetone elution. C18 extracts were observed to have a higher promutagenicity than XAD2 and CN extracts. The mutagenicity of smokers' urine depended on the smoking habits, and a strong correlation was observed between urinary promutagenicity, daily cigarette consumption, and the tobacco type (black or blond). Smokers of black tobacco had a higher urinary genotoxicity than smokers of blond tobacco, after taking into account the level of tobacco consumption. Urinary promutagenicity did not appear to depend on the tar level of cigarettes.

Mutation spectra of chemical fractions of a complex mixture: role of nitroarenes in the mutagenic specificity of municipal waste incinerator emissions

Using an ion-exchange procedure coupled to a microsuspension Salmonella assay, we fractionated the dichloromethane-extractable particulate organics emitted by a municipal waste incinerator. Most (80-95%) of the mutagenic activity resided in the neutral/base fraction; however, the polar neutral fraction accounted for 12% of the direct-acting mutagenic activity. The mutagenic potencies of the whole extract and the various fractions were 4-15 times greater in the absence than in the presence of S9. Results with strains deficient in classical nitroreductase (TA98NR) and transacetylase (TA98/1,8-DNP6) indicated that a majority of the direct-acting mutagenicity was due to nitroarenes. This was confirmed by bioassay-directed subfractionation of the neutral/base faction by a cyanopropyl/HPLC method. The mutations in -3,000 revertants (approximately 400 each induced in TA98 by the whole extract, the neutral/base and polar neutral fractions from the ion-exchange column and 3 of the neural/base subfractions from the HPLC column; along with 200 revertants each induced by the model nitroarene 1-nitropyrene (1NP) in strains TA98, TA1538 and TA100) were analyzed by probe hybridization and PCR/DNA sequence analysis. The results indicated that nitroarenes such as 1NP that eluted in the neutral/base fraction accounted for at least 50% of the direct-acting mutagenicity and induced only a hotspot 2-base deletion in the sequence (CG)4 in TA98. In contrast, most of the complex frameshifts (a frameshift with a flanking base substitution) induced by the whole extract were induced by nitroarenes other than 1NP that were activated by transacetylation and that eluted in the polar neutral fraction. This study (1) identifies nitroarenes as an important contributor to the mutagenic activity of the emissions from municipal waste incinerators; (2) confirms our previous conclusion that the mutation spectrum of a complex mixture reflects the dominance of particular classes of chemical mutagens within the mixture; and (3) demonstrates the possibility of isolating certain chemical fractions of a complex mixture that induce certain classes of mutations produced by the whole, unfractionated mixture.

Analysis of the ciprofloxacin-induced mutations in Salmonella typhimurium

The mutagenic events induced by ciprofloxacin, a potent antimicrobial agent, have been characterized. For this, a battery of His mutants of Salmonella typhimurium (hisG428, his G46, His C9070, and his G1775 targets) that detects the six possible transitions and transversions [Levin and Ames (1986): Environ Mutagen 8:9-28] and two additional His strains (hisC3076 and his D3052 targets) carrying frameshift mutations have been used. Our results indicate that GC-TA transversions are the major base-pair substitution induced by ciprofloxacin and that GC-At transitions are also produced, but to a lesser degree. However, we cannot discard the fact that At-Ta transversions are also induced. In addition, the data indicate that the mutational specificity of ciprofloxacin depends on the location of the target. Intragenic base-pair substitutions are the most frequent mutations at the hisG428 target when it is on the chromosome, whereas 3 or 6 base-pair deletions are the major mutagenic events when this target is on the plasmid pAQ1. We have shown that ciprofloxacin also induces deletions/insertions at the hisC3076 and hisD3052 frameshift targets. Therefore, this inhibitor of DNA gyrase promotes a wide pattern of mutations including different kinds of base-pair substitutions, 3 or 6 base-pair deletions, and insertions/deletions resulting in frameshifts. All of these mutagenic events require the MucAb proteins involved in the error-prone repair, with the exception of base-pair insertions/deletions at the hisD3052 target, which are independent of the presence of plasmid pKM101.

Examination of the additivity assumption using the spiral and standard Salmonella assays to evaluate binary combinations of mutagens

Binary combinations of pure chemicals and complex mixtures were evaluated for their ability to produce additive mutagenicity responses in the spiral and standard Salmonella mutagenicity assays. Single chemicals were selected that were representative of the primary chemical class responsible for much of the mutagenic activity of each complex mixture. The following agents were evaluated in the absence of S9: 1-nitropyrene, diesel exhaust extract, and the chlorinated drinking water mutagen 3-chloro-4-dichloromethyl-5-hydroxy-2-[5H]-furanone (MX). In the presence of S9, the following agents were evaluated: 4-aminobiphenyl, benzo[a]pyrene, and an organic extract from the particulate emissions resulting from the combustion of polyethylene in a rotary kiln incinerator. Binary combinations of the agents within each S9 group were tested. The results were analyzed for additivity by determining whether the difference between the expected response of the binary mixture was significantly different from the observed response. In general, the combinations of mutagens produced additive responses at low doses in both assays. However, at high doses, the results generally departed from additivity, especially for combinations of indirect-acting mutagens. A requirement for exogenous metabolic activation imposes conditions, such as different S9 optima for each mutagen, that complicate the application of the additivity assumption to binary combinations of indirect-acting mutagens. Although the two bioassays generally gave similar results for each binary combination of mutagens, the spiral assay permitted a gradient of mutagen and/or S9 concentrations to be evaluated, and it allowed the mutagens to be evaluated in the absence of solvents, eliminating any potential solvent-mutagen interactions. These features of the spiral assay may be advantageous when studying chemical interactions.

Mutation spectra in Salmonella of sunlight, white fluorescent light, and light from tanning salon beds: induction of tandem mutations and role of DNA repair

We evaluated the mutagenicity of sunlight (SUN), uncovered coolwhite fluorescent light (FLR), and light from a tanning salon bed (TAN) at the base-substitution allele hisG46 of Salmonella in four DNA repair backgrounds (wild type, uvrB, pKM101, and uvrB + pKM101). Approximately 80% of the radiation emitted by TAN was within the ultraviolet (UV) range, whereas only approximately 10% of the SUN and approximately 1% of the FLR radiation was UV. TAN emitted similar amounts of UVA and UVB, whereas SUN emitted 50-60x and FLR emitted 5-10x more UVA relative to UVB. Based on total dose (UV + visible), the mutagenic potency ranking was TAN > FLR > SUN. Using colony probe hybridization and PCR/DNA sequence analysis, approximately 3000 revertants were analyzed to determine the mutational specificity of the three light sources. The mutation spectra and those induced by 254-nm UV had common features. The uvrB mutation enhanced the mutagenicity of the environmental UV sources more (20-216x) than did the pKM101 plasmid (approximately 20x) relative to wild type DNA repair. All light sources induced equal proportions of transitions and transversions in excision repair-proficient strains, but they induced more transitions relative to transversions in uvrB-containing strains. The majority of the mutations were G.C-->A.T transitions that were induced equally frequently at the first or second position of the CCC codon of the hisG46 allele in all strains except TA1535 (uvrB), where SUN and FLR induced transitions preferentially at the first position, and TAN induced them preferentially at the second position. Identified or presumptive multiple mutations, which constituted the only mutational class enhanced by all three light sources in the presence of uvrB and pKM101 either alone or together, accounted for 3-5% of the induced mutations in the plasmid-containing strains, and their increases (38-82-fold) in TA100 (uvrB, pKM101) were the highest of any mutational class. Of the TAN-induced multiple mutations, 83% (19/23) were CC-->TT tandem transitions. These results show that exposures to the nonsolar environmental UV sources FLR and TAN produce mutations similar to those produced by SUN, a known carcinogen.

Mutagenicity and mutation spectra of 2-acetylaminofluorene at frameshift and base-substitution alleles in four DNA repair backgrounds of Salmonella

We used colony probe hybridization procedures to determine the mutations in approximately 600 revertants of the -1 frameshift allele hisD3052 and approximately 200 revertants of the base-substitution allele hisG46 of Salmonella typhimurium induced by 2-acetylaminofluorene (2-AAF) in the presence of Aroclor-induced rat liver S9. 2-AAF was primarily a frameshift mutagen, exhibiting 5 times more frameshift than base-substitution activity. The only frameshift mutation 2-AAF induced at the hisD3052 allele was a hotspot (-2) deletion within the sequence CGCGCGCG. The addition of the pKM101 plasmid had a small effect on the mutagenic potency of 2-AAF at this allele in a uvr+ background and no effect on the mutation spectra in either a uvr+ or uvr- background. The small amount of base-substitution activity exhibited by 2-AAF at the hisG46 allele required the presence of both the pKM101 plasmid and the uvrB mutation. The base substitutions were G.C-->T.A transversions (86%) and G.C-->A.T transitions (14%), and 85% of the substitutions were at the second position of the CCC target of the hisG46 allele; the remainder were at the first position. We propose that the hotspot frameshift may be initiated by N-acetyl-2-aminofluorene adducts located at the C(8) position of any of the guanines except the first one in the CGCGCGCG hotspot sequence. The mutation might then result from correct incorporation of cytosine opposite the adducted guanine, followed by a 2-base slippage according to our recently proposed correct-incorporation/slippage model. The hotspot mutation may also result from a 2-AAF-induced B- to Z-DNA transition at the repeating GpC site as well as by the action of enzymes involved in DNA metabolism, such as DNA resolvases or topoisomerases, on DNA structures that have been distorted by 2-AAF adducts. The small amount of 2-AAF-induced base-substitution activity may be due to mispairing of adenine opposite the minor aminofluorene adduct at the C(8) position of guanine.

Increased frequency of mutations at A:T base pairs in the bone marrow of B6C3F1 lacI transgenic mice exposed to 1,3-butadiene

We have examined the spectra of mutations in a collection of 74 lacI mutants isolated from the bone marrow of B6C3F1 lacI transgenic mice exposed to 1,250 ppm 1,3-butadiene (BD). Of the 49 independent mutations analyzed in the present study, 30 of 49 (61%) were point mutations at G:C base pairs, and 10 of 49 (20%) were point mutations at A:T base pairs. The remaining mutations consisted of small deletions and insertions and a single tandem change. An analysis of variance (ANOVA) on the frequency of specific mutations observed in each animal in this mutagenicity experiment [present study; also Sisk SC et al. (1994): Carcinogenesis 15:471-477] indicated that the frequency of point mutations at A:T base pairs is significantly greater (P < 0.05) in BD-exposed mice than in the air controls. In addition, there was a decrease (P < 0.05; Fisher's exact test) in the frequency of G:C-->A:T transitions at 5'-CpG-3' sites in BD-exposed mice (27%) relative to air controls (51%). These data indicate that subchronic exposures to BD induces an increased frequency of in vivo mutation at A:T base pairs in the bone marrow of B6C3F1 lacI transgenic mice.

Mutation spectra in salmonella of chlorinated, chloraminated, or ozonated drinking water extracts: comparison to MX

Drinking water samples were prepared in a pilot-scale treatment plant by chlorination (Cl2), chloramination (NH2Cl), ozonation (O3), or O3 followed by Cl2 or NH2Cl; and the nonvolatile acidic organics of the raw and treated waters were extracted by XAD/ethyl acetate and evaluated for mutagenicity in Salmonella (-S9). The extracts were 2-8 times more mutagenic in TA100 than in TA98, and the mutagenic potencies of the water extracts ranked similarly in both strains: Cl2 > O3 + Cl2 > NH2Cl > O3 + NH2Cl > O3 > raw. 3-Chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX), which was estimated to account for approximately 20% of the mutagenic activity of the extracts, was shown to be the most potent compound tested thus far in a prophage-induction assay in Escherichia coli and a forward-mutation assay in Salmonella TM677. The mutations in approximately 2,000 revertants of TA98 and TA100 induced by MX and the water extracts were analyzed by colony probe hybridization and polymerase chain reaction/DNA sequence analysis. The water extracts and MX produced similar mutation spectra, which consisted in TA100 of predominantly of GC-->TA transversions in the second position of the CCC (or GGG) target of the hisG46 allele. This spectrum resembles that produced by large aromatic compounds and is distinct from that produced by alkylating agents and the semivolatile drinking water mutagen dichloroacetic acid. In TA98, MX and those water extracts resulting from the introduction of the chlorine atom produced 50-70% hotspot 2-base deletions and 30-50% complex frameshifts (frameshifts with an adjacent base substitution--mostly GC-->TA transversions as found in TA100). No other compound or mixture is known to induce such high frequencies of complex frameshifts. These results suggest that MX and "MX-like" compounds (possibly halogenated aromatics, such as halogenated polycyclic aromatic hydrocarbons) account for much of the mutagenic activity and specificity of the nonvolatile organics in drinking water and that these halogenated organics are especially capable of promoting misincorporation by the DNA replication complex. This study provides further evidence that the mutation spectrum of a complex mixture reflects the dominance of one or a few classes of chemical mutagens within the mixture.

Mutational spectrum of revertants in the hisD3052 allele of Salmonella typhimurium induced by hydrogen peroxide-activated benzidine

Benzidine is mutagenic in a modified Ames (Salmonella typhimurium) assay, which uses hydrogen peroxide-dependent peroxidative activation. The mutational specificity of benzidine was investigated in tester strain TA98, which reverts by frameshifts of the hisD3052 allele. The most frequently observed mutation is a deletion of two bases from a (CG)4 run. This deletion was elevated in frequency among benzidine-induced revertants, relative to spontaneous revertants. Many other mutations were also observed, including additions, deletions, and complex events. Only small frameshifts were observed among the benzidine-induced revertants, whereas some larger deletions were observed among the spontaneous revertants.

Mutation spectra in Salmonella of complex mixtures: comparison of urban air to benzo[a]pyrene

We used an ion-exchange procedure coupled to the Salmonella assay to fractionate the dichloromethane-extractable particulate organics from an urban air sample collected in Boise, Idaho. A resulting base/neutral fraction contained 81% of the mutagenic activity but only 36% of the mass of the unfractionated sample. Chemical analysis showed that polycyclic aromatic hydrocarbons (PAHs) accounted for much of the mutagenic activity of the air sample. Colony probe hybridization, PCR, and DNA sequence analysis were then used to determine the mutations induced by the complex mixtures and a model PAH, benzo[a]pyrene (BAP) in approximately 900 revertants of the frameshift hisD3052 allele and approximately 400 revertants of the base-substitution hisG46 allele. The majority (93-94%) of the mutations induced at the frameshift allele in strain TA98 by the whole or base/neutral fraction of the urban air sample was a hotspot 2-base deletion of a CG or GC within the sequence CGCGCGCG. The remaining mutations were complex frameshifts that consisted of -2 or +1 frameshifts associated with a flanking base substitution. BAP induced a somewhat similar pattern of mutations, with 70% being the hotspot mutation, 23% being complex frameshifts, and the remaining being deletions. The inferred base-substitution specificity associated with the complex frameshifts at the hisD3052 allele (primarily G.C-->T.A transversions) was consistent with the observation that this same transversion was the primary mutation induced by the whole urban air sample and BAP at the base-substitution allele in strain TA100. At the frameshift allele, adducts that promote correct incorporation/slippage could account for hotspot mutations, whereas those that promote misincorporation/slippage could account for complex frameshifts. At the base-substitution allele, a mixture of adducts or of adducts with multiple conformations could account for the observed proportion of transitions and transversions. Combined with the bioassay-directed chemical analysis, these results from the first mutation spectra of a complex mixture suggest that such spectra reflect the dominance of particular classes of chemical mutagens within the mixture.

Mutation spectra of Glu-P-1 in Salmonella: induction of hotspot frameshifts and site-specific base substitutions

We used colony probe hybridization and PCR/DNA sequence analysis to determine the mutations in approximately 1,640 revertants of the -1 frameshift allele hisD3052 and approximately 260 revertants of the base substitution allele hisG46 of Salmonella typhimurium induced by the heterocyclic amine cooked food mutagen 2-amino-6-methyldipyrido[1,2-a:3',2'-d]imidazole (Glu-P-1). All of the mutations were at sites containing guanine, which is the base at which Glu-P-1 forms DNA adducts. A hotspot mutation involving the deletion of a CG or GC within the sequence CGCGCGCG accounted for 100% of the Glu-P-1-induced mutations at the frameshift allele in strains TA1978 (uvr+) and TA1538 (delta uvrB) and 99% in TA98 (delta uvrB, pKM101). To explain the induction of these hotspot mutations by Glu-P-1, we describe here a more detailed version of our recently proposed correct incorporation/slippage model [Genetics:136:731, 1994]. We propose that after cytosine is incorporated correctly opposite a Glu-P-1-adducted guanine, various slipped intermediates may form (a total of 18), depending on which guanine is adducted and whether it remains within the helix or becomes extrahelical. This variety of mutational pathways may account for the high mutability of the hotspot sequence by Glu-P-1. Although the pKM101 plasmid does not influence the mutagenic potency or mutational spectrum of Glu-P-1 at the frameshift allele, it is required by Glu-P-1 to revert the base substitution allele, where Glu-P-1 induces G-C --> T-A transversions (75%) and G-C --> tA-T transitions (25%) exclusively at a single site (the second position of the CCC codon of the hisG46 allele). The limited (20-30 times less) base substitution mutagenic potency of Glu-P-1 relative to its frameshift mutagenic potency as well as the extreme site specificity exhibited by Glu-P-1 for base substitutions may have bearing on the lack of base substitutions identified in ras genes in Glu-P-1-induced rat colon tumors.

QSAR models for both mutagenic potency and activity: application to nitroarenes and aromatic amines

We studied the molecular determinants that discriminate between mutagenic and inactive compounds for: a) aromatic and heteroaromatic amines; b) nitroarenes. Mutagenic activity (data from literature) had been previously assessed in Salmonella typhimurium and Escherichia coli (SOS repair). The Quantitative Structure-Activity Relationships (QSAR) found were compared with those obtained in the laboratory of Professor C. Hansch for the mutagenic potency of the same compounds. It appears that there is a dramatic difference between the QSARs for potency, and those for yes/no activity: hydrophobicity played a major role in determining the potency of the active compounds, whereas mainly electronic factors differentiated the actives from the inactives. The electronic factors were those expected on the basis of the hypothesized metabolic pathways of the chemicals. Our interpretation is that the electronic factors (together with size/shape, possibly) determine the minimum requirement for the chemicals to be metabolized, whereas the hydrophobicity determines the extent of activity of chemicals that can be metabolized (actives). Moreover, the different QSARs found for the Salmonella strains TA98 and TA100 were discussed in the light of recent progress in the understanding of the molecular mechanisms of mutagenicity in these organisms. It is concluded that the nonlinear relationship observed for these chemicals between the two types of QSAR should be taken into account both when planning QSAR studies, and when using mutagenicity data for risk assessment.