Mutation and DNA replication in Escherichia coli treated with low concentrations of N-methyl-N'-nitro-N-nitrosoguanidine

Adaptation and preadaptation of Salmonella enterica to Bile

Bile possesses antibacterial activity because bile salts disrupt membranes, denature proteins, and damage DNA. This study describes mechanisms employed by the bacterium Salmonella enterica to survive bile. Sublethal concentrations of the bile salt sodium deoxycholate (DOC) adapt Salmonella to survive lethal concentrations of bile. Adaptation seems to be associated to multiple changes in gene expression, which include upregulation of the RpoS-dependent general stress response and other stress responses. The crucial role of the general stress response in adaptation to bile is supported by the observation that RpoS⁻ mutants are bile-sensitive. While adaptation to bile involves a response by the bacterial population, individual cells can become bile-resistant without adaptation: plating of a non-adapted S. enterica culture on medium containing a lethal concentration of bile yields bile-resistant colonies at frequencies between 10⁻⁶ and 10⁻⁷ per cell and generation. Fluctuation analysis indicates that such colonies derive from bile-resistant cells present in the previous culture. A fraction of such isolates are stable, indicating that bile resistance can be acquired by mutation. Full genome sequencing of bile-resistant mutants shows that alteration of the lipopolysaccharide transport machinery is a frequent cause of mutational bile resistance. However, selection on lethal concentrations of bile also provides bile-resistant isolates that are not mutants. We propose that such isolates derive from rare cells whose physiological state permitted survival upon encountering bile. This view is supported by single cell analysis of gene expression using a microscope fluidic system: batch cultures of Salmonella contain cells that activate stress response genes in the absence of DOC. This phenomenon underscores the existence of phenotypic heterogeneity in clonal populations of bacteria and may illustrate the adaptive value of gene expression fluctuations.

This study describes mechanisms employed by the bacterium Salmonella enterica to survive bile: adaptation, mutation, and non-mutational preadaptation. Adaptation is easily observed in the laboratory: when a Salmonella culture is grown in the presence of a sublethal concentration of the bile salt sodium deoxycholate (DOC), the minimal inhibitory concentration of DOC increases. Adaptation appears to be associated to multiple changes in gene expression induced by DOC. Mutational bile resistance is also a common phenomenon: plating on agar containing a lethal concentration of bile yields bile-resistant colonies. Fluctuation analysis indicates that such colonies derive from bile-resistant cells present in the previous culture. However, selection on lethal concentrations of bile also provides bile-resistant isolates that are not mutants. Non-mutational preadaptation, a non-canonical phenomenon a priori, suggests that batch cultures contain rare Salmonella cells whose physiological state permits survival upon encountering bile. The view that non-mutational preadaptation may be a consequence of phenotypic heterogeneity is supported by the observation that Salmonella cultures contain cells that activate stress response genes in the absence of DOC.

Using genomic sequencing for classical genetics in E. coli K12

We here develop computational methods to facilitate use of 454 whole genome shotgun sequencing to identify mutations in Escherichia coli K12. We had Roche sequence eight related strains derived as spontaneous mutants in a background without a whole genome sequence. They provided difference tables based on assembling each genome to reference strain E. coli MG1655 (NC_000913). Due to the evolutionary distance to MG1655, these contained a large number of both false negatives and positives. By manual analysis of the dataset, we detected all the known mutations (24 at nine locations) and identified and genetically confirmed new mutations necessary and sufficient for the phenotypes we had selected in four strains. We then had Roche assemble contigs de novo, which we further assembled to full-length pseudomolecules based on synteny with MG1655. This hybrid method facilitated detection of insertion mutations and allowed annotation from MG1655. After removing one genome with less than the optimal 20- to 30-fold sequence coverage, we identified 544 putative polymorphisms that included all of the known and selected mutations apart from insertions. Finally, we detected seven new mutations in a total of only 41 candidates by comparing single genomes to composite data for the remaining six and using a ranking system to penalize homopolymer sequencing and misassembly errors. An additional benefit of the analysis is a table of differences between MG1655 and a physiologically robust E. coli wild-type strain NCM3722. Both projects were greatly facilitated by use of comparative genomics tools in the CoGe software package (http://genomevolution.org/).

Induction of enzymes involved in DNA repair and mutagenesis

Three phenomena examined here have been claimed to reflect the operation of inducible repair systems. It has been postulated that 'SOS repair' involves the induction by DNA-damaging agents of an error-prone repair system that is capable of affecting the replication of damaged DNA. This system works with bacteriophages and animal viruses, in which it is possible to separate the effects of DNA damage on the viral DNA from that on the host cell. Whether this system also operates in repair of the cell's own DNA is, however, controversial. The system appears to have little effect on survival of bacterial cells and its operation in cellular mutagenesis is still not proven, at least in bacteria with otherwise normal repair capacity. 'Adaptation' is the response of bacteria to low doses of methylating agents. Adapted bacteria are more resistant to the lethal and mutagenic action of alkytlating agents. The process includes the induction of an enzyme that 'removes' O6-alkylated bases from DNA and which, unusually, is consumed during the course of the reaction. The reaction itself is also unknown; it does not depend on a nuclease, glycosylase or demethylase, but could use a transmethylase. There is some evidence that an analogous process occurs in animals. The third process affects the synthesis of high molecular weight DNA in cultured mammalian cells that have been exposed to split doses of DNA-damaging agents. It has been postulated that this system is inducible and error-free, but detailed analysis suggests that the observed effect is an artifact arising from an abnormal distribution of sizes of nascent DNA after the second dose, and as a result of exposure to the first dose. Inducible DNA repair systems may be expected to influence kinetics of the dose--response relationships obtained after exposure of cells to mutagens and carcinogens. The interactions between these effects and those produced by inducible pathways of metabolic activation and detoxification are discussed.

Bile-induced DNA damage in Salmonella enterica

In the absence of DNA adenine methylase, growth of Salmonella enterica serovar Typhimurium is inhibited by bile. Mutations in any of the mutH, mutL, and mutS genes suppress bile sensitivity in a Dam(-) background, indicating that an active MutHLS system renders Dam(-) mutants bile sensitive. However, inactivation of the MutHLS system does not cause bile sensitivity. An analogy with Escherichia coli, in which the MutHLS system sensitizes Dam(-) mutants to DNA-injuring agents, suggested that bile might cause DNA damage. In support of this hypothesis, we show that bile induces the SOS response in S. enterica and increases the frequency of point mutations and chromosomal rearrangements. Mutations in mutH, mutL, or mutS cause partial relief of virulence attenuation in a Dam(-) background (50- to 100-fold by the oral route and 10-fold intraperitoneally), suggesting that an active MutHLS system reduces the ability of Salmonella Dam(-) mutants to cope with DNA-damaging agents (bile and others) encountered during the infection process. The DNA-damaging ability of bile under laboratory conditions raises the possibility that the phenomenon may be relevant in vivo, since high bile concentrations are found in the gallbladder, the niche for chronic Salmonella infections.

How heterologously expressed Escherichia coli genes contribute to understanding DNA repair processes in Saccharomyces cerevisiae

DNA-damaging agents constantly challenge cellular DNA; and efficient DNA repair is therefore essential to maintain genome stability and cell viability. Several DNA repair mechanisms have evolved and these have been shown to be highly conserved from bacteria to man. DNA repair studies were originally initiated in very simple organisms such as Escherichia coli and Saccharomyces cerevisiae, bacteria being the best understood organism to date. As a consequence, bacterial DNA repair genes encoding proteins with well characterized functions have been transferred into higher organisms in order to increase repair capacity, or to complement repair defects, in heterologous cells. While indicating the contribution of these repair functions to protection against the genotoxic effects of DNA-damaging agents, heterologous expression studies also highlighted the role of the DNA lesions that are substrates for such processes. In addition, bacterial DNA repair-like functions could be identified in higher organisms using this approach. We heterologously expressed three well characterized E. coli repair genes in S. cerevisiae cells of different genetic backgrounds: (1) the ada gene encoding O(6)-methylguanine DNA-methyltransferase, a protein involved in the repair of alkylation damage to DNA, (2) the recA gene encoding the main recombinase in E. coli and (3) the nth gene, the product of which (endonuclease III) is responsible for the repair of oxidative base damage. Here, we summarize our results and indicate the possible implications they have for a better understanding of particular DNA repair processes in S. cerevisiae.

Increased repair in DNA growing point regions after treatment of human lymphoma cells with N-methyl-N'-nitro-N-nitrosoguanidine

Benzoylated naphthoylated DEAE-cellulose columns can be used to separate DNA growing point regions from the bulk of the DNA. We used the columns to estimate DNA excision repair in both fractions. Repair induced by acetoxy acetyl aminofluorene (AAAF), bromomethyl benz(alpha) anthracene (BMBA), and methyl methanesulfonate (MMS) occurs to an equal extent in growing point and non-replicating regions of the DNA. Excision repair induced by methyl nitrosourea (MNNU) and methyl nitronitrosoguanidine (MNNG) occurs to a greater extent in growing point regions of the DNA. The overall amount of methyl nitronitrosoguanidine-induced alkylation is the same for replicating and non-replicating regions of the DNA treated in vitro. We conclude that there is some special interaction between methyl-nitronitrosoguanidine and the growing point region in vivo. We suppose that strand displacement and branch migration return DNA lesions at the growing point to a double stranded configuration at which repair is possible.

N-methyl-N'-nitro-N-nitrosoguanidine-induced resistance to ionizing radiation

N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) pretreatments increase the resistance of Escherichia coli to gamma-radiation. The increased resistance is dependent on functional polA, recA, recB, recC, and lexA genes and is partly dependent on recN. The MNNG-induced resistance is additive to resistance induced by pretreatment with gamma-radiation but not by increases induced by hydrogen peroxide. The MNNG-induced resistance occurs in adaptive response mutants and at pretreatment levels of MNNG that do not activate cells to reactivate UV-inactivated lambda phage. The MNNG-induced resistance appears to be distinct from other inductions to gamma-radiation resistance.

Enhancement by cysteamine of N-methyl-N-nitrosourea mutagenesis in E. coli

Cysteamine (MEA) is comutagenic to methylnitrosourea (MNU) in E. coli AB 1157 but not in the nonadaptable mutant derivative ada-6 of that strain. The comutagenic action of MEA was eliminated by cysteine at low concentrations, which also lowered mutation frequencies in AB1157 but not in ada-6. In model experiments it was shown that cysteine counteracted the inhibition by MEA of beta-galactosidase induction in both bacterium strains. The comutagenic action of MEA is interpreted as being due to an inhibition of induction of methyltransferase during treatment with MNU.

A model for the mechanism of alkylation mutagenesis

The phenomenology of mutagenesis by N-methyl-N'-nitro-N-nitrosoguanidine and related alkylating agents is reviewed and a three-step model for the molecular events of mutagenesis is presented. The first step is the production of miscoding lesions, especially O6-methylguanine, and the induction and synthesis of methyltransferase. The second step is the generation of DNA sequences in which O6-methylguanine is paired with thymine. The third step is the conversion of this abnormal base pair to an adenine-thymine pair completing the production of a transition mutation. At each of these steps, factors which affect the ultimate mutation frequency are outlined. The model is then described formally and the limits of the model are discussed.

Genetic effects of N-methyl-N'-nitro-N-nitrosoguanidine and its homologs

Since the discovery of the mutagenic activity of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) in 1960, this compound has become one of the most widely used chemical mutagens. The present paper gives a survey on the chemistry, metabolism, and mode of interaction of MNNG with DNA and proteins, and of the genotoxic effects of this agent on microorganisms, plants, and animals, including human cells cultured in vitro. Data on the carcinogenicity and teratogenicity of MNNG as well as on the genotoxic effects of homologs of MNNG are also presented.

An Escherichia coli mutant refractory to nitrosoguanidine mutagenesis

A newly-isolated Escherichia coli mutant suffers only about 10% as many mutations as normal strains on exposure to nitrosoguanidine. The responsible mutation, inm-1, maps at approximately minute 79 in the current E. coli genetic map. The mutant is normal for overall growth, nitrosoguanidine lethality, spontaneous mutagenesis, ultraviolet light lethality and mutagenesis, ethyl methanesulfonate lethality and mutagenesis, and the adaptive repair induced by alkylating agents. The existence of this mutation proves that nitrosoguanidine mutagenesis is not merely the result of reactions between the chemical and DNA, but requires specific cellular function(s), and underscores the peculiarity of nitrosoguanidine as a mutagen.

Forward mutations to arabinose resistance in Salmonella typhimurium strains: a sensitive assay for mutagenicity testing

The forward-mutation assay using the L-arabinose-sensitive strain SV3 of Salmonella typhimurium has been calibrated against a selected set of mutagens. Strain SV3 is sensitive to chemicals causing base-pair substitutions, frameshift mutations and deletions. New strains deficient for the excision-repair system or the lipopolysaccharide barrier or both have been selected from strain SV3. The additional mutations do not affect the independence of the assay from experimental artifacts due to physiological or lethal damage or differences in plating density. The new strains are more sensitive than SV3 to certain mutagens. Techniques for using this set of strains are presented and their relative advantages discussed.

A mutagen assay detecting forward mutations in an arabinose-sensitive strain of Salmonella typhimurium

Strain SV3 of Salmonella typhimurium is sensitive to arabinose, that is, unable to grow in a medium containing arabinose plus glycerol as carbon source. Arabinose resistance is the consequence of the mutational inactivation of one of at least three different genes. The selection of arabinose-resistant mutants provides a simple and sensitive assay for the detection of weak mutagens and for refined quantitative studies of strong ones. The assay is not influenced by experimental artifacts derived from physiological or lethal effects or from differences in plating density. Such artifacts are common with other bacterial mutagen assays, including those using strains analogous to SV3. As practical examples, the assay was used with N-methyl-N'-nitro-N-nitrosoguanidine and the fungicide captafol.

The role of pre-replication and post-replication processes in mutation induction in Haemophilus influenzae by N-methyl-N'-nitro-N-nitrosoguanidine

Studies were carried out on the repair and fixation of premutational damage induced in Haemophilus influenzae by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). The studies employed a temperature-sensitive DNA elongation mutant (dna9) and its combinations with mutants defective in pyrimidine dimer excision (uvr1, uvr2) and in recombination (rec1). The dna9 mutant is shown to be leaky, allowing about 1% of the normal rate of DNA synthesis at the restrictive temperature. Repair of premutational lesions was detected by a decline in mutation frequency with increasing delay in DNA replication in dna9 at the restrictive temperature. This repair is unaffected by the pyrimidine dimer excision system. Mutation fixation was detected by the ability of DNA from treated and then lysed cells to transfer mutants to recipient cells by transformation. Some fixation occurred at the restrictive temperature but much less than at the non-restrictive temperature suggesting that an appreciable minority of the mutations resulted from lesions introduced near the replication fork but that the majority of mutations arise from lesions introduced at some distance from the fork, perhaps randomly. The DNA synthesized immediately after MNNG treatment is of lower molecular weight than normal and returns to normal with time. This return is blocked in the rec1 mutant, suggesting that recombination is involved. The possible role of this process in MNNG mutagenesis is discussed.

The relation of repair phenomena to mutation induction in bacteria

The relation of various processes to mutation induction by radiation and chemicals is discussed for for various species of bacteria. A variety of repair processes have been identified at the molecular level that can eliminate many kinds of potentially mutagenic lesions before they can be converted to final mutation. Fixation often but not always occurs at replication. A number of mutagens, including UV light, ionizing radiation, and a number of chemicals, induce an error-prone process, perhaps a modification of the proof-reading system, that allows bacteria to survive after potentially lethal damage at the expense of making errors. Some mutagens, notably monofunctional alkylating agents and base analogues, produce mutations by other processes. Even in these cases, repair processes play an important role. There is some evidence that error-free as well as error-prone repair processes can be induced. A brief discussion is given of the relation of these findings to the practical problems of hazards estimations.

Antimutagenic effects of caffeine during nitrosoguanidine-induced mutagenesis of Salmonella typhimurium cells and phages

The effect of caffeine on nitrosoguanidine-induced mutagenesis of Salmonella typhimurium and its P22 and L phages was studied. The detected mutations included phage "clear" mutations, reversions of phage "amber" mutation, and prototrophic reversions of the his- auxotroph of Salmonella typhimurium. Neither the recA mutation of the host nor the erf mutation of the phage genome were found to affect the nitrosoguanidine-induced mutagenesis of the phage during vegetative growth. Beginning with a concentration of 0.2 mg/ml, caffeine decreased the frequency of mutants by 30--60%, attaining a maximum effect at 1.5 mg/ml and retaining this effect even at higher concentrations. A similar antimutagenic effect was observed with the mutagenesis of the host cells. The nitrosoguanidine-induced mutagenesis does not seem to be related to the function of the recA cell gene or the erf phage gene. The mechanism of mutagenesis by nitrosoguanidine probably has two components, one of them caffeine sensitive, the other caffeine-resistant.

Physiological modification of alkylating agent induced mutagenesis. II. Influence of the numbers of chromosome replicating forks and gene copies on the frequency of mutations induced in Escherichia coli

The frequency of reversions induced in Escherichia coli K-12 trpA58 by any of five different monofunctional alkylating agents increased as the growth rate of the organism was raised prior to mutagen treatment. The increase in mutation frequency did not correlate with growth rate-dependent changes in cell area or total cellular protein and DNA. After treatment of cells with N-methyl-N-nitrosourea (MNUA), no growth rate-dependent change was observed in the total DNA alkylation or percentage of O6-methylguanine present in the DNA extracted. The frequency of reversions induced by one mutagen, methyl methanesulphonate (MMS), increased in proportion to the average number of trpA gene copies per cell, whereas the frequency of reversions induced by the other compounds was dependent on the average number of chromosome replicating forks per cell. This difference was attributed to the different ratios of DNA base alkylation products observed, formed after treatment with MMS, an SN2-type reagent, or after treatment with the SN1-type reagents ethyl methanesulphonate (EMS), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), MNUA and N-ethyl-N-nitrosourea (ENUA). Possible reasons for the dependence of mutation frequency on the number of replicating forks per cell are discussed.

Methyl methanesulfonate mutagenesis of synchronized Chlamydomonas

Methyl methanesulfonate (MMS) mutagenesis of Chlamydomonas reinhardtii at different stages of the synchronous cell-cycle revealed the following results. (1) Induction of phenotypically distinct Mendelian (nuclear), str-50 and non-Mendelian (chloroplast) str-500P, streptomycin resistant mutants was relatively high during the first portion of the cell-cycle when chloroplast DNA replication is known to occur. (2) A second and more pronounced interval of enhanced Mendelian, str-50 mutant induction was observed near the middle of the cell-cycle when the initial stages of nuclear DNA replication occur. Induction of non-Mendelian, str-500P mutants was inconsistent during this period. (3) The incidence of mutants from a second phenotypically distinct class of non-Mendelian streptomycin-resistant mutants (str-500D) was not increased over control levels at any stage of the cell-cycle examined. It is concluded that MMS, like N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), may not be the most suitable general mutagen for this alga because its enhanced mutagenesis of cells in the nuclear S phase could result in multiple closely linked mutations.

Mutation induction by MNNG in a bacteriophage of Haemophilus influenzae

Three temperature-sensitive mutants of the Haemophilus influenzae phage HP1c1 were tested for reversion to wild type (ts leads to ts+). Treatment with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) produced revertants at levels up to 0.1% of the total progeny phage from treated lysogens. Cells treated with MNNG after infection with whole ts phage produced progeny phage with similar reversion frequencies, but when the uninfected cells or the phage were treated alone no reversion was induced. Fixation of premutational lesions was shown to occur with no evidence for host-cell DNA synthesis, indicating that phage DNA synthesis may be responsible for fixation of mutation in phage DNA. Evidence is given which shows that prophage DNA replicating by the cells' replicating system after treatment and before induction, produces the same number of revertants per survivor as phage DNA which is replicated outside the host genome. Two of the phage mutants (ts1 and ts2) reverted at similar frequencies, while one of the mutants (ts3) exhibited a much lower induced reversion frequency.

Lethal and mutagenic effects of nitrosoguanidine on synchronized Chlamydomonas

The lethal and mutagenic effects of 5 mug/ml N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) were maximal during the nuclear S-period of synchronously grown Chlamydomonas reinhardtii. This was revealed by a 50% drop in survival and a 50- to 100-fold increase in the recovery of slow-growth mutants (up to 40% of the survivors) which were first recognized as small colonies on agar medium. Partial characterization of these isolates revealed about 50% to be stable on subculture, and several were demonstrated to be either acetate-dependent, dark-lethal (light-dependent), or acetate-sensitive mutants. There was no significant increase of lethality or of slow-growth mutants correlated with treatment during the chloroplast DNA replication phase of the cell-cycle. The results of genetic analysis with 13 mutants induced during the nuclear S-period were consistent with their nuclear origin. These analyses were hampered by the high proportion of lethality among the progeny of most crosses. It is concluded that the enhanced mutant induction among nuclear S-phase cells may indicate preferential mutagenesis of replication fork DNA and induction of multiple-closely-linked mutations, as in some bacteria. Consequently, for C. reinhardtii, caution should be exercised in drawing relationships between abnormal behavioral and biochemical phenotypes in MNNG-induced mutants.

The effect of nitrosoguanidine upon DNA synthesis in vitro

Both the polymerase and the exonuclease activities of DNA polymerase III are inactivated by treatment with nitrosoguanidine. The treatment of the DNA template with the mutagen does not affect the template in supporting DNA synthesis. No effect of nitrosoguanidine upon fidelity of replication in vitro was detected.