The origin of mutants

A constant rate of spontaneous mutation in DNA-based microbes

In terms of evolution and fitness, the most significant spontaneous mutation rate is likely to be that for the entire genome (or its nonfrivolous fraction). Information is now available to calculate this rate for several DNA-based haploid microbes, including bacteriophages with single- or double-stranded DNA, a bacterium, a yeast, and a filamentous fungus. Their genome sizes vary by approximately 6500-fold. Their average mutation rates per base pair vary by approximately 16,000-fold, whereas their mutation rates per genome vary by only approximately 2.5-fold, apparently randomly, around a mean value of 0.0033 per DNA replication. The average mutation rate per base pair is inversely proportional to genome size. Therefore, a nearly invariant microbial mutation rate appears to have evolved. Because this rate is uniform in such diverse organisms, it is likely to be determined by deep general forces, perhaps by a balance between the usually deleterious effects of mutation and the physiological costs of further reducing mutation rates.

On the origins of genetic variants

Two contrasting mechanisms responsible for the creation of genetic variants are described: one is the manifestation of the limited accuracy of the cellular machinery for DNA replication, the other results from the ability of cells to repair damaged DNA. Replication-dependent variants and those caused by episodical DNA damage enhance the probability that a small fraction of a cell population may survive a sudden (physical or biological) change of environmental conditions. Replication-independent variants arise during persistent but not immediately lethal stress (e.g. starvation) of a non-dividing population. The variants observed under these conditions are of selective advantage because they are able to cope with the particular stress situation. The molecular basis of their creation is a matter of intensive debate.

Adaptive evolution that requires multiple spontaneous mutations: mutations involving base substitutions

A previous study has demonstrated that adaptive missense mutations occur in the trp operon of Escherichia coli. In this study it is shown that, under conditions of intense selection, a strain carrying missense mutations in both trpA and trpB reverts to Trp+ 10(8) times more frequently than would be expected if the two mutations were the result of independent events. Comparison of the single mutation rates with the double mutation rate and information obtained by sequencing DNA from double revertants show that neither our classical understanding of spontaneous mutation processes nor extant models for adaptive mutations can account for all of the observations. Despite a current lack of mechanistic understanding, it is clear that adaptive mutations can permit advantageous phenotypes that require multiple mutations to arise and that they appear enormously more frequently than would be expected.

Tandem duplications of the lac region of the Escherichia coli chromosome

Tandem duplications are caused by unequal crossing over between homologous sequences. Duplications in the lac region of the Escherichia coli chromosome were isolated by two methods. Duplication frequency using a method involving P1 transduction increased from 0.4% with no UV to 2.0% following UV irradiation at 35 J/m2. Duplication frequency in lac using a second generalizable method that does not involve P1 transduction increased from 0.7 to 12% at 35 J/m2 UV. In both cases the duplication frequency began to plateau at UV doses of 12 J/m2 and 24 J/m2. According to segregation analysis of sixteen duplications there may be at least seven classes of duplications isolated by each method. Pulsed-field gel electrophoresis was used to measure the duplications isolated without P1 transduction. The minimum size of the duplications ranged from 30 to 320 kb but could be much larger.

Increased spontaneous mutation and alkylation sensitivity of Escherichia coli strains lacking the ogt O6-methylguanine DNA repair methyltransferase

Escherichia coli expresses two DNA repair methyltransferases (MTases) that repair the mutagenic O6-methylguanine (O6MeG) and O4-methylthymine (O4MeT) DNA lesions; one is the product of the inducible ada gene, and here we confirm that the other is the product of the constitutive ogt gene. We have generated various ogt disruption mutants. Double mutants (ada ogt) do not express any O6MeG/O4MeT DNA MTases, indicating that Ada and Ogt are probably the only two O6MeG/O4MeT DNA MTases in E. coli. ogt mutants were more sensitive to alkylation-induced mutation, and mutants arose linearly with dose, unlike ogt+ cells, which had a threshold dose below which no mutants accumulated; this ogt(+)-dependent threshold was seen in both ada+ and ada strains. ogt mutants were also more sensitive to alkylation-induced killing (in an ada background), and overexpression of the Ogt MTase from a plasmid provided ada, but not ada+, cells with increased resistance to killing by alkylating agents. The induction of the adaptive response was normal in ogt mutants. We infer from these results that the Ogt MTase prevents mutagenesis by low levels of alkylating agents and that, in ada cells, the Ogt MTase also protects cells from killing by alkylating agents. We also found that ada ogt E. coli had a higher rate of spontaneous mutation than wild-type, ada, and ogt cells and that this increased mutation occurred in nondividing cells. We infer that there is an endogenous source of O6MeG or O4MeT DNA damage in E. coli that is prevalent in nondividing cells.

On the dependence of spontaneous mutation rates on the functional state of genes

Spontaneous mutation of some genes was studied in haploid adenine and leucine auxotrophic yeast Saccharomyces. It was shown that a decrease in the amount of adenine (from 500 to 0 mg l-1) or leucine (from 300 to 0.3 mg l-1) in the medium, simultaneously with the transition from repression to derepression of the biosynthesis of these metabolites, resulted in a 15- to 150-fold increase in the reversion rate of genes ade 2 and leu2, respectively, for different strains. At the same time the mutation rate of suppressor genes varied relatively little (up to five-fold), and that of gene lys did not change at all. It was also demonstrated (on gene leu2) that the mutation rate is determined by the composition of the nutrient medium at the time of the S-phase of the cell cycle and it does not depend on the cultivation conditions during the presynthetic period. We discuss the hypothesis that derepressed genes mutate with a significantly higher rate than genes in the repressed state.

Properties of plasmids responsible for production of extended-spectrum beta-lactamases

The extended-spectrum beta-lactamases are believed to arise by mutations which alter the configuration around the active site of TEM- and SHV-type enzymes so as to increase their efficiency with otherwise nonhydrolyzable cephalosporins and monobactams. This hypothesis predicts that the genes for these new enzymes should be found on the same wide variety of plasmids that encode TEM-1, TEM-2, and SHV-1 beta-lactamases and that at least some of them should be mediated by transposons. Fifteen plasmids, each encoding an extended-spectrum beta-lactamase, were examined. Unlike the average TEM plasmid, all were large, ranging in size from 80 to 300 kb. All determined resistance to multiple antimicrobial agents, ranging from 5 to 11, and some conferred resistance to heavy metals and UV radiation as well. The plasmids belonged to a limited number of incompatibility (Inc) groups, including IncC, IncFI, IncHI2, and IncM. Because most of the mutations giving rise to extended-spectrum activity are G.C----A.T transitions and some of the mutant genes have as many as four base substitutions, a plasmid-determined mutator gene was searched for, but no such property was found. Several techniques were used to detect transposition of the extended-spectrum beta-lactamase genes, but a mobile genetic element could not be demonstrated even though eight of the plasmids hybridized with a DNA probe derived from the tnpR gene of Tn3. The genesis of extended-spectrum beta-lactamases may not be as simple as has been supposed.

msDNA of bacteria

The msDNA-retron element represents the first prokaryotic member of the large and diverse retroelement family found in many eukaryotic genomes (Table II). This prokaryotic retroelement exists as a single copy element in the chromosome of two different bacterial groups: the common soil microbe M. xanthus and the enteric bacterium E. coli. It encodes an RT similar to the polymerases found in retroviruses, containing most of the strictly conserved amino acids found in all RTs. The RT is responsible for the production of an unusual extrachromosomal RNA-DNA molecule known as msDNA. Each composed of a short single strand of RNA and a short single strand of DNA, msDNAs vary considerably in their primary nucleotide sequences, but all share certain secondary structural features, including the unique 2',5' branch linkage that joins the 5' end of the DNA chain to the 2' position of an internal guanosine residue of the RNA strand. It is proposed that msDNA is synthesized by reverse transcription of a precursor RNA transcribed from a region of the retron containing the genes msr (encoding the RNA portion) and msd (encoding the DNA portion) and the ORF (encoding the RT). The precursor RNA transcript folds into a stable secondary structure that serves as both the primer and the template for the synthesis of msDNA. The msDNA-retron elements of E. coli are found in less than 10% of all strains observed, are heterogeneous in nature, and have an atypical aminoacid codon usage for this species, suggesting that this element was transmitted to E. coli by some other source. The presence of directly repeated 26-base-pair sequences flanking the junctions of the Ec67-retron of E. coli also suggests that it may be a mobile element. However, the msDNA-retrons of M. xanthus appear to be as old as other genes native to this species, based on codon-usage data for the RT genes and the fact that every strain of M. xanthus appears to have the same type of msDNA. If the msDNA-retron element originated with the myxobacteria, it would place the existence of retrons before the appearance of eukaryotic cells, suggesting that the bacterial element is perhaps the ancestral gene from which eukaryotic retroviruses and other retroelements evolved.(ABSTRACT TRUNCATED AT 400 WORDS)

Organization of the bacterial chromosome

Recent progress in studies on the bacterial chromosome is summarized. Although the greatest amount of information comes from studies on Escherichia coli, reports on studies of many other bacteria are also included. A compilation of the sizes of chromosomal DNAs as determined by pulsed-field electrophoresis is given, as well as a discussion of factors that affect gene dosage, including redundancy of chromosomes on the one hand and inactivation of chromosomes on the other hand. The distinction between a large plasmid and a second chromosome is discussed. Recent information on repeated sequences and chromosomal rearrangements is presented. The growing understanding of limitations on the rearrangements that can be tolerated by bacteria and those that cannot is summarized, and the sensitive region flanking the terminator loci is described. Sources and types of genetic variation in bacteria are listed, from simple single nucleotide mutations to intragenic and intergenic recombinations. A model depicting the dynamics of the evolution and genetic activity of the bacterial chromosome is described which entails acquisition by recombination of clonal segments within the chromosome. The model is consistent with the existence of only a few genetic types of E. coli worldwide. Finally, there is a summary of recent reports on lateral genetic exchange across great taxonomic distances, yet another source of genetic variation and innovation.

Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli

Multicopy single-stranded DNA (msDNA), a branched DNA-RNA molecule, has been shown in Escherichia coli B and clinical strain Cl-1 to be synthesized by reverse transcriptase. We report that 13% of the strains of the ECOR collection, a sample of 72 E. coli isolates representing the breadth of genetic variation of the species, produce msDNA. Three of the four major subspecific groups include msDNA-producing strains. Screening of 25 isolates that are genetically related to msDNA-producing clinical strains uncovered 22 additional msDNA-producing strains. A phylogenetic tree based on allelic variation detected electrophoretically at 20 enzyme-encoding loci revealed two major clusters and several deep branches composed of strains that synthesize msDNA. Although E. coli K-12 does not harbor msDNA, other closely related strains of the K-12 family do. The results support the hypothesis that msDNA-synthesizing systems, including reverse transcriptase genes, were acquired recently and independently in different lineages of E. coli.

The efficiency of antibody affinity maturation: can the rate of B-cell division be limiting?

It has been known for many years that the affinity of antibodies for antigen increases with time during an immune response. It is now clear that two processes play fundamental roles in this affinity 'maturation' in the mouse - V gene somatic mutation and antigen affinity-based selection. Exactly how these two processes work in concert is not fully understood. In this article Tim Manser argues that models of affinity maturation based on the assumption that somatic mutation, antigen selection and B-cell division are interdependent may not explain the high efficiency of the process, and he suggests an alternative model.

surA, an Escherichia coli gene essential for survival in stationary phase

Mutations in genes not required for exponential growth but essential for survival in stationary phase were isolated in an effort to understand the ability of wild-type Escherichia coli cells to remain viable during prolonged periods of nutritional deprivation. The phenotype of these mutations is referred to as Sur- (survival) and the genes are designated sur. The detailed analysis of one of these mutations is presented here. The mutation (surA1) caused by insertion of a mini-Tn10 element defined a new gene located near 1 min on the E. coli chromosome. It was located directly upstream of pdxA and formed part of a complex operon. Evidence is presented supporting the interpretation that cells harboring the surA1 mutation die during stationary phase while similar insertion mutations in other genes of the operon do not lead to a Sur- phenotype. Strains harboring surA1 had a normal doubling time in both rich and minimal medium, but cultures lost viability after several days in stationary phase. Analysis of revertants and suppressors of surA1, which arose after prolonged incubation in stationary phase, indicates that DNA rearrangements (excisions and duplications) occurred in cultures of this strain even when the viable-cell counts were below 10(2) cells per ml. Cells containing suppressing mutations then grew in the same culture to 10(8) cells per ml, taking over the population. The implications of these observations to our understanding of stationary-phase mutagenesis are discussed.

The significance of biological heterogeneity

Heterogeneity of expression for a variety of characteristics is found among malignant cells in the organism and in culture. Normal cells are relatively uniform when organized in a tissue, but become heterogeneous for many characteristics when they are dispersed and grown in monolayer culture. The heterogenizing effect of growth in culture indicates that the morphology and behavior of normal cells is ordered by their topological relations in tissues and other homeostatic influences of the organism. Weakening of these ordering relations may contribute to malignant transformation, as it usually does in rodent cell culture. Although phenotypic differences among cells of a given type may be transient, they can be perpetuated by protracted exposure to selective conditions. Examples are cited of selection which leads to an adapted state that is heritable for many cell generations after removal of the selective conditions. Such heritable adaptations are analogous to the Dauermodifikationen, or lingering changes, first described in ciliated protozoa and shown there to be under cytoplasmic control. The concept of progressive state selection is introduced to account for heritable adaptation at the cellular level. It depends on the spontaneous occurrence of transient, variant states and their successive selection to progressively higher levels of adaptation to an altered microenvironment. Although the process is basically epigenetic, it may be stabilized by genetic change. The concept is consistent with our present knowledge of tumor development, including progression to metastasis, and with epigenetic aspects of normal development.

The RecE recombination pathway mediates recombination between partially homologous DNA sequences: structural analysis of recombination products

Escherichia coli generalized recombination, utilizing the RecA RecB recombination pathway, requires large stretches (70-200 bp) of complete DNA sequence homology. In contrast, we have found that the RecE pathway can promote recombination between DNA with only short stretches of homology. A plasmid containing 10 partially homologous direct repeats was linearized by digestion with specific restriction enzymes. After transformation, a RecE+ (sbcA) host was able to circularize the plasmid by recombination between partially homologous direct repeat sequences. Recombination occurred in regions of as little as 6 bp of perfect homology. Recombination was enhanced in the regions adjacent to restriction sites used to linearize the plasmid, consistent with a role of double-strand breaks in promoting recombination. A mechanism is proposed in which the 5' exonuclease, ExoVIII, produces 3' single-stranded ends from the linearized plasmid. These pair with other sequences of partial homology. Partial homologies in the sequences flanking the actual join serve to stabilize this recombination intermediate. Recombination is completed by a process of "copy and join." This recombination mechanism requires less homology to stabilize intermediates than the degree of homology needed for mechanisms involving strand invasion. Its role in nature may be to increase genomic diversity, for example, by enhancing recombination between bacteriophages and regions of the bacterial chromosome.

Mechanism for induction of adaptive mutations in Escherichia coli

When bacterial cells are subjected to a strong selective pressure it often induces specific mutations. Here a model is considered in which errors are introduced at random in one of the strands of the DNA molecule: a nick in one of the strands can initiate strand displacement rendering a region of the chromosome single-stranded. Upon conversion back to double-stranded DNA there is a certain probability of introducing errors creating a heteroduplex. If an error results in the production of an mRNA molecule encoding a product which provides a selective advantage, growth will be stimulated and the mutation can be immortalized by chromosomal replication. Otherwise, the error can be corrected by the DNA 'proof-reading' enzymes.

New data on excisions of Mu from E. coli MCS2 cast doubt on directed mutation hypothesis

According to the directed mutation hypothesis, certain mutations in bacteria occur more frequently in environments in which the resulting phenotype is selectively favoured than in non-selective environments. This hypothesis therefore challenges the fundamental tenet that mutations occur spontaneously, irrespective of effects on the organism's fitness. One purported case of directed mutation is the excision of a Mu sequence from Escherichia coli strain MCS2 in minimal lactose-arabinose medium. Here, we show that this case can be more simply explained by an accelerated rate of excision mutation in response to non-specific physiological stresses of starvation and by slight growth of MCS2 on minimal lactose-arabinose medium.

Phenotypic drift inBradyrhizobium japonicum populations after introduction into soils as established by numerical analysis

The degree of phenotypic variation of the bacterial strains USDA 125-Sp, USDA 138 and USDA 138-SmBradyrhizobium japonicum a long time after introduction was studied in three experimental fields. A total of 54 phenotypic characters were analyzed by constructing a dendrogram based on an hierarchic classification. Strong similarities (92.6, 94 and 95%) were found between the isolates introduced into soil 8, 10 and 13 years ago and between their respectiveB. japonicum parental clones. The dendrogrammic analysis detected a small amount of phenotypic drift, however, between soil isolates and parental clones belonging to the same serogroup (selective effects were found to have generated 0 to 3.9% variation for the USDA 125-Sp inoculum introduced 8 years ago, and 3.2-3.5% after 10 and 13 years, respectively, for the USDA 138 and USDA 138-Sm bacterial inocula) and within the serogroup 125 soil isolates (2.7%). We found a similar evolution of serogroup 125 isolates when compared with parental clones conserved on slant agar at 4°C. When a drift was observed, the isolates from soil presented a lower activity for several enzymes and lower diversity compared with the parental clones.

The biological equilibrium of base pairs

An inherent feature of double-stranded DNA is the possible replacement of any base pair by another one upon replication. A replication-dependent substitution mutation of a matched base pair requires the temporary formation of a mismatched base pair (mispair). A functionally complementary pair of mispairs is ascribed to each of the four types of substitution mutations. Provided that all types of mispairs can be formed, a dynamic biological equilibrium between the four matched base pairs must exist in all DNA, which is directly related to the formation and stability of the corresponding eight mispairs in vivo. Each nucleotide position in a genome can therefore be described as a system of six dynamic equilibria between the four matched base pairs. After a sufficient number of replications, these equilibrium states will express an overall mutation-selection balance for each individual base pair. In a thermodynamic context, the mispairs represent intermediate states on the transformation pathways between the matched base pairs. Catalysts change the stability and probability of formation of intermediate states. Mutagenic proteins are proposed as hypothetical substitution mutation catalysts in vivo. Functionally, they would be capable of recognizing a particular DNA sequence, tautomerizing a nucleotide base thereof, and hence efficiently inducing a specific misincorporation. Phenomenologically such catalysts would accelerate the rates of substitution mutations and provide pathways for directional mutation pressure.

Mycoplasma pulmonis V-1 surface protein variation: occurrence in vivo and association with lung lesions

The V-1 antigen of Mycoplasma pulmonis is exposed to the surface of the mycoplasma and has an immunoblot banding pattern that varies in vitro between and within strains. To determine if V-1 variation occurs in vivo, we infected C3H/HeNCr mice intranasally with 5 X 10(8) colony-forming units of M. pulmonis strain 5782C. We isolated M. pulmonis clones from the respiratory tracts of mice up to 28 days post-infection, then used anti-V-1 monoclonal antibody P39 to visualize their V-1 immunoblot banding patterns. By the 28th day following infection, 92% of the recovered clones had variant V-1 banding patterns. Additionally, there was a significant correlation between the severity of lung lesions and the percentage of V-1 variant clones recovered from the respiratory tracts of individual mice. These studies prove that V-1 variation does occur in vivo, and suggest that mice with more severe pulmonary lesions tend to have more V-1 variant clones as a percentage of the M. pulmonis population. Thus, variation in the V-1 protein may be a mechanism by which M. pulmonis persists in the in vivo environment, possibly by evasion of host immune surveillance or by alteration of its surface membrane to take better advantage of its environmental niche in the host.

Differential activity of a transposable element in Escherichia coli colonies

In Escherichia coli colonies, patterns of differential gene expression can be visualized by the use of Mu d(lac) fusion elements. Here we report that patterned beta-galactosidase expression in colonies of strain MS1534 resulted from a novel mechanism, spatially localized replication of the Mu dII1681 element causing lacZ transposition to active expression sites. Mu dII1681 replication did not occur constitutively with a fixed probability but was dependent on the growth history of the bacterial population. The bacteria in which Mu dII1681 replication and lacZ transposition had occurred could no longer form colonies. These results lead to several interesting conclusions about cellular differentiation during colony development and the influence of bacterial growth history on gene expression and genetic change.

Herpes simplex virus and the rheumatic diseases

A viral aetiology for rheumatoid arthritis and inflammatory connective tissue diseases has been sought in general terms first, by studying viral growth patterns in lymphocytes from the blood and lesions of patients affected second, by analysing lymphocyte concentrations of the interferon-induced enzyme 2-5 oligo-adenylate synthetase (2-5 A); and third, by probing Southern blots of lymphocyte DNA with viral probes. Indirect evidence consistent with a viral aetiology has been found in several such diseases, but direct proof has been difficult to adduce. There is some suggestion that herpes simplex viral (HSV) DNA is present in Behcet's blood lymphocytes, but the findings are inconsistent. It is also plausible that viruses such as HSV do not induce these diseases through classic immunopathological mechanisms, but as "promoters" of abnormal lymphoproliferation in individuals with predisposing defects, possibly related to selective DNA repair defects.

Analysis of relative reversion frequencies for IS2 insertion mutations in the regulatory region of the galOPETK operon of Escherichia coli

Two previously characterized mutations in the galOPETK operon of Escherichia coli, galOP-3 and galOPE-490, contain IS2 insertions only 1 bp apart in the gal regulatory region; yet only the former yields Gal+ phenotypic revertants at a detectable frequency. We have shown that the galOPE-490 allele comprises two mutations--an IS2(I) insertion at bp+(2-6) (relative to the gal mRNA start site) plus a C/G to A/T transversion at bp + 59. The latter creates an ochre stop codon and lies within the internal site of the bipartite gal operator; it acts as an operator mutation in an in vivo repressor titration assay. Analysis of a newly isolated allele (galOP-490*) which retains the IS2 of galOPE-490 but is galE+ reveals a reversion frequency approximately 30-fold higher than that of galOP-3. Reversion of galOPE-490 is at least 10,000-fold lower and has not been detectable even under conditions conducive to enhanced double mutations in other systems.

Ability to perceive androstenone can be acquired by ostensibly anosmic people

Nearly half the adult human population does not perceive an odor when sniffing androstenone (5 alpha-androst-16-en-3-one), a volatile steroid found in human perspiration, boar saliva, some pork products (e.g., bacon), truffles, and celery. This variation in ability to perceive androstenone has a significant heritable component, suggesting that androstenone insensitivity is in part determined genetically. We now report that the ability to perceive androstenone was induced in 10 of 20 initially insensitive subjects who were systematically exposed to androstenone. Since olfactory neurons of the olfactory epithelium undergo periodic replacement from differentiating basal cells, and assuming the induction of sensitivity to be peripheral, we propose that a portion of the apparently anosmic human population does in fact possess olfactory neurons with specific receptors for androstenone. Such neurons may undergo clonal expansion, or selection of lineages with more receptors or receptors of higher affinity, in response to androstenone stimulation, much in the manner of lymphocytes responding to antigenic stimulation, thus raising odor stimulation to the level of conscious perception. As a guide to further study of the genetics and mechanism of variation of androstenone perception, we provisionally envisage three categories of human subjects, the truly anosmic, the inducible, and those subjects who either are constitutionally sensitive or have already experienced incidental induction.

The inheritance of acquired epigenetic variations

There is evidence that the functional history of a gene in one generation can influence its expression in the next. In somatic cells, changes in gene activity are frequently associated with changes in the pattern of methylation of the cytosines in DNA; these methylation patterns are stably inherited. Recent work suggests that information about patterns of methylation and other epigenetic states can also be transmitted from parents to offspring. This evidence is the basis of a model for the inheritance of acquired epigenetic variations. According to the model, an environmental stimulus can induce heritable chromatin modifications which are very specific and predictable, and might result in an adaptive response to the stimulus. This type of response probably has most significance for adaptive evolution in organisms such as fungi and plants, which lack distinct segregation of the soma and germ line. However, in all organisms, the accumulation of specific and random chromatin modifications in the germ line may be important in speciation, because these modifications could lead to reproductive isolation between populations. Heritable chromatin variations may also alter the frequency and distribution of classical mutations and meiotic recombination. Therefore, inherited epigenetic changes in the structure of chromatin can influence neo-Darwinian evolution as well as cause a type of "Lamarckian" inheritance.

Transcriptional bias: a non-Lamarckian mechanism for substrate-induced mutations

In bacterial cultures in the stationary phase, substrates can selectively stimulate mutations that lead to their own utilization, but because of apparent conflict with the neo-Darwinian view of evolution the phenomenon has encountered widespread resistance. Building on further evidence for this process, Cairns et al. [Cairns, J., Overbaugh, J. & Miller, S. (1988) Nature (London) 335, 142-145] have suggested a Lamarckian mechanism of directed mutation. This paper proposes an alternative mechanism: transcription induced by the substrate introduces a bias in the random process of mutation, because the resulting single-stranded regions of DNA are more mutable. This stimulation of adaptive mutations by the environment has implications for evolution similar to those of directed mutation, but without contradicting the central "dogma" of molecular genetics. In addition, in eukaryotic cells a mutagenic effect of induction on protooncogenes could contribute to the stimulatory effect of proliferation on carcinogenesis.

Genetic and physiological relationships among the miaA gene, 2-methylthio-N6-(delta 2-isopentenyl)-adenosine tRNA modification, and spontaneous mutagenesis in Escherichia coli K-12

The miaA tRNA modification gene was cloned and located by insertion mutagenesis and DNA sequence analysis. The miaA gene product, tRNA delta 2-isopentenylpyrophosphate (IPP) transferase, catalyzes the first step in the biosynthesis of 2-methylthio-N6-(delta 2-isopentenyl)-adenosine (ms2i6A) adjacent to the anticodon of several tRNA species. The translation start of miaA was deduced by comparison with mod5, which encodes a homologous enzyme in yeasts. Minicell experiments showed that Escherichia coli IPP transferase has a molecular mass of 33.5 kilodaltons (kDa). Transcriptional fusions, plasmid and chromosomal cassette insertion mutations, and RNase T2 mapping of in vivo miaA transcription were used to examine the relationship between miaA and mutL, which encodes a polypeptide necessary for methyl-directed mismatch repair. The combined results showed that miaA, mutL, and a gene that encodes a 47-kDa polypeptide occur very close together, are transcribed in the same direction in the order 47-kDa polypeptide gene-mutL-miaA, and likely form a complex operon containing a weak internal promoter. Three additional relationships were demonstrated between mutagenesis and the miaA gene or ms2i6A tRNA modification. First, miaA transcription was induced by 2-aminopurine. Second, chromosomal miaA insertion mutations increased the spontaneous mutation frequency with a spectrum distinct from mutL mutations. Third, limitation of miaA+ bacteria for iron, which causes tRNA undermodification from ms2i6A to i6A, also increased spontaneous mutation frequency. These results support the notion that complex operons organize metabolically related genes whose primary functions appear to be completely different. In addition, the results are consistent with the idea that mechanisms exist to increase spontaneous mutation frequency when cells need to adapt to environmental stress.

Properties of genetic instability during the vegetative growth of Coprinus radiatus

In Coprinus radiatus, a mutation at the Nic-2 locus unstable at meiosis has been previously described. Further studies have now shown that this mutation is also unstable, although with lower frequency, during vegetative growth. This 'vegetative instability', which is thermosensitive, is not a random process but an aggregative process, perhaps depending on the physiological state of the mycelium.

The nature of spontaneous mutations

The induction of mutations is often expressed in relation to spontaneous mutations and designated for instance by the doubling-dose concept. A problem in that context is the fact that the mutational spectrum for spontaneous and induced mutations is not the same and it can furthermore vary considerably between loci. This is illustrated by molecular characterization of spontaneous and ionizing-radiation-induced mutations in mammalian cells. Furthermore changes of the genetic machinery are not limited to those endpoints usually measured in mutational assays, that is, base substitutions, frameshifts, classical chromosomal aberrations and numerical alterations of chromosomes. Additional alterations, of which far less is known, include insertion mutations, recombinogenic events and disproportionate replication of DNA giving rise to gene amplifications, and changes of gene expression through methylation of cytosine. There are reasons to believe that these endpoints are of importance in the development of tumors. Amplification of oncogenes is a well-known phenomenon in tumorigenicity and lately mutations by the insertion of mobile DNA elements have been demonstrated in cancer cells. Often these alterations are induced by stress and they constitute a manifestation of the dynamics and instability of DNA and the genetic system revealed in recent years. It is of interest in that context that the flow of genetic information does not only occur in one direction that is, DNA-RNA-protein, but also from RNA to DNA through reverse transcription and possibly even from the protein end of the sequence.

Mutation and selection in bacterial populations: alternatives to the hypothesis of directed mutation

Bacterial populations have served as model systems for studying evolutionary processes ever since the classic experiments of Luria and Delbrück, which demonstrated the occurrence of mutations prior to selection for the traits they conferred. However, several authors have recently presented experiments suggesting that bacteria may have mechanisms for directing which mutations occur, such that the rate of adaptive mutations is enhanced. Before the hypothesis of directed mutation is accepted, it is imperative to consider alternative hypotheses that might account for the same observations. To this end, we expand upon existing mathematical theory of the dynamics of mutation and selection in clonal populations for two cases of particular interest. The first case concerns selection against mutants before plating; this selection occurs as the result of differences in growth rate between mutants and nonmutants. We demonstrate that this selection model gives rise to distributions of mutants, obtained by plating from sister cultures, that are very similar to those expected when some mutations are induced by the selective environment. The second case concerns the sequential incorporation of two mutations as the result of selection for an intermediate genotype after plating. We demonstrate that this two-step mutation model also yields distributions that are similar to those expected when some mutations are induced by the selective environment. These two cases therefore provide alternatives to the hypothesis of directed mutation. We suggest experiments that might be used to examine our alternative hypotheses. We also contrast the hypothesis of directed mutation with the notion of inheritance of acquired characteristics.