A colicin-tolerant mutant of Escherichia coli with reduced levels of cyclic AMP and a strong bias towards lambda lysogeny

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Colorado River near Rifle, CO. Virus abundance ranged from 8.0 × 104 to 1.0 × 106 mL-1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 104 to 6.1 × 105 mL-1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to understand subsurface biogeochemical cycling and contaminant mobility.

Correlation between viral production and carbon mineralization under nitrate-reducing conditions in aquifer sediment

A variety of microbially mediated metabolic pathways impact biogeochemical cycling in terrestrial subsurface environments. However, the role that viruses have in influencing microbial mortality and microbial community structure is poorly understood. Here we investigated the production of viruses and change in microbial community structure within shallow alluvial aquifer sediment slurries amended with (13)C-labeled acetate and nitrate. Biostimulation resulted in production of viruses concurrent with acetate oxidation, (13)CO2 production and nitrate reduction. Interestingly, change in viral abundance was positively correlated to acetate consumption (r(2)=0.6252, P<0.05) and (13)CO2 production (r(2)=0.6572, P<0.05); whereas change in cell abundance was not correlated to acetate consumption or (13)CO2 production. Viral-mediated cell lysis has implications for microbial community structure. Betaproteobacteria predominated microbial community composition (62% of paired-end reads) upon inoculation but decreased in relative abundance and was negatively correlated to changes in viral abundance (r(2)=0.5036, P<0.05). As members of the Betaproteobacteria decreased, Gammaproteobacteria, specifically Pseudomonas spp., increased in relative abundance (82% of paired-end reads) and was positively correlated with the change in viral abundance (r(2)=0.5368, P<0.05). A nitrate-reducing bacterium, Pseudomonas sp. strain Alda10, was isolated from these sediments and produced viral-like particles with a filamentous morphology that did not result in cell lysis. Together, these results indicate that viruses are linked to carbon biogeochemistry and community structure in terrestrial subsurface sediments. The subsequent cell lysis has the potential to alter available carbon pools in subsurface environments, additionally controlling microbial community structure from the bottom-up.

Relationship between cellular RecA protein concentration and untargeted mutagenesis in Escherichia coli

We measured the production of untargeted mutations in the cI and cII genes of untreated lambda phage undergoing a lytic cycle in UV-irradiated bacterial hosts. As previously shown, treatment with 4 micrograms/ml of rifampicin during post-irradiation incubation inhibited amplification of the RecA protein in these cells. In addition, we observed a decreased mutation rate compared to the untreated, irradiated bacteria. Treatment with 4 micrograms/ml or 8 micrograms/ml rifampicin did not prevent the UV induction of the umuDC operon, as judged by assay of beta-galactosidase activity in a umuC-lacZ fusion strain. In contrast, the UV-induction of beta-galactosidase in the sulA-lacZ fusion strain was decreased by 4 micrograms/ml rifampicin. The inhibition of untargeted mutagenesis by this drug treatment was also observed in a strain constitutive for SOS functions (lexA (Def)) as well as in a RecA-overproducing plasmid strain, suggesting the requirement of other factor(s) in wild-type recA+ cells. An htpR165-carrying strain, that blocks induction of heat-shock proteins, exhibited normal UV-promoted mutagenesis. A correlation was observed between the cellular concentration of RecA protein, increased spontaneously by a temperature shift in a lexA(Ts) strain, and the extent of UV-promoted untargeted mutagenesis. These results suggest a mechanistic role of RecA protein in this process.

Genetic analysis of clear-plaque mutations induced in bacteriophage lambda by 9-aminoacridine

Clear-plaque mutations were induced in the cI and cII genes of lambda by treating lysogenic cells with 9-aminoacridine (9AA). Mapping of the mutations revealed that there were two hot spots for 9AA mutagenesis in cI, and one strong hot spot in cII. The hot spots in cI mapped close to 1 of the 3 runs of 4 G/C base-pairs and near the only run of 5 G/Cs, respectively, in this gene. Of 36 cI mutations tested, at most one mapped near a run of 6 A/T base-pairs. By analogy, the sequence responsible for the strong hot spot in cII may be the run of 6 G/Cs in this gene.

Methodologies for the determination of various genetic effects in permeable strains of E. coli K-12 differing in DNA repair capacity. Quantification of DNA adduct formation, experiments with organ homogenates and hepatocytes, and animal-mediated assays

Derivatives of E. coli K-12 strain 343/113 differing in DNA repair capacity, in permeability to large molecules, and in some metabolizing activities (nitroreductase, glutathione), were constructed for the quantitative determination of the induction of various genetic effects, such as forward and back mutations, lysogenic induction of prophage lambda, and repairable DNA damage. These E. coli strains can be used in assay procedures which allow variation and control over several experimental conditions, such as oxygen tension, time, pH, temperature of incubation and growth phase of the indicator cells. Methods are described for the simultaneous determination of genetic effects and of DNA-adduct formation during mutagen treatment, i.e. by using radio-labeled compounds or by means of an enzyme-linked immunosorbent assay (ELISA). Mammalian biotransformation of xenobiotics can be investigated by including various fractions of mammalian organs in the system. Examples of the relative effectiveness of the activating potential of S9, S100 and isolated hepatocytes for dialkylnitrosamines and other carcinogens are presented. Host-mediated assays, finally, are described which, in addition to gene mutations, can also be used for the determination of repairable DNA damage in bacteria present in different organs, including the liver, spleen, lungs, kidneys, pancreas, and the blood stream of chemically treated mice. It is concluded that quantitative tests in vitro for assessment of induced mutagenic spectrum and genotoxic potency, combined with the host-mediated assay as a monitor, in vivo, of genotoxic factors present in various organs of animals, may become useful in the assessment of genotoxic (and possibly tumor-initiating) properties of chemicals for which long-term in-vivo mutagenicity and/or carcinogenicity data are not yet available.

Damaged-site independent mutagenesis of phage lambda produced by inducible error-prone repair

The existence of damaged-site independent mutagenesis is confirmed here by scoring the appearance of clear-plaque (c-) or virulent (vir) forward mutations on intact (non-irradiated) phage lambda grown on UV-irradiated E. coli K12 hosts. The mutation frequency was measured as a function of the incubation time between the occurrence of host DNA lesions and phage infection. The time course of mutagenesis of intact phage followed the induction pattern observed upon UV-reactivation of UV-damaged phage by Defais et al. (1976). Intact phage did not mutate in UV-irradiated hosts carrying the uvm-25 mutation known to prevent the occurrence of UV-reactivation. These findings suggest that damaged-site independent mutagenesis results from inducible error-prone repair. Clear-plaque mutations arising on intact phage were mostly found in phage bursts consisting of clear and turbid plaque formers whereas UV-damaged phage gave rise to mostly clear-plaque formers. Contrarily to damaged-site dependent mutagenesis, damaged-site independent mutagenesis can arise even at late times during the phage replication cycle. Our data indicate that about half of the phage mutations that arise upon UV-reactivation are damaged-site independent mutations. Replication of intact phage DNA in a host during induction of SOS functions provides a sensitive assay for the detection of damaged-site independent mutagenesis.

Effects of the rex gene of phage lambda on lysogeny

Mutations in therexgene of phage λ affect lysogeny. λrex−phages have an increased probability of forming abortive lysogens instead of stable lysogens. In addition, established lysogens produce elevated levels of cured cells during anaerobic but not aerobic growth. It is suggested that the function of therexgene is related to excision or repressor function.

Repressor and int synthesis of bacteriophage lambda in the E. coli host mutant ER437

Analysis of lambda phage infection of the host mutant ER437 by SDS polyacrylamide gel electrophoresis and autoradiography has revealed altered expression of repressor and integration function (Int). We show that in this host Int as well as repressor synthesis is not dependent upon the lambdacIII gene product in the usual manner, nor is their synthesis turned off in the normal way.

Kinetics of induction of error-prone repair of bacteriophage lambda by temperature shift in an Escherichia coli dnaB mutant

Preincubation at 42 degrees, before infection at permissive temperature by phage lambda, of an Escherichia coli dnaB mutant, provokes a significant increase in survival and mutagenesis of ultraviolet irradiated phage as well as mutagenesis of untreated phage. Similarly to UV irradiation and many chemical mutagens, the inhibition of DNA synthesis by temperature shift of this dnaB mutant induces SOS repair. This work shows that replication blockage in bacterial DNA is not only mutagenic for bacterial DNA itself (Witkin, 1975) but also for normally replicating lambda DNA, probably due to induction of diffusible products.

Membrane mutation affecting energy-linked functions in Escherichia coli K 12

A small-colony forming variant of Escherichia coli with a mutation in the ncf gene was analysed. The alternation of the protein composition in the cytoplasmic membrane and the interaction with K and E group colicins indicated a membrane mutation. The effect of this mutation on some membrane-bound processes, the activity of Mg2+-activated ATPase, the growth on different carbon sources and the active transport of amino acids, is described. This mutation does not exert any effect on the electron transport system.

A bacterial RNA polymerase mutant that renders lambda growth independent of the N and cro functions at 42 degrees C

We describe a bacterial RNA polymerase mutation, rif 501, which confers rifampicin resistance and thermosensitivity to E. coli K 12. The purified RNA polymerase enzyme from rif 501 bacteria shows increased heatsensitivity in vitro at 51 degrees C. However, in vivo, at 42 degrees C the non-permissive temperature, mutant bacteria continue to grow and to synthesize RNA for 90 min. On a lawn of the mutant bacteria, at 40-41 degrees C, phage lambda forms clear plaques (LycA phenotype); this is probably due to an enhancement of cro function; we surmise that at 42 degrees C the transcription originating from the pR (but not from the pL) promoter on the lamdba genome becomes N-independent and less sensitive to the absence of the cro product. We discuss the possibility that both the N and cro proteins of phage lambda interact directly with the bacterial RNA polymerase. These observations indicate that the loss of viability of the rif 501 mutant at the restrictive temperature is not a consequence of an immediate inactivation of RNA polymerase; rather we feel it is due to a modification of the activity of RNA polymerase, leading to a disruption of the cellular regulation.

Evidence for a dual control of the initiation of host-cell lysis caused by phage lambda

The timing of host-cell lysis by coliphage lambda is controlled by two separable systems. The lambdaS gene product acts as a positive effector of lysis while another protein, the lysis regulator, is an inhibitor of lysis. If the continuous function of the lysis regulator is interrupted in phage infected cells immediate lysis ensues. This lysis requires metabolic energy but not S gene activity. In contrast, S protein activity is stimulated by agents which uncouple and which block oxidative phosphorylation. The lysis regulator is thermolabile and several lines of evidence suggest that it may be the lambdarex gene product.

Genetics of resistance to colicins in Escherichia coli K-12: cross-resistance among colicins of group A

By using each of the available colicins, we have isolated a large number of colicin-resistant mutants. They included both receptor and tolerant mutants and each was screened for cross-resistance to all other colicins. On the basis of the cross-resistance of these mutants it was possible to place known colicins into two mutually exclusive groups, group A and group B. Mutants selected as resistant to colicins of group A may or may not be cross-resistant to other colicins of group A, BUT Are never resistant to colicins of group B. The reverse also applies. The mutants isolated as resistant to colicins of group A (A, E1, E2, E3, K, L, N, S4, and X) have been divided into 21 phenotypic classes on the basis of their colicin resistance patterns. These include most of the tolerant and receptor mutants previously isolated, some of which were previously shown to also have an increased sensitivity to certain antibiotics and detergents. Type strains from each of the phenotypic classes were therefore tested for sensitivity to a range of antibiotics, detergents, and surfactants that included all those previously used. With these new data, it has been possible to speculate informatively on the mode of action of the different colicins. We have confirmed the position of previously isolated mutations on the Escherichia coli K-12 genetic map, and located approximately the loci conferring colicin resistance in some of the newly isolated mutants.

Mutant of Salmonella typhimurium that channels infecting bacteriophage P22 toward lysogenization

A slowly growing, polymyxin-sensitive mutant of Salmonella typhimurium was isolated. Wild-type phage P22 form plaques on the mutant at 5 x 10(-4), the frequency observed on wild-type hosts. All P22 clear mutants form plaques with near normal frequency. The inability of the mutant to form plaques is correlated with an increase in lysogenization frequency. The cause of the increased lysogenization frequency is not known, but it is not the result of overproduction of cyclic adenosine 5'-monophosphate.

Escherichia coli females defective in conjugation and in adsorption of a single-stranded deoxyribonucleic acid phage

We predicted that, among mutants resistant to infection by single-stranded deoxyribonucleic acid viruses, there would be some also resistant to "infection" by single-stranded conjugal deoxyribonucleic acid. Approximately 5% of the Escherichia coli K-12 females selected for resistance to phage ST-1 were defective as recipients in conjugation. These spontaneous mutants fell into two classes. Type A accepted both plasmid and chromosomal markers at greatly reduced frequencies (<10(-6) of normal for at least one strain), formed "rough" colonies, and (unlike their parent) were nonflagellated. Type B strains accepted both chromosomal and plasmid markers at reduced frequencies (10(-2) to 10(-1) of normal), were temperature sensitive for growth, and showed increased susceptibility towards antibiotics and deoxycholate. Both classes of mutants also were resistant to certain female-specific viruses.

The roles of the lambda c3 gene and the Escherichia coli catabolite gene activation system in the establishment of lysogeny by bacteriophage lambda

Maximum lysogenization of E. coli by bacteriophage lambda requires both the lambdacIII gene function and the host catabolite gene activation system mediated by adenosine 3':5'-cyclic monophosphate. Whereas considerable lysogenization occurs in the presence of either system alone, lysogenization is absolutely prevented in the absence of both systems. Neither system is, however, required for efficient lysogenization when the host bears an hfl(-) mutation. It is argued that the normal function of these two systems is to negate the antagonistic effect of the Hfl(+) protein upon lysogenization. It is further argued that both the lambdacIII gene function and the Hfl(+) protein do not directly affect the host catabolite gene activation system.