DNA polymerases II and V mediate respectively mutagenic (-2 frameshift) and error-free bypass of a single N-2-acetylaminofluorene adduct

The NarI sequence represents a strong mutation hot spot for -2 frameshift mutations induced by N-2-acetylaminofluorene (AAF), a strong chemical carcinogen. Only when bound to the third (underlined) guanine (5'-GGCGCC-->GGCC) can AAF trigger frameshift mutations, suggesting the involvement of a slipped replication intermediate with a two-nucleotide bulge. While base substitutions induced by UV light or abasic sites require DNA polymerase V (Pol V; umuDC), the AAF-induced -2 frameshift pathway requires DNA polymerase II, the polB gene product. Interestingly, error-free bypass of the G-AAF adduct requires Pol V. The genes encoding both Pol II and Pol V are induced by the SOS regulon, a co-ordinated cellular response to environmental stress. A given lesion, G-AAF, can thus be bypassed by two SOS-controlled DNA polymerases (II and V), generating mutagenic (-2 frameshifts) and error-free replication products respectively. Therefore both Pol II and Pol V can compete for the blocked replication intermediate in the vicinity of the lesion and engage in replication by transiently replacing the replicative DNA Pol III. Our data suggest that, in order to cope with the large diversity of existing DNA lesions, cells use a single or a combination of translesional DNA polymerases to achieve translesion synthesis.

Sequence-dependent modulation of frameshift mutagenesis at NarI-derived mutation hot spots

The NarI sequence is known to be the strongest mutation hot spot for induced frameshift mutagenesis. Indeed, a single N-2-acetylaminofluorene (AAF) adduct induces -2 frameshift mutations (5'-GGCGAAFCC--> 5'-GGCC) more than 10(7)-fold over background mutagenesis in Escherichia coli. The mechanism of induction of the frameshift mutation involves a two nucleotide primer-template misalignment event during replication of the adduct-containing sequence. The slipped mutagenic intermediate (SMI) that is thus formed is strongly stabilised by the AAF residue. In order to understand the origin of the extreme susceptibility of this sequence to frameshift mutagenesis, we analysed AAF-induced mutagenesis at sequences 5'-NaGCGAAFCNb-3' containing the core dinucleotide GCGC repeat present in the NarI sequence flanked by variable nucleotides Na and Nb. The nature of nucleotide Nb was found to strongly modulate the frequency of induced -2 frameshift mutagenesis (up to 30 to 50-fold), while little if any effect could be attributed to nucleotide Na. The induction of -2 frameshifts, regardless of nucleotides Na and Nb, was found to be SOS-inducible but umuDC-independent as previously found for the authentic NarI sequence. The NarI sequence (GGCGCC) and sequence TGCGCA (Na=T, Nb=A) were found to be equally "hot" for -2 frameshift mutation induction compared to the sequence AGCGCT where induced mutagenesis was 30 to 50-fold lower.The analysis of replication events using constructions containing a strand marker across from the adduct site allowed us to demonstrate that the large difference in -2 frameshift mutagenesis is due to an intrinsic difference in the propensity of these sequences to slip during replication. How the nature of the nucleotide flanking the adduct on its 3'-side (Nb) differentially stabilises the SMI will be discussed in the light of recent structural data and theoretical models.

Cellular strategies for accommodating replication-hindering adducts in DNA: control by the SOS response in Escherichia coli

The replication of double-stranded plasmids containing a single adduct was analyzed in vivo by means of a sequence heterology that marks the two DNA strands. The single adduct was located within the sequence heterology, making it possible to distinguish trans-lesion synthesis (TLS) events from damage avoidance events in which replication did not proceed through the lesion. When the SOS system of the host bacteria is not induced, the C8-guanine adduct formed by the carcinogen N-2-acetylaminofluorene (AAF) yields less than 1% of TLS events, showing that replication does not readily proceed through the lesion. In contrast, the deacetylated adduct N-(deoxyguanosin-8-yl)-2-aminofluorene yields approximately 70% of TLS events under both SOS-induced and uninduced conditions. These results for TLS in vivo are in good agreement with the observation that AAF blocks DNA replication in vitro, whereas aminofluorene does so only weakly. Induction of the SOS response causes an increase in TLS events through the AAF adduct (approximately 13%). The increase in TLS is accompanied by a proportional increase in the frequency of AAF-induced frameshift mutations. However, the polymerase frameshift error rate per TLS event was essentially constant throughout the SOS response. In an SOS-induced delta umuD/C strain, both US events and mutagenesis are totally abolished even though there is no decrease in plasmid survival. Error-free replication evidently proceeds efficiently by means of the damage avoidance pathway. We conclude that SOS mutagenesis results from increased TLS rather than from an increased frameshift error rate of the polymerase.

Sequence determinants for -2 frameshift mutagenesis at NarI-derived hot spots

The recognition sequence of the NarI restriction enzyme is known to be a strong hot spot for -2 frameshift mutations (G1G2CG3CC-->GGCC) induced by the chemical carcinogen N-2-acetylaminofluorene (AAF). In an attempt to define a "consensus sequence" for this mutation hot spot, we have investigated the role of the bases flanking the central dinucleotide GpC repeat in the NarI sequence (NaGCGCNb) on the mutation frequency induced by the carcinogen. Construction and random modification with AAF of the 16 plasmids resulting from the replacement of Na and Nb by A,T,G and C, respectively, have been undertaken. All 16 sequences tested are found to be -2 frameshift mutation hot spots. Indeed, a level of modification of approximately five AAF adducts per plasmid molecule induces a mutation frequency ranging between 500 and 5000-fold above background. The mutations observed are mainly (90%) deletion of a dinucleotide CpG in the targeted sequence NaGCGCNb. Previous studies on NarI mutagenesis (G1G2CG3CC-->GGCC) have shown that only AAF adducts at G3 in the template for lagging strand synthesis induce -2 frameshift mutagenesis at a high level. When the mutation data obtained in this work are analyzed as originating essentially from adducts to guanines in this strand, we find that it is the nucleotide Nb located 3' to the central dinucleotide GpC repeat that strongly modulates the mutation frequency, while the nucleotide Na located on the 5' side has little effect. Our present model of frameshift mutagenesis at NarI sites involves a template-primer misalignment step with a two-nucleotide slipped mutagenic intermediate. In the context of this model, the modulation of mutagenesis by nucleotide Nb located two nucleotides 3' from the putative adduct site in the template strand can be explained in view of the fact that the replication complex encounters this nucleotide before it encounters the adduct.

Mutation spectra of the two guanine adducts of the carcinogen 4-nitroquinoline 1-oxide in Escherichia coli. Influence of neighbouring base sequence on mutagenesis

When the chemical carcinogen 4-nitroquinoline 1-oxide binds to DNA in vitro, two major adducts are formed, both at guanine residues, but at different positions, i.e. the C8 or the N2 position. Well-defined adducts (either C8 or N2 guanine adducts) can be formed in vitro by reacting DNA with 4-actoxyaminoquinoline 1-oxide (Ac-4HAQO) under different reaction conditions. Forward mutations induced by each of both main 4NQO adducts in the tetracycline resistance gene of pBR322 were determined. In total, 30 independent 4NQO-induced mutations were characterized, showing mainly base-pair substitution mutations and some frameshift mutations. We have observed that the 5' neighbouring base influences the specificity of dGuo-N2-AQO induced base-pair substitutions mutagenesis; a similar effect does not occur with dGuo-C8-AQO. This study reveals the importance of the N2 guanine adduct in the mutagenesis induced by 4NQO in vivo.

N-acetoxy-N-acetyl-2-aminofluorene-induced mutagenesis in the lacI gene of Escherichia coli

To study the mechanisms of mutagenesis by the carcinogen N-acetyl-2-aminofluorene (AAF), we determined by DNA sequencing the spectrum of mutations in the Escherichia coli lacI gene induced by the ultimate metabolite N-acetoxy-N-acetyl-2-aminofluorene, using an E. coli derivative with increased permeability to this compound. Several different classes of mutations were recovered, including base substitutions (11%), single-base frameshifts (11%), double-base frameshifts (22%), deletions (21%), duplications (2%) and 'spontaneous hot-spot' mutations [26%; the gain (19%) or loss (7%) of TGGC at the sequence TGGCTGGCTGGC]. Among the base substitutions, both transitions and transversions occurred. The single-base frameshifts were all the loss of a base. The double-base frameshifts represented the loss of a (GpC) or (ApC) dinucleotide from alternating (GpC)n or (ApC)n sequences. The deletion, duplication and hot-spot mutations showed relative G,C-richness at their endpoints, suggesting that AAF-induced lesions at or near the endpoints promoted their occurrence. Taken together, the data are consistent with several previous findings on AAF mutagenesis, extending in particular the importance of frameshift mutagenesis at alternating purine-pyrimidine sequences and establishing deletion and duplication mutations as an important consequence of treatment with this carcinogen.

Genetic control of AAF-induced mutagenesis at alternating GC sequences: an additional role for RecA

In a previous study, the forward mutation spectrum induced by the chemical carcinogen N-acetoxy-N-2-acetylaminofluorene was determined (Koffel-Schwartz et al. 1984). It was found that 90% of the induced mutations are frameshift mutations located within specific sequences (mutation hot spots). Two classes of mutation hot spots were found: (i) -1 frameshift mutations occurring within runs of guanines (i.e. GGGG----GGG; (ii) -2 frameshift mutations occurring within the NarI recognition sequence (GGCGCC----GGCC). In the present work, we further investigate the genetic requirements of these frameshift events by using specific reversion assays. Like UV-induced mutagenesis, frameshift mutations occurring within runs of G's (also referred to as the "slippage pathway") require the activated form of the RecA protein (RecA*). On the other hand, frameshift mutations occurring at the NarI site (the "NarI mutation pathway") require a LexA-controlled function(s) that is not UmuDC. The LexA-controlled gene(s) that is (are) involved in this pathway remain to be identified. Moreover, this pathway does not require RecA* for the proteolytic processing of a protein other than LexA (like the cleavage of UmuD in UV-induced mutagenesis). An "additional" role of RecA can be defined as follows: (i) The non-activated form of the RecA protein acts as an inhibitor in the NarI mutation pathway. (ii) This inhibition is relieved upon activation of RecA by UV irradiation of the bacteria. (iii) A recA deletion mutant is totally proficient in the NarI mutation pathway provided the SOS system is derepressed [lexA (Def) allele]. Therefore, RecA does not actively participate in the fixation of the mutation. A molecular model for this "additional" role of RecA is proposed.

Specific strand loss in N-2-acetylaminofluorene-modified DNA

N-2-Acetylaminofluorene (AAF), a well-known chemical carcinogen, when covalently linked to guanine residues constitutes a premutagenic lesion that is converted in vivo into frameshift mutations. In Escherichia coli, it is thought that -AAF adducts block the replication fork and that the mutagenic processing of the -AAF adducts is mediated by the SOS response. The construction in vitro of plasmids containing -AAF adducts in one strand only of a double-stranded DNA molecule enabled us to investigate the segregation of the strands and the mutagenicity of the lesions in vivo. The two DNA strands were "genetically labelled" by means of a single base-pair mismatch in the tetracycline-resistance gene, one strand carrying the wild-type allele and the other strand a mutant tetracycline-sensitive allele. The two strands contained either no -AAF adducts, -AAF adducts in one strand or -AAF adducts in both strands. When such constructions are used to transform bacterial cells the following are found. When no -AAF adducts are present on either strand of the DNA, a mixture of plasmids having information from both parent strands is found in 80% of the transformed bacterial clones. With -AAF adducts present in one strand only, in 90% of the transformants there is a consistent loss of the parent strand information that contained the -AAF adducts. In the constructions having -AAF adducts in both strands, the transformed bacteria carry either one or the other allele in a pure form. Our results suggest that when blocking lesions (-AAF adducts) are present in one strand only, they trigger the specific loss of that strand. The forward mutation frequency (i.e. the tetracycline-resistance gene inactivation frequency) was found to be more than ten times lower when the -AAF adducts are bound to one strand only compared with the situation where both strands carry the premutagenic lesions. Moreover, when the isolated mutants were sequenced, the mutations were found to consist of a mixture of true -AAF-induced mutations (i.e. -1 or -2 frameshift mutation at previously determined mutation hot spots) and of mutations that are not targeted at -AAF adducts. We suggest that these "background" mutants arose from the mutagenic processing of cryptic lesions present in our DNA. The low mutagenic efficiency of -AAF adducts, when present in one strand only of a duplex DNA, most probably results from the above-described loss of the damaged strand.(ABSTRACT TRUNCATED AT 400 WORDS)

Covalent binding of a carcinogen as a probe for the dynamics of deoxyribonucleic acid

In order to determine the kinetic parameters of the binding to DNA of two closely related ultimate carcinogens, 2-(N-acetoxy-N-acetylamino)fluorene (N-Aco-AAF) and 2-(N-hydroxyamino)fluorene (N-OH-AF), three kinds of experiments were performed: measurement of the final amount of adduct (N-Aco-AAF and N-OH-AF), determination of the initial rate, and study of the reaction with deoxyguanosine (N-Aco-AAF only) at temperatures between 4 and 50 degrees C. The kinetic treatment of the chemical equations relies on two main assumptions: (i) binding of carcinogen to the C8 of guanine (G) could occur either with the classical B conformation or with a transient conformational state of the sugar--phosphate chain at the level of the guanine and denoted by G*; (ii) the equilibrium between G and G* is fast as compared to the chemical rate of carcinogen binding. These two assumptions have been verified by comparing experimental and calculated values of some of the data. From experimental data it is possible then to determine the characteristic independent parameters of the reaction: the constant K of the G in equilibrium G* and the enthalpy change delta H of the process, the rate constant k3 of the binding to the C8 of G, and the rate constant k1 of hydrolysis of the carcinogen with their corresponding activation enthalpies E3 and E1. Some essential results obtained are as follows: (a) The amount of G* that represents about 10% of the G at room temperature increases with temperature and is higher in denatured than in native DNA. (b) The values of delta H (approximately 9 kcal mol-1) and delta S (approximately 27 cal K-1 mol-1) of the G in equilibrium G* equilibrium are close to those associated with single base pair opening [Wartell, R.M., & Benight, A.S. (1982) Biopolymers 21, 2069]. (c) N-Aco-AAF reacts only with the G* conformation while N-OH-AF binds preferentially to the "classical" G (B conformation). Therefore, the electrophilic carcinogens behave as probes of the dynamic state of the DNA, but the rate of the G in equilibrium G* exchange is fast as compared to the binding rate of the carcinogen.(ABSTRACT TRUNCATED AT 400 WORDS)

Carcinogen-induced mutation spectrum in wild-type, uvrA and umuC strains of Escherichia coli. Strain specificity and mutation-prone sequences

Forward mutations induced by the ultimate carcinogen N-acetoxy-N-2-acetylaminofluorene (N-Aco-AAF) in the tetracycline resistance gene carried on plasmid pBR322 are shown to be dependent upon the induction of the host SOS functions in wild-type and umuC Escherichia coli cells. The mutation frequency in the umuC strain is equal to about 40% of the mutation frequency observed in the umu+ background. In the excision-repair-deficient uvrA mutant strain the mutagenic response is the same as in SOS-induced wild-type cells whether or not the uvrA bacteria are SOS-induced. Equal mutation frequencies are obtained in both the wild-type and the uvrA strains for equal modification levels although the survival of AAF-modified plasmid DNA is greatly reduced in the uvrA strain as compared to the wild-type strain. Sequence analysis of the mutations reveals that more than 90% of the N-Aco-AAF-induced mutations are frameshift mutations. Two types of mutational hotspots are observed occurring either at repetitive sequences or at non-repetitive sequences. Both types of mutants appear at similar locations and frequencies in both the wild-type and the uvrA strains. On the other hand, only the non-repetitive sequence mutants are obtained in the umuC background. These non-repetitive sequence mutants preferentially occur within the sequence 5' G-G-C-G-C-C 3' (the NarI restriction enzyme recognition sequence). The analysis of the -AAF binding spectrum to the same DNA fragment shows that there is no direct correlation between the modification spectrum and the mutation spectrum. We suggest that certain sequences are "mutation-prone" in the sense that only these sequences can be efficiently mutated as the result of an active processing mediated by specific proteins. When a sequence is said to be mutation-prone it probably corresponds to a particular structure that is induced within this sequence as a result of the binding to the DNA of the mutagen. This sequence-specific conformational change is the substrate for the protein(s) that fixes the mutation. The mutagenic processing pathway(s) is part of the cellular response to DNA-damaging agents (the so-called SOS response). Two pathways for frameshift mutagenesis are suggested by the data: an umuC-dependent pathway, which is involved in the mutagenic processing of lesions within repetitive sequences; an umuC-independent pathway responsible for the fixation of mutations within specific non-repetitive sequences.