cAMP-dependent SOS induction and mutagenesis in resting bacterial populations

Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli

The SOS response in UV-irradiated Escherichia coli includes the upregulation of several dozen genes that are negatively regulated by the LexA repressor. Using DNA microarrays containing amplified DNA fragments from 95.5% of all open reading frames identified on the E. coli chromosome, we have examined the changes in gene expression following UV exposure in both wild-type cells and lexA1 mutants, which are unable to induce genes under LexA control. We report here the time courses of expression of the genes surrounding the 26 documented lexA-regulated regions on the E. coli chromosome. We observed 17 additional sites that responded in a lexA-dependent manner and a large number of genes that were upregulated in a lexA-independent manner although upregulation in this manner was generally not more than twofold. In addition, several transcripts were either downregulated or degraded following UV irradiation. These newly identified UV-responsive genes are discussed with respect to their possible roles in cellular recovery following exposure to UV irradiation.

An aerobic recA-, umuC-dependent pathway of spontaneous base-pair substitution mutagenesis in Escherichia coli

Antimutator alleles indentify genes whose normal products are involved in spontaneous mutagenesis pathways. Mutant alleles of the recA and umuC genes of Escherichia coli, whose wild-type alleles are components of the inducible SOS response, were shown to cause a decrease in the level of spontaneous mutagenesis. Using a series of chromosomal mutant trp alleles, which detect point mutations, as a reversion assay, it was shown that the reduction in mutagenesis is limited to base-pair substitutions. Within the limited number of sites than could be examined, transversions at AT sites were the favored substitutions. Frameshift mutagenesis was slightly enhanced by a mutant recA allele and unchanged by a mutant umuC allele. The wild-type recA and umuC genes are involved in the same mutagenic base-pair substitution pathway, designated "SOS-dependent spontaneous mutagenesis" (SDSM), since a recAumuC strain showed the same degree and specificity of antimutator activity as either single mutant strain. The SDSM pathway is active only in the presence of oxygen, since wild-type, recA, and umuC strains all show the same levels of reduced spontaneous mutagenesis anaerobically. The SDSM pathway can function in starving/stationary cells and may, or may not, be operative in actively dividing cultures. We suggest that, in wild-type cells, SDSM results from basal levels of SOS activity during DNA synthesis. Mutations may result from synthesis past cryptic DNA lesions (targeted mutagenesis) and/or from mispairings during synthesis with a normal DNA template (untargeted mutagenesis). Since it occurs in chromosomal genes of wild-type cells, SDSM may be biologically significant for isolates of natural enteric bacterial populations where extended starvation is often a common mode of existence.

Mutator natural Escherichia coli isolates have an unusual virulence phenotype

A small percentage of natural Escherichia coli isolates (both commensal and pathogenic) have a mutator phenotype related to defects in methyl-directed mismatch repair (MR) genes. We investigated whether there was a direct link between the mutator phenotype and virulence by (i) studying the relationships between mutation rate and virulence in a mouse model of extraintestinal virulence for 88 commensal and extraintestinal pathogenic E. coli isolates and (ii) comparing the virulence in mice of MR-deficient and MR-proficient strains that were otherwise isogenic. The results provide no support for the hypothesis that the mutator phenotype has a direct role in virulence or is associated with increased virulence. Most of the natural mutator strains studied displayed an unusual virulence phenotype with (i) a lack of correspondence between the number of virulence determinants and pathogenicity in mice and (ii) an intermediate level of virulence. On a large evolutionary scale, the mutator phenotype may help parasites to achieve an intermediate rate of virulence which mathematical models predict to be selected for during long-term parasite-host interactions.

Adaptive mutation: implications for evolution

Adaptive mutation is defined as a process that, during nonlethal selections, produces mutations that relieve the selective pressure whether or not other, nonselected mutations are also produced. Examples of adaptive mutation or related phenomena have been reported in bacteria and yeast but not yet outside of microorganisms. A decade of research on adaptive mutation has revealed mechanisms that may increase mutation rates under adverse conditions. This article focuses on mechanisms that produce adaptive mutations in one strain of Escherichia coli, FC40. These mechanisms include recombination-induced DNA replication, the placement of genes on a conjugal plasmid, and a transient mutator state. The implications of these various phenomena for adaptive evolution in microorganisms are discussed.

No genetic barriers between Salmonella enterica serovar typhimurium and Escherichia coli in SOS-induced mismatch repair-deficient cells

Conjugational crosses trigger SOS induction in Escherichia coli F(-) cells mated with Salmonella enterica serovar Typhimurium Hfr donors. Using an epigenetic indicator of SOS induction, we showed that a strong SOS response occurring in a subpopulation of mated mismatch repair-deficient cells totally abolishes genetic barriers between these two genera.

Mutators and sex in bacteria: conflict between adaptive strategies

Bacterial mutation rates can increase and produce genetic novelty, as shown by in vitro and in silico experiments. Despite the cost due to a heavy deleterious mutation load, mutator alleles, which increase the mutation rate, can spread in asexual populations during adaptation because they remain associated with the rare favorable mutations they generate. This indirect selection for a genetic system generating diversity (second-order selection) is expected to be highly sensitive to changes in the dynamics of adaptation. Here we show by a simulation approach that even rare genetic exchanges, such as bacterial conjugation or transformation, can dramatically reduce the selection of mutators. Moreover, drift or competition between the processes of mutation and recombination in the course of adaptation reveal how second-order selection is unable to optimize the rate of generation of novelty.

Colonization strategies and conjugal gene transfer of inoculated Pseudomonas syringae on the leaf surface

Survival, colonization and activity of Pseudomonas syringae bacteria inoculated onto the leaf surface of the common bean (Phaseolus vulgaris) was studied. Inoculated Ps. syringae cells shortened by half their size in 100% humidity and by an average of one fifth in 40-60% humidity. The respiring portion of the population, measured by the formation of 5-cyano-2,3-ditolyl tetrazolium chloride (CTC)-formazan crystals, decreased more in 40-60% humidity than in 100% humidity. In scanning electron micrographs, the bacterial cells on leaf surfaces were seen embedded in a mucoid matrix. Intraspecies conjugation of plasmid RP1 also occurred in 40-60% humidity conditions. The portion of transconjugants temporally rose higher than the same portion in 100% humidity conditions. Therefore, although only a small proportion of the inoculated cells remained active on the leaf surface in 40-60% humidity, a relatively high rate of conjugation was still seen. Gene spreading was thus efficient on the leaf surface also when conditions did not allow bacterial population growth.

The SOS response regulates adaptive mutation

Upon starvation some Escherichia coli cells undergo a transient, genome-wide hypermutation (called adaptive mutation) that is recombination-dependent and appears to be a response to a stressful environment. Adaptive mutation may reflect an inducible mechanism that generates genetic variability in times of stress. Previously, however, the regulatory components and signal transduction pathways controlling adaptive mutation were unknown. Here we show that adaptive mutation is regulated by the SOS response, a complex, graded response to DNA damage that includes induction of gene products blocking cell division and promoting mutation, recombination, and DNA repair. We find that SOS-induced levels of proteins other than RecA are needed for adaptive mutation. We report a requirement of RecF for efficient adaptive mutation and provide evidence that the role of RecF in mutation is to allow SOS induction. We also report the discovery of an SOS-controlled inhibitor of adaptive mutation, PsiB. These results indicate that adaptive mutation is a tightly regulated response, controlled both positively and negatively by the SOS system.

lon incompatibility associated with mutations causing SOS induction: null uvrD alleles induce an SOS response in Escherichia coli

The uvrD gene in Escherichia coli encodes a 720-amino-acid 3'-5' DNA helicase which, although nonessential for viability, is required for methyl-directed mismatch repair and nucleotide excision repair and furthermore is believed to participate in recombination and DNA replication. We have shown in this study that null mutations in uvrD are incompatible with lon, the incompatibility being a consequence of the chronic induction of SOS in uvrD strains and the resultant accumulation of the cell septation inhibitor SulA (which is a normal target for degradation by Lon protease). uvrD-lon incompatibility was suppressed by sulA, lexA3(Ind(-)), or recA (Def) mutations. Other mutations, such as priA, dam, polA, and dnaQ (mutD) mutations, which lead to persistent SOS induction, were also lon incompatible. SOS induction was not observed in uvrC and mutH (or mutS) mutants defective, respectively, in excision repair and mismatch repair. Nor was uvrD-mediated SOS induction abolished by mutations in genes that affect mismatch repair (mutH), excision repair (uvrC), or recombination (recB and recF). These data suggest that SOS induction in uvrD mutants is not a consequence of defects in these three pathways. We propose that the UvrD helicase participates in DNA replication to unwind secondary structures on the lagging strand immediately behind the progressing replication fork, and that it is the absence of this function which contributes to SOS induction in uvrD strains.

Evolution-driving genes

Genomic sequences provide evidence for a common origin of life and its evolution via selection of genetic variants created by mutation and recombination. Two classes of genes are known to accelerate mutation and/or recombination rates in bacterial populations: stress-inducible wild-type genes, usually part of the SOS regulon, and genes whose functional loss, or downregulation, increases the rate of genetic variability (mutator and/or hyper-rec mutants).

A role for the umuDC gene products of Escherichia coli in increasing resistance to DNA damage in stationary phase by inhibiting the transition to exponential growth

The umuDC gene products, whose expression is induced by DNA-damaging treatments, have been extensively characterized for their role in SOS mutagenesis. We have recently presented evidence that supports a role for the umuDC gene products in the regulation of growth after DNA damage in exponentially growing cells, analogous to a prokaryotic DNA damage checkpoint. Our further characterization of the growth inhibition at 30 degrees C associated with constitutive expression of the umuDC gene products from a multicopy plasmid has shown that the umuDC gene products specifically inhibit the transition from stationary phase to exponential growth at the restrictive temperature of 30 degrees C and that this is correlated with a rapid inhibition of DNA synthesis. These observations led to the finding that physiologically relevant levels of the umuDC gene products, expressed from a single, SOS-regulated chromosomal copy of the operon, modulate the transition to rapid growth in E. coli cells that have experienced DNA damage while in stationary phase. This activity of the umuDC gene products is correlated with an increase in survival after UV irradiation. In a distinction from SOS mutagenesis, uncleaved UmuD together with UmuC is responsible for this activity. The umuDC-dependent increase in resistance in UV-irradiated stationary-phase cells appears to involve, at least in part, counteracting a Fis-dependent activity and thereby regulating the transition to rapid growth in cells that have experienced DNA damage. Thus, the umuDC gene products appear to increase DNA damage tolerance at least partially by regulating growth after DNA damage in both exponentially growing and stationary-phase cells.

Identification of genetic factors altering the SOS induction of DNA damage-inducible yebG gene in Escherichia coli

The yebG gene of Escherichia coli is a novel SOS regulon gene, but details of its regulation mechanism and biological function are not yet known. To characterize the regulation of yebG gene as a SOS gene, we identified the genetic factors affecting the SOS induction of yebG gene using yebG-lacZ operon fusion plasmid. We found that the SOS induction of yebG occurs as the cells enter into the stationary growth phase, but its induction is not observed in LB medium in the presence of 1% glucose. A stationary phase SOS induction of the yebG gene does not require the global regulator of stationary phase-specific genes, rpoS, or gyrA functions, but requires cya encoding the adenylate cyclase and hns encoding the histone-like protein H-NS functions. Our results demonstrated that the induction of a DNA damage-inducible yebG gene of E. coli is dependent on cyclic AMP and H-NS.

The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis

In Escherichia coli, the dinB gene is required for the SOS-induced lambda untargeted mutagenesis pathway and confers a mutator phenotype to the cell when the gene product is overexpressed. Here, we report that the purified DinB protein is a DNA polymerase. This novel E. coli DNA polymerase (pol IV) is shown to be strictly distributive, devoid of proofreading activity, and prone to elongate bulged (misaligned) primer/template structures. Site-directed mutagenesis experiments of dinB also demonstrate that the polymerase activity of DinB is required for its in vivo mutagenicity. Along with the sequence homologies previously found within the UmuC-like protein family, these results indicate that the uncovered DNA polymerase activity may be a common feature of all these homologous proteins.

Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria

Selection of mutator alleles, increasing the mutation rate up to 10, 000-fold, has been observed during in vitro experimental evolution. This spread is ascribed to the hitchhiking of mutator alleles with favorable mutations, as demonstrated by a theoretical model using selective parameters corresponding to such experiments. Observations of unexpectedly high frequencies of mutators in natural isolates suggest that the same phenomenon could occur in the wild. But it remains questionable whether realistic in natura parameter values could also result in selection of mutators. In particular, the main parameters of adaptation, the size of the adapting population and the height and steepness of the adaptive peak characterizing adaptation, are very variable in nature. By simulation approach, we studied the effect of these parameters on the selection of mutators in asexual populations, assuming additive fitness. We show that the larger the population size, the more likely the fixation of mutator alleles. At a large population size, at least four adaptive mutations are needed for mutator fixation; moreover, under stronger selection stronger mutators are selected. We propose a model based on multiple mutations to illustrate how second-order selection can optimize population fitness when few favorable mutations are required for adaptation.

Mechanisms of genome-wide hypermutation in stationary phase

Stationary-phase mutation (a subset of which was previously called adaptive mutation) occurs in apparently nondividing, stationary-phase cells exposed to a nonlethal genetic selection. In one experimental system, stationary-phase reversion of an Escherichia coli F'-borne lac frameshift mutation occurs by a novel molecular mechanism that requires homologous recombination functions of the RecBCD system. Chromosomal mutations at multiple loci are detected more frequently in Lac+ stationary-phase revertants than in cells that were also exposed to selection but did not become Lac+. Thus, mutating cells represent a subpopulation that experiences hypermutation throughout the genome. This paper summarizes current knowledge regarding stationary-phase mutation in the lac system. Hypotheses for the mechanism of chromosomal hypermutation are discussed, and data are presented that exclude one hypothetical mechanism in which chromosomal mutations result from Hfr formation.

Evolution of evolvability

Genomic sequence data provide evidence for a common origin of life and for its evolution by genetic variation via mutation and recombination. This paper discusses the fundamental dialectic paradigm of evolution--stability versus variability--at the crossroads of molecular genetics, population genetics, ecology, and the emerging science of experimental evolution. Experimental evolution of molecules, viruses, and bacteria can be used not only to test some basic evolutionary hypotheses but also to create new organisms for applications in biotechnology, agriculture, and medicine.

Barriers to horizontal gene transfer by natural transformation in soil bacteria

Bacteria can utilize horizontally transferred DNA from other bacterial species to adapt and evolve to their changing environments. Natural transformation is a process that allows bacteria, which are able to express a regulated physiological state of competence, to take up and integrate free DNA from their surroundings. This uptake of DNA does not necessarily depend on DNA sequence, thus, indicating the potential of gene transfer from diverged donor organisms. Barriers active against such interspecies transfer are present at different phases of the transformation process. The functionality of these barriers will be discussed, and seen in relation to mechanisms that may enable bacterial cells to respond to environmental stress by adaptive evolution.

Glucose and related catabolite repressors are powerful inhibitors of pKM101-enhanced UV mutagenesis in Escherichia coli

When stationary phase Escherichia coli K12 trp (amber) cells were exposed to UV doses ranging from 180-540 J m(-2), we found that we could not recover any induced Trp+ revertants unless the irradiated cultures were first supplied with the Muc+ mutation-enhancing IncP plasmid pKM101 (by conjugation). We also found that the numbers of UV-induced Trp+ revertants recovered from pKM101+ cultures varied quite dramatically depending upon which of several commonly-used carbon sources were present in the post-irradiation plating medium, e.g., there were always significantly fewer revertants on minimal glucose plates than on minimal glycerol plates. More importantly, there were also fewer UV-induced revertants on glycerol + glucose plates than on 'glycerol-only' plates. We then tested two glucose-related compounds which are known to depress intracellular cyclic AMP (cAMP) levels even more effectively than glucose (glucose-6-phosphate and the non-utilisable methyl-alpha-D-glucopyranoside) and found that they too were able to exert powerfully antimutagenic effects in UV-treated pKM101-containing bacteria. Taken together, these results provide strong additional support for our working hypothesis that at least one component of the mutational pathway which operates in UV-irradiated pKM101-containing cells is extremely sensitive to classical cAMP-mediated catabolite repression.

Generation of a genetic polymorphism in clonal populations of the bacterium Streptomyces ambofaciens: characterization of different mutator states

In Streptomyces ambofaciens, colony pigmentation is an unstable character. Very unstable mutants selected from twelve wild type (WT) subclones of S. ambofaciens ATCC23877 were investigated. This research showed that the polymorphism in colony pigmentation had distinct features. The first aspect is the coexistence of four types of colonies: pigmented colonies (Pig+), pigment-defective colonies (Pigcol-), pigmented colonies harboring pigment-defective sectors (Pigsec+) or pigment-defective papillae (Pigpap+). The second feature was revealed by the study on Pigpap+ colonies. We showed that WT progeny after 14 days of growth consisted almost totally of Pigpap+ colonies. Pigpap+ colonies were also found to be genetically different from each other. Characterization of twelve colonies presenting more than 20 papillae (Hyperpap colonies) led to the isolation of twelve mutator strains which produced at high frequency Pigcol- and Hyperpap colonies. Each exhibited a specific mutator phenotype and were distinct from each other. Such strains constituted a part of the polymorphism observed in each of the WT progeny and also generated a high variability. Finally, we showed that pigment-defective papillae were mutants and constituted a new form of genetic instability.

The identification of exported proteins with gene fusions to invasin

Exported proteins are integral to understanding the biology of bacterial organisms. They have special significance in pathogenesis research because they can mediate critical interactions between pathogens and eukaryotic cell surfaces. Further, they frequently serve as targets for vaccines and diagnostic tests. The commonly used genetic assays for identifying exported proteins use fusions to alkaline phosphatase or beta-lactamase. These systems are not ideal for identifying outer membrane proteins because they identify a large number of inner membrane proteins as well. We addressed this problem by developing a gene fusion system that preferentially identifies proteins that contain cleavable signal sequences and are released from the inner membrane. This system selects fusions that restore outer membrane localization to an amino terminal-truncated Yersinia pseudotuberculosis invasin derivative. In the present study, a variety of Salmonella typhimurium proteins that localize beyond the inner membrane were identified with gene fusions to this invasin derivative. Previously undescribed proteins identified include ones that share homology with components of fimbrial operons, multiple drug resistance efflux pumps and a haemolysin. All of the positive clones analysed contain cleavable signal sequences. Moreover, over 40% of the genes identified encode putative outer membrane proteins. This system has several features that may make it especially useful in the study of genetically intractable organisms.

Inhibition of Escherichia coli RecA coprotease activities by DinI

In Escherichia coli, the SOS response is induced upon DNA damage and results in the enhanced expression of a set of genes involved in DNA repair and other functions. The initial step, self-cleavage of the LexA repressor, is promoted by the RecA protein which is activated upon binding to single-stranded DNA. In this work, induction of the SOS response by the addition of mitomycin C was found to be prevented by overexpression of the dinI gene. dinI is an SOS gene which maps at 24.6 min of the E.coli chromosome and encodes a small protein of 81 amino acids. Immunoblotting analysis with anti-LexA antibodies revealed that LexA did not undergo cleavage in dinI-overexpressed cells after UV irradiation. In addition, the RecA-dependent conversion of UmuD to UmuD' (the active form for mutagenesis) was also inhibited in dinI-overexpressed cells. Conversely, a dinI-deficient mutant showed a slightly faster and more extensive processing of UmuD and hence higher mutability than the wild-type. Finally, we demonstrated, by using an in vitro reaction with purified proteins, that DinI directly inhibits the ability of RecA to mediate self-cleavage of UmuD.

Transient and heritable mutators in adaptive evolution in the lab and in nature

Major advances in understanding the molecular mechanism of recombination-dependent stationary-phase mutation in Escherichia coli occurred this past year. These advances are reviewed here, and we also present new evidence that the mutagenic state responsible is transient. We find that most stationary-phase mutants do not possess a heritable stationary-phase mutator phenotype, although a small proportion of heritable mutators was found previously. We outline similarities between this well-studied system and several recent examples of adaptive evolution associated with heritable mutator phenotype in a similarly small proportion of survivors of selection in nature and in the lab. We suggest the following: (1) Transient mutator states may also be a predominant source of adaptive mutations in these latter systems, the heritable mutators being a minority (Rosenberg 1997); (2) heritable mutators may sometimes be a product of, rather than the cause of, hypermutation that gives rise to adaptive mutations.

Mutagenesis and more: umuDC and the Escherichia coli SOS response

The cellular response to DNA damage that has been most extensively studied is the SOS response of Escherichia coli. Analyses of the SOS response have led to new insights into the transcriptional and post-translational regulation of processes that increase cell survival after DNA damage as well as insights into DNA-damage-induced mutagenesis, i.e., SOS mutagenesis. SOS mutagenesis requires the recA and umuDC gene products and has as its mechanistic basis the alteration of DNA polymerase III such that it becomes capable of replicating DNA containing miscoding and noncoding lesions. Ongoing investigations of the mechanisms underlying SOS mutagenesis, as well as recent observations suggesting that the umuDC operon may have a role in the regulation of the E. coli cell cycle after DNA damage has occurred, are discussed.

Adaptive mutation: has the unicorn landed?

Reversion of an episomal Lac- allele during lactose selection has been studied as a model for adaptive mutation. Although recent results show that the mutations that arise during selection are not "adaptive" in the original sense, the mutagenic mechanism that produces these mutations may nonetheless be of evolutionary significance. In addition, a transient mutational state induced in a subpopulation of starving cells could provide a species with a mechanism for adaptive evolution.

Spontaneous cAMP-dependent derepression of gene expression in stationary phase plays a role in recombinant expression instability

E. coli recombinant expression systems that utilize lac operon control elements to modulate gene expression are known to produce some amount of uninduced (leaky) gene expression. Previously, we showed that high levels of uninduced gene expression was a major cause of instability in the pET expression system. We show here that the pET system, in which the phage T7 RNA polymerase gene is expressed via lac operon control elements, exhibits leaky expression that increases markedly as cells grown in complex medium enter stationary phase. Moreover, we found that this phenomenon occurs with the chromosomal lac operon as well. Further investigation revealed that stationary phase leaky expression requires cyclic AMP, and that substantial leaky expression could be effected in log phase cells by adding cyclic AMP and acetate at pH6.0. Finally, a comparison of otherwise isogenic cya and wild-type hosts showed that expression stability and plasmid maintenance in the cya host is greatly enhanced, even when cells are passaged repeatedly in non-selection medium. These findings both provide a method to enhance the stability of lac-based recombinant expression systems, and suggest that derepression of the lac operon in the absence of inducer may be part of a general cellular response to nutrient limitation.

Catabolite repressors are potent antimutagens in Escherichia coli plate incorporation assays: experiments with glucose, glucose-6-phosphate and methyl-alpha-D-glucopyranoside

Having previously found that the yields of spontaneous valine-resistant (Val(r)) Escherichia coli mutants which appeared on plates containing 40 microg/ml of valine were always much lower when glucose was present in the glycerol-containing defined medium normally used to select them, we now sought to determine whether or not the global regulatory mechanism known as catabolite repression (formerly also called glucose repression) might be involved. We therefore tested glucose (the archetypal catabolite repressor), glycerol (a non catabolite-repressing substrate), glucose-6-phosphate (G6P, an exceptionally powerful catabolite repressor) and methyl-alpha-D-glucopyranoside (alphaMG, a strongly catabolite-repressing but non-utilisable glucose analogue), as potential inhibitors of spontaneous mutagenesis in plate incorporation assays, using three distinct mutation detection systems. We found that the numbers of spontaneous Val(r) and Lac+ mutations appearing on the selective plates tended to be highest when the medium contained only a non-repressing primary carbon source (glycerol in the Val(s) --> Val(r) system, lactose in the Lac- --> Lac+ system) and lowest when it had been supplemented with a strongly catabolite-repressing compound such as alphaMG, G6P or glucose. These results would seem to establish that catabolite repression is an important factor in determining the outcome of the spontaneous mutation generation process in E. coli and hence that the numbers of spontaneous mutations which can be expected to arise in any given set of mutation assay conditions may often be dependent upon the levels of catabolite repression which prevail during the course of the assay. The implications of these results for conventional plate-incorporation mutation assays are discussed.

Natural genetic transformation of Pseudomonas stutzeri in a non-sterile soil

Natural transformation of the soil bacterium Pseudomonas stutzeri JM300 in a non-sterile brown earth microcosm was studied. For this purpose, the microcosm was loaded with purified DNA (plasmid or chromosomal DNA, both containing a high-frequency-transformation marker, his+, of the P. stutzeri genome), the non-adsorbed DNA was washed out with soil extract and then the soil was charged with competent cells (his-1). Both chromosomal and plasmid transformants were found among the P. stutzeri cells recovered from the soil. The number of plasmid transformants increased in a linear fashion with the amount of DNA added [10-600 ng (0.7 g soil)-1]. The observed efficiency of transformation, the time course of transformant formation and the complete inhibition of transformation by DNase I, when added to the soil, were similar to that seen in optimized transformations in nutrient broth. Addition of cells as late as 3 d after loading the soil with plasmid DNA still yielded 3% of the initial transforming activity. This suggests that nucleases indigenous to the soil destroyed the transforming DNA, but at a rate allowing considerable DNA persistence. Transformants were also obtained when intact P. stutzeri cells were introduced into the soil to serve as plasmid DNA donors. Apparently, DNA was released from the cells, adsorbed to the soil material and subsequently taken up by recipient cells. The results indicate that competent cells of P. stutzeri were able to find access to and take up DNA bound on soil particles in the presence of micro-organisms and DNases indigenous to the soil.

Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA

dinP is an Escherichia coli gene recently identified at 5.5 min of the genetic map, whose product shows a similarity in amino acid sequence to the E. coli UmuC protein involved in DNA damage-induced mutagenesis. In this paper we show that the gene is identical to dinB, an SOS gene previously localized near the lac locus at 8 min, the function of which was shown to be required for mutagenesis of nonirradiated lambda phage infecting UV-preirradiated bacterial cells (termed lambdaUTM for lambda untargeted mutagenesis). A newly constructed dinP null mutant exhibited the same defect for lambdaUTM as observed previously with a dinB::Mu mutant, and the defect was complemented by plasmids carrying dinP as the only intact bacterial gene. Furthermore, merely increasing the dinP gene expression, without UV irradiation or any other DNA-damaging treatment, resulted in a strong enhancement of mutagenesis in F'lac plasmids; at most, 800-fold increase in the G6-to-G5 change. The enhanced mutagenesis did not depend on recA, uvrA, or umuDC. Thus, our results establish that E. coli has at least two distinct pathways for SOS-induced mutagenesis: one dependent on umuDC and the other on dinB/P.

Mutation for survival

Adaptive mutations appear in response to selection. In the best-studied system, the two most controversial issues were resolved this year. The mutations are neither Lamarckian nor a peculiarity of bacterial sex, as had been suggested. They occur genome-wide in a hypermutable subpopulation of stressed cells. Genomic 'hot' and 'cold' regions may explain previous failures to detect similar mutations in other systems and at other sites. Stationary phase specific limitation of mismatch repair has also been discovered.

Genetic requirements and mutational specificity of the Escherichia coli SOS mutator activity

To better understand the mechanisms of SOS mutagenesis in the bacterium Escherichia coli, we have undertaken a genetic analysis of the SOS mutator activity. The SOS mutator activity results from constitutive expression of the SOS system in strains carrying a constitutively activated RecA protein (RecA730). We show that the SOS mutator activity is not enhanced in strains containing deficiencies in the uvrABC nucleotide excision-repair system or the xth and nfo base excision-repair systems. Further, recA730-induced errors are shown to be corrected by the MutHLS-dependent mismatch-repair system as efficiently as the corresponding errors in the rec+ background. These results suggest that the SOS mutator activity does not reflect mutagenesis at so-called cryptic lesions but instead represents an amplification of normally occurring DNA polymerase errors. Analysis of the base-pair-substitution mutations induced by recA730 in a mismatch repair-deficient background shows that both transition and transversion errors are amplified, although the effect is much larger for transversions than for transitions. Analysis of the mutator effect in various dnaE strains, including dnaE antimutators, as well as in proofreading-deficient dnaQ (mutD) strains suggests that in recA730 strains, two types of replication errors occur in parallel: (i) normal replication errors that are subject to both exonucleolytic proofreading and dnaE antimutator effects and (ii) recA730-specific errors that are not susceptible to either proofreading or dnaE antimutator effects. The combined data are consistent with a model suggesting that in recA730 cells error-prone replication complexes are assembled at sites where DNA polymerization is temporarily stalled, most likely when a normal polymerase insertion error has created a poorly extendable terminal mismatch. The modified complex forces extension of the mismatch largely at the exclusion of proofreading and polymerase dissociation pathways. SOS mutagenesis targeted at replication-blocking DNA lesions likely proceeds in the same manner.

Viral spread within ageing bacterial populations

The viral spread within isolated host populations has been studied throughout the growth of P22-infected Salmonella cell colonies. By using an integration mutant of this bacteriophage, horizontal and vertical transmission have been analyzed independently. The data obtained show that both strategies are not simultaneous but consecutive during the colony development. Lytic cycles are tightly repressed during the exponential cell growth but stimulated in independent colonies with remarkable synchrony when the cell division rate decreases. The coincidence of the viral outburst and the decay of bacterial replicative fitness is a new example of the extreme viral competence in exploiting the host cells as dissemination vehicles for viral genomes.

Carbon starvation of Salmonella typhimurium does not cause a general increase of mutation rates

Mutation rates in bacteria can vary depending on the genetic target studied and the specific growth conditions of the cells. Here, two different methods were used to determine how rates of mutation to antibiotic resistance, auxotrophy, and prototrophy were influenced by carbon starvation on agar plates. The rate of mutation to rifampin resistance was increased by starvation as measured by fluctuation tests, similar to what has been reported previously for Escherichia coli. In contrast, the rates of mutation to various types of auxotrophy were unaffected or decreased as measured by both fluctuation tests and a repeated-streaking procedure. Similarly, the rates of reversion to prototrophy of his and lac nonsense and missense mutations were unaffected by starvation. Thus, mutation rates of different genetic targets can be affected differently by starvation and we conclude that carbon starvation is not generally mutagenic in Salmonella typhimurium.

A genetic strategy to demonstrate the occurrence of spontaneous mutations in nondividing cells within colonies of Escherichia coli

A genetic strategy was designed to examine the occurrence of mutations in stationary-phase populations. In this strategy, a parental population of cells is able to survive under both permissive and restrictive conditions whereas mutants at a particular target locus exhibit a conditional-lethal phenotype. Thus, by growing the population to stationary phase under restrictive conditions and then shifting it to permissive conditions, mutations that had arisen in stationary phase can be studied without confounding effects caused by the occurrence of similar mutations during growth of the population. In two different applications of this strategy, we have studied the reversion to Lac+ in stationary phase of several Lac- mutations in Escherichia coli. Our results indicate that a variety of spontaneous point mutations and deletions, particularly those that are sensitive to the mechanisms of replication slippage (for their generation) and methyl-directed mismatch repair (for their correction), can arise in nondividing populations of cells within a colony. The frequency of their occurrence was also elevated in mutS strains, which are defective in such mismatch repair. These data have relevance to the ongoing debate on adaptive or directed mutations in bacteria.

Genetic variability and adaptation to stress

Besides an immediate cellular adaptation to stress, organisms can resist such challenges through changes in their genetic material. These changes can be due to mutation or acquisition of pre-evolved functions via horizontal transfer. In this chapter we will review evidence from bacterial genetics that suggests that the frequency of such events can increase in response to stress by activating mutagenic response (e.g. the SOS response) and by inhibiting antimutagenic activities (e.g. mismatch repair system, MRS). Natural selection, by favoring adaptations, can also select for the mechanism(s) that has/have generated the adaptive changes by hitchhiking. These mutator mechanisms can sometimes respond very specifically, though blindly, to the challenge of the environment. Such stress-induced increases in mutation rates enhance genetic polymorphism, which is the structural component of the barrier to genetic exchange. Since SOS and MRS are the enzymatic controls of this barrier, the modulation of these systems can lead to a burst of speciation.

Mismatch repair protein MutL becomes limiting during stationary-phase mutation

Postsynthesis mismatch repair is an important contributor to mutation avoidance and genomic stability in bacteria, yeast, and humans. Regulation of its activity would allow organisms to regulate their ability to evolve. That mismatch repair might be down-regulated in stationary-phase Escherichia coli was suggested by the sequence spectrum of some stationary-phase ("adaptive") mutations and by the observations that MutS and MutH levels decline during stationary phase. We report that overproduction of MutL inhibits mutation in stationary phase but not during growth. MutS overproduction has no such effect, and MutL overproduction does not prevent stationary-phase decline of either MutS or MutH. These results imply that MutS and MutH decline to levels appropriate for the decreased DNA synthesis in stationary phase, whereas functional MutL is limiting for mismatch repair specifically during stationary phase. Modulation of mutation rate and genetic stability in response to environmental or developmental cues, such as stationary phase and stress, could be important in evolution, development, microbial pathogenicity, and the origins of cancer.

Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria

Speciation involves the establishment of genetic barriers between closely related organisms. The extent of genetic recombination is a key determinant and a measure of genetic isolation. The results reported here reveal that genetic barriers can be established, eliminated, or modified by manipulating two systems which control genetic recombination, SOS and mismatch repair. The extent of genetic isolation between enterobacteria is a simple mathematical function of DNA sequence divergence. The function does not depend on hybrid DNA stability, but rather on the number of blocks of sequences identical in the two mating partners and sufficiently large to allow the initiation of recombination. Further, there is no obvious discontinuity in the function that could be used to define a level of divergence for distinguishing species.

Mutation in Escherichia coli under starvation conditions: a new pathway leading to small deletions in strains defective in mismatch correction

Strains of Escherichia coli carrying the mutY mutation lack a mismatch correction glycosylase that removes adenines from various mismatch situations. In growing bacteria, 8-oxoguanine-adenine mispairs persist and can give rise to G-->T transversions during subsequent replication cycles. We now show that when trpA23 mutY bacteria are held under tryptophan starvation conditions the tryptophan-independent mutants that arise include small in-frame deletions in addition to transversions. The trpA23 reversion system appears to be unusual in that small in-frame deletions occurring in a particular region of the gene can lead to the production of a functional protein. We suggest that this is a consequence of the deletion causing the polar group on the arginine at the trpA23 site to be pulled away from the active site of the enzyme. Such deletions are also found with starved bacteria defective in methyl-directed mismatch correction activity (mutH, mutL or mutS), and deletion mutations are also found among the much lower number of mutants that arise in bacteria wild-type for mismatch correction. There is thus a pathway, hitherto undetected, leading to deletions probably from mismatches under conditions of growth restraint. RecA, UmuC, UvrA, MutH,L,S, SbcC and SbcD proteins are not required for the operation of the deletion pathway. A possible explanation is that the deletion pathway is not dependent upon further replication and that it fails to be discernible in growing cells because it is relatively slow acting and mismatches are likely to encounter a DNA replication fork before the initial step of the deletion pathway.