Interaction of an antimutator gene with DNA repair pathways in Escherichia coli K-12

Summary A mutation in the purB gene of E. coli K-12, isolated and partially characterized by Geiger and Speyer (1977), confers a temperature sensitive requirement for adenine and an antimutator phenotype at 30°C. Several hypotheses about the mechanism of action of this mutation, named mud for mutation defective, were tested in the present work. The mud mutation has no effect upon the induction of the SOS response, so the antimutator phenotype is unlikely to be due to repression of mutagenic repair. Mud cells are resistant to the cytotoxic and mutagenic effects of alkylating agents such as MNNG, but this resistance is not due simply to derepression of the adaptive response. DNA isolated from mud cells is not undermethylated relative to DNA from purB ⁺ cells, so the antimutator phenotype of mud cannot be due to reduced hotspot base-substitution mutation at methylated cytosine residues. Nor is there a longer lag in post-replicative DNA methylation, which indicates that there is no enhancement of mismatch repair resulting from an extended time window for strand discrimination. Measurement of nucleotide pool levels demonstrated an elevation of dCTP in mud cells and a reduction of all other nucleoside triphosphates.This work was supported in part by Public Health Service grants numbers GM15697 and CA32182     

TheisfA mutation inhibits mutator activity and processing of UmuD protein inEscherichia coli recA730 strains

Further studies on theisfA mutation responsible for anti-SOS and antimutagenic activities inEscherichia coli are described. We have previously shown that theisfA mutation inhibits mutagenesis and other SOS-dependent phenomena, possibly by interfering with RecA coprotease activity. TheisfA mutation has now been demonstrated also to suppress mutator activity inE. coli recA730 andrecA730 lexA51(Def) strains that constitutively express RecA coprotease activity. We further show that the antimutator activity of theisfA mutation is related to inhibition of RecA coprotease-dependent processing of UmuD. Expression of UmuD' from plasmid pGW2122 efficiently restores UV-induced mutagenesis in therecA730 isfA strain and partially restores its mutator activity. On the other hand, overproduction of UmuD'C proteins from pGW2123 plasmid markedly enhances UV sensitivity with no restoration of mutability.     

Prophage induction in Escherichia coli K12 cells deficient in DNA polymerase I.

Summary The induction of prophage by ultraviolet light has been measured inE. coli K12 lysogenic cells deficient in DNA polymerase I. The efficiency of the induction process was greater inpolA1 polC(dnaE) double mutants incubated at the temperature that blocks DNA replication than inpolA ⁺ polC single mutants. Similarly, thepolA1 mutation sensitizedtif-promoted lysogenic induction in apolA1 tif strain at 42°. In strains bearing thepolA12 mutation, which growth normally at 30°, induction of the prophage occured after the shift to 42°. It is concluded that dissapearance of the DNA polymerase I activity leads to changes in DNA replication that are able, per se, to trigger the prophage induction process.     

TheisfA mutation inhibits mutator activity and processing of UmuD protein inEscherichia coli recA730 strains

Further studies on theisfA mutation responsible for anti-SOS and antimutagenic activities inEscherichia coli are described. We have previously shown that theisfA mutation inhibits mutagenesis and other SOS-dependent phenomena, possibly by interfering with RecA coprotease activity. TheisfA mutation has now been demonstrated also to suppress mutator activity inE. coli recA730 andrecA730 lexA51(Def) strains that constitutively express RecA coprotease activity. We further show that the antimutator activity of theisfA mutation is related to inhibition of RecA coprotease-dependent processing of UmuD. Expression of UmuD' from plasmid pGW2122 efficiently restores UV-induced mutagenesis in therecA730 isfA strain and partially restores its mutator activity. On the other hand, overproduction of UmuD'C proteins from pGW2123 plasmid markedly enhances UV sensitivity with no restoration of mutability.     

Doublet frequencies and codon weighting in the DNA ofEscherichia coli and its phages

Summary A compilation of nucleic acid sequences fromE.coli and its phages has been analysed for the frequency of occurrence of nearest neighbour base doublets and codons. Several statistically significant deviations from random are found in both doublet and codon frequencies. The deviations inE.coli also appear to occur in and in the coat protein gene of MS2, whereas T4 and other parts of the MS2 genome show different sequence properties. These and other findings are discussed in relation to the hypothesis that rapidity of translation of mRNAs in theE. coli system is dependent on doublet frequency and codon usage patterns.     

Selection againstdam methylation sites in the genomes of DNA of enterobacteriophages

Summary Postreplicative methylation of adenine inEscherichia coli DNA to produce G^6m ATC (where^6mA is 6-methyladenine) has been associated with preferential daughter-strand repair and possibly regulation of replication. An analysis was undertaken to determine if these, or other, as yet unknown roles of GATC, have had an effect on the frequency of GATC inE. coli or bacteriophage DNA. It was first ascertained that the most accurate predictions of GATC frequency were based on the observed frequencies of GAT and ATC, which would be expected since these predictors take into account preferences in codon usage. The predicted frequencies were compared with observed GATC frequencies in all available bacterial and phage nucleotide sequences. The frequency of GATC was close to the predicted frequency in most genes ofE. coli and its RNA bacteriophages and in the genes of nonenteric bacteria and their bacteriophages. However, for DNA enterobacteriophages the observed frequency of DNA enterobacteriophages the observed frequency of GATC was generally significantly lower than predicted when assessed by the chi square test. No elevation in the rate of mutation of^6mA in GATC relative to other bases was found when pairs of DNA sequences from closely related phages or pairs of homologous genes from enterobacteria were compared, nor was any preferred pathway for mutation of^6mA evident in theE. coli DNA bacteriophages. This situation contrasts with that of 5-methylcytosine, which is hypermutable, with a preferred pathway to thymine. Thus, the low level of GATC in enterobacteriophages is probably due not to^6mA hypermutability, but to selection against GATC in order to bypass a GATC-mediated host function.     

Ribonuclease III reduces the efficiency of bacteriophage gy1 propagation inE. coli

TheE. coli rnc gene encodes the double-stranded, RNA-specific ribonuclease III (RNaseIII). A novel bacteriophage, gy1, was isolated, and its propagation inE. coli was shown to depend on the expression of RNaseIII in the cell. (a) gyl has a low efficiency of plating on rnc⁺ strains and a high efficiency of plating on a rnc^– E. coli strain harboring the rnc 105 point mutation that renders its RNaseIII product inactive. (b) gy1 has a high efficiency of plating on rnc^– strains in which thernc gene is disrupted by a Tn10 insertion. (c) Plasmids harboring a rnc⁺ gene that were introduced into the rnc^– strains described above reduced the efficiency of plating of gy1.     

Transfer ofF′ fromEscherichia coli K 12 toEscherichia coli B and to strains ofParacolobacter andKlebsiella

The transfer of theF episome fromEscherichia coli K 12 toE. coli B,Paracolobacter andKlebsiella was studied. The frequency of transfer of the episomal markers toE. coli B was very low. The large majority ofE. coli B cells which had received the episomal markerslac ⁺ orgal ⁺ were F^–, which indicates that the episomal markers were stably integrated on the chromosome. Recombinants from K 12 F⁺ × B F^– crosses were mostly F^–. These results suggest that the multiplication of theF-factor ofE. coli K 12 is restricted inE. coli B. The transfer of theF-lac ⁺ Ad ⁺ episome fromE. coli K 12 toParacolobacter andKlebsiella strains was in most cases only possible when donor and acceptor strain were plated together on selective media. Stable incorporation of episomal markers was also found withParacolobacter coliforme. Paracolobacter aerogenoides andKlebsiella aerogenes strains could be infected withF-lac ⁺ Ad ⁺. The episomal markers were not incorporated and the episomes were easily lost, which indicates that these strains contained theF factor in the autonomous state.     

Effects of mutations in genesfadR,fabB, fadE,andenvC ofEscherichia coli on the action of the lysis gene of bacteriophageϕX174

The lytic effect of the expression of the cloned geneE of bacteriophage X174 inEscherichia coli is considerably amplified by a mutation in thefadR gene, which primarily affects the regulation of fatty acid degradation. In contrast, reduction of the fluidity of the cell membranes by use of thefabB andfadE mutations, which interfere with the synthesis and the oxidation of unsaturated fatty acids, severely inhibits the action of the X174 lysis gene product. A chain-forming mutant carrying a pleiotropic mutation in theenvC locus is also refractory to the X174 lysis protein. As shown by reversion and complementation of theenvC mutatation, a defect in at least one additional gene (rle) is involved in the generation of this refractoriness.     

Analyses of<Emphasis Type="Italic"> cis</Emphasis> -acting elements that affect the transposition of<Emphasis Type="Italic"> Mos1 mariner</Emphasis> transposons in vivo

The left (5) inverted terminal repeat (ITR) of the Mos1 mariner transposable element was altered by site-directed mutagenesis so that it exactly matched the nucleotide sequence of the right (3) ITR. The effects on the transposition frequency resulting from the use of two 3 ITRs, as well as those caused by the deletion of internal portions of the Mos1 element, were evaluated using plasmid-based transposition assays in Escherichia coli and Aedes aegypti. Donor constructs that utilized two 3 ITRs transposed with greater frequency in E. coli than did donor constructs with the wild-type ITR configuration. The lack of all but 10 bp of the internal sequence of Mos1 did not significantly affect the transposition frequency of a wild-type ITR donor. However, the lack of these internal sequences in a donor construct that utilized two 3 ITRs resulted in a further increase in transposition frequency. Conversely, the use of a donor construct with two 3 ITRs did not result in a significant increase in transposition in Ae. aegypti. Furthermore, deletion of a large portion of the internal Mos1 sequence resulted in the loss of transposition activity in the mosquito. The results of this study indicate the possible presence of a negative regulator of transposition located within the internal sequence, and suggest that the putative negative regulatory element may act to inhibit binding of the transposase to the left ITR. The results also indicate that host factors which are absent in E. coli, influence Mos1 transposition in Ae. aegypti.Communicated by G. P. Georgiev     

Molecular cloning and expression ofBacillus subtilis bglS gene inSaccharomyces cerevisiae

A 2.7-kb EcoRI DNA fragment carrying aBacillus subtilis endo--1,3-1,4-glucanase gene (bglS) from theE. coli plasmid pFG1 was cloned into anEscherichia coli/yeast shuttle vector to construct a hybrid plasmid YCSH. The hybrid plasmid was used to transformSaccharomyces cerevisiae, and thebglS gene was expressed. Variation between levels ofbglS gene expression inS. cerevisiae was about 2.3-fold, depending on the orientation of the 2.7-kb DNA fragment. Assay of substrate specificity and optimal pH of the enzyme demonstrated that the enzyme encoded by YCSH (bglS) was identical with that found inB. subtilis, but the expression level ofbglS gene inS. cerevisiae (YCSH) was much lower than that inE. coli (YCSH).     

Restoration of Growth Phenotypes of Escherichia coli DH5α in Minimal Media through Reversal of a Point Mutation in purB

A point mutation (E115K) resulting in slower growth of Escherichia coli DH5α and XL1-Blue in minimal media was identified in the purB gene, coding for adenylosuccinate lyase (ASL), through complementation with an E. coli K-12 genomic library and serial subcultures. Chromosomal modification reversing the mutation to the wild type restored growth phenotypes in minimal media.The Escherichia coli DH5α strain possesses many beneficial genotypes (recA, deoR, gyrA, and endA1) and has been widely used for many purposes, such as gene cloning and protein production (5). However, E. coli DH5α also exhibits inferior growth phenotypes, especially in minimal media, compared to other E. coli strains. As such, the utilization of this bacterium has been limited to the laboratory despite its numerous advantages. We can assume that these inferior growth phenotypes have resulted from unknown accumulated mutations during the strain development process (5). Some of those mutations, which might impact growth in minimal media, have been characterized, including the phenotypes for thiamine requirement and relaxed amino acid synthesis (5). Still, there may be other uncharacterized mutations whose interactions hamper the growth of E. coli DH5α in minimal media.Based on successful identifications (6, 7) of gene targets for metabolic engineering (3), we performed serial subcultures of E. coli DH5α transformants with an E. coli K-12 genomic library based on a multicopy plasmid (9) to isolate genes that improve growth phenotypes in minimal media. The M9 minimal medium and R medium (11) were chosen for enrichment experiments because of their popular use in metabolic engineering (1, 2, 7) and in high-cell-density fermentation (8, 10, 11). After 11 serial transfers of the transformants in the M9 medium, and 27 transfers in the R medium, cultured cells were diluted and plated onto LB agar for single-colony isolation. Although more than 10 colonies were picked, only three distinctive plasmids, containing different inserts, were isolated from the transformants enriched in M9 medium. In the case of R medium enrichment, all isolated plasmids were identical. Sequencing of the isolated plasmids revealed the exact genome coordinates of each insert. A diagram of the inserts in the context of the E. coli genome sequence is shown in Fig. ​Fig.1.1. Interestingly, all of the isolated plasmids contained similar regions of genomic DNA. mnmA (tRNA 5-methylaminomethyl-2-thiouridylate-methyltransferase), purB (adenylosuccinate lyase), and hflD (lysogenization regulator) were the annotated genes in the overlapping region among distinctive isolated fragments. However, since the N-terminal portions of mnmA and hflD were truncated in some of the inserts, we selected only the M3 and R1 plasmids for further experimentation. These two plasmids were retransformed into E. coli DH5α for confirmation of their beneficial effects on growth of E. coli in minimal media. The newly transformed strains showed growth phenotypes almost identical to those of the previously isolated transformants. When cultured in flasks, the specific growth rate of E. coli DH5α with the R1 plasmid was 1.5-fold higher (0.53 versus 0.36 h⁻¹) than the rate of cells transformed with a control plasmid (pZE). The R1 transformant reached the stationary phase much earlier, arriving at an optical density at 600 nm (OD₆₀₀) of 10 within 16 h, whereas the control transformant reached this cell density after 24 h. However, the final cell densities were almost equivalent. Acetate accumulation, as well as glucose consumption, by the R1 transformant was much higher than that of the control transformant (2.2 versus 0.3 g acetate/liter). The increased accumulation of acetate could be the result of increased cell density. These findings confirm that the enhanced growth phenotypes of the isolated transformants were conferred not by accumulated spontaneous mutations in the genome during enrichment but by the introduced plasmids.Open in a separate windowFIG. 1.Diagram of open reading frames in the identified genomic DNA fragments. M1, M2, and M3 were isolated from the serial subculture using M9 medium. R1 was isolated from the serial subculture using R medium.The open reading frame (ORF) of purB was amplified and cloned into a multicopy plasmid under the control of a strong promoter (rrnB). Transformation of the resulting plasmid (pZE-purB) into E. coli DH5α resulted in a growth phenotype almost identical to that of the R1 transformant. This result suggested that overexpression of purB is a specific genetic perturbation improving growth phenotypes of E. coli DH5α in minimal media. We also performed 1-liter batch fermentation experiments with three DH5α transformants: one containing the control plasmid (pZE), one with the isolated plasmid (R1), and a third with the purB overexpression plasmid (pZE-purB). Growth phenotypes of these strains were very similar to results obtained from shaker flask experiments (Fig. ​(Fig.2).2). Next, we tested whether the overexpression of purB is beneficial to the growth of other E. coli strains by introducing the R1 and pZE-purB plasmids into various other strains (K-12, BL21, and XL1-Blue) that are commonly used in biotechnological research. Among the four strains tested in our various experiments, the positive effects of purB overexpression on growth phenotypes were observed only in DH5α and XL1-Blue, both of which have been favored in molecular cloning. These results suggest that an uncharacterized mutation might have been introduced into both strains during strain development. This unknown mutation might cause growth inhibition, which can be suppressed by the overexpression of purB. Therefore, we concluded that expression of an exogenous, K-12-derived copy of the purB gene under a constitutive promoter can enhance growth phenotypes of E. coli DH5α and XL1-Blue strains in minimal media.Open in a separate windowFIG. 2.Comparison of levels of cell growth (♦) (OD₆₀₀), glucose consumption (▪) (g/liter), and acetate production (▴) (g/liter) by E. coli DH5α transformants with a control plasmid (A), the isolated R1 plasmid (B), and the pZE-purB plasmid (C) in R medium with glucose in a bioreactor.However, it is plausible that a mutation is located in the purB locus of DH5α and XL1-Blue that decreases the activity of the encoded enzyme. In order to identify a putative mutation in purB, we sequenced the chromosomal purB gene of DH5α and XL1-Blue. A point mutation resulting in the transition of nucleotide 343 of purB from guanine (G) to adenine (A) was identified in the genomes of both strains. This mutation causes a change of the 115th residue of adenylosuccinate lyase from glutamate to lysine (E115K). This finding explains why the expression of exogenous, K-12-derived purB in DH5α and XL1-Blue strains enhances growth phenotypes in minimal media. The E115K mutation of purB was named purB20 for simple notation.Chromosomal modification of the mutant allele in E. coli DH5α or XL1-Blue might be desirable for practical applications. To this end, the purB20 mutant allele was replaced by purB amplified from E. coli K-12 through recombination based on phage lambda Red recombinase (4). The resulting strain (SC1) showed growth phenotypes similar to those of E. coli DH5α strains harboring the pZE-purB or R1 plasmid. The specific growth rate of SC1 in M9 medium was 40% higher than that of DH5α (0.50 versus 0.36 h⁻¹). These results show that what we had originally interpreted as overexpression of the purB gene was actually complementation of the mutant purB20 allele with wild-type purB. We also tested whether the modification from purB20 to wild-type purB elicits a change in the transformation efficiency. Chemically induced competent SC1 cells exhibited approximately 2.5-fold lower transformation efficiency than E. coli DH5α cells did when induced under identical conditions (1.8 ± 0.1 × 10⁶ versus 4.6 ± 0.3 × 10⁶ CFU/μg pUC19 DNA). Still, the transformation efficiency of the SC1 strain was of the same order of magnitude as that of E. coli DH5α, suggesting that the SC1 strain would be useful for many biotechnological applications, such as the mass production of DNA vectors and recombinant proteins.     

Expression of the tryptophan operon in merodiploids of Escherichia coli. I. Gene dosage, gene position and marker effects

Summary Under conditions of derepression,Escherichia coli K12 strains diploid for thetrp operon specify more than twice as much enzyme as a haploid. The disproportionate increase probably occurs because episomally carriedtrp genes tend to specify more enzyme than do chromosomal genes.Operons harboring the nonsense mutationtrpA2 or the missense mutationtrpBYS-101 specify less protein than do wild-type operons. This effect varies with operon location in the case oftrpBYS-101.In a homozygoustrp merodiploid A46/F A46 reversion totrp ⁺ occurs three times as frequently in episomal DNA as in chromosomal DNA. Thus, if the chromosome: Ftrp episome ratio inE. coli is one, as demonstrated by Helinski and co-workers, the rate of gene expression and the rate of mutation can vary and depends upon the location of the DNA within the cell.Supported by Grant AM-12150 from the National Institutes of Health. Journal Paper No. 3973 of Purdue Agricultural Experiment Station.     

Comparison of the in situ survival and activity ofKlebsiella pneumoniae andEscherichia coli in tropical marine environments

A near-shore coastal mangrove island receiving untreated sewage and a coastal cove receiving rum distillery effluent in Puerto Rico were examined for their ability to support survival and activity ofKlebsiella pneumoniae andEscherichia coli. Pure cultures of both bacteria were monitored for 96 hours in situ at both locations using membrane diffusion chambers.K. pneumoniae survived at all sites as measured by AODC and Coulter Counter direct counts. However, at the mangrove island less than 20% of theK. pneumoniae population was active (AODC) after the first 3 hours and less than 10% of this population was respiring (INT). In contrast, the coastal area which was receiving rum distillery effluent was able to maintain 40% of theK. pneumoniae population in an active state with 90% respiring. TheE. coli population declined by two orders of magnitude at the mangrove island, but remained unchanged at the rum distillery outfall. TheE. coli population had a higher proportion of active cells and respiring cells thanK. pneumoniae at all sites. At the rum distillery site, theE. coli population was remarkable in that 95% remained active and 99% were respiring. This study suggests that, when sufficient organic loading exists,E. coli, a nonsurvivor, can overcome the bactericidal effects of tropical marine waters.K. pneumoniae, a survivor, could survive under all conditions but could not maintain the activity or respiration that theE. coli population could, even when high organic loads were present. Morphological changes related to nutrient stress in the tropical marine environment were apparent inE. coli, but not inK. pneumoniae. Based on physiological activityE. coli is just as much a survivor asK. pneumoniae in tropical marine waters.     

Heat shock-induced protein synthesis inLactococcus lactis subsp.lactis

Heat shock inLactococcus lactis subsp.lactis may induce as many as 16 proteins after a temperature shift from 30° to 40°C. Five induced proteins were found to be immunologically related to theEscherichia coli GroEL, DnaK, DnaJ, and GrpE proteins, and to theBacillus subtilis ⁴³ factor. From these initial studies we conclude that, inL. lactis subsp.lactis, a heat shock response similar to that known to occur in other prokaryotes might exist.     

High-frequency electroporation and maintenance of pUC- and pBR-based cloning vectors inPseudomonas stutzeri

A number ofEscherichia coli cloning vectors, based on ColE1-like replicons, were shown to be maintained inPseudomonas stutzeri ATCC 17588. A restrictionless mutant ofP. stutzeri was isolated, and this strain was used to develop an efficient electroporation system. With theE. coli cloning vector pHSG298, transformation frequencies of up to 2×10⁷ transformants/g DNA were achieved. This frequency is comparable to that obtained for CaCl₂-mediated transformation ofE. coli; thus, direct cloning of DNA intoP. stutzeri is feasible. As will be discussed, this may prove useful for cloning DNA from high mol% G+C genera in cases in whichE. coli is not a suitable heterologous cloning host.     

Isolation of the pullulanase gene fromClostridium thermosulfurogenes (DSM 3896) and its expression inEscherichia coli

The pullulanase gene fromClostridium thermosulfurogenes (DSM 3896) was cloned and expressed inEscherichia coli with pUC18 as cloning vector. Two clones showed expression of amylolytic enzymes which were active at high temperatures. One of the recombinant plasmids (pCT3) containing a 5.3 kbp insert coded for the pullulanase gene; the other (pCT4, 4.4 kbp insert) carried the same-amylase gene as the previously described plasmid pCT2 (2.9 kpb insert, 7). The pullulanase gene was efficiently transcribed inE. coli, apparently using its own promoter; the enzyme was not secreted into the medium. No difference in the temperature optimum and thermostability between the original and the heterologously expressed (inE. coli) enzyme could be found.     

Molecular cloning,expression, and characterization of a new endoglucanase gene fromFibrobacter succinogenes S85

A DNA fragment coding for a carboxymethylcellulase (CMCase) ofFibrobacter succinogenes S85 was isolated from a pUC18 gene library inEscherichia coli JM109. The CMCase gene was present as a single copy in theF. succinogenes S85 genome and was found in all the otherF. succinogenes strains tested. The gene was expressed from an endogenous promoter inE. coli and was not subject to glucose repression. Most of the CMCase activity was located in the membrane ofE. coli. Zymogram analysis and³⁵S labeling of the proteins encoded by the CMCase gene-containing plasmid indicated that the enzyme has a molecular mass of 58,000. The optimal pH and temperature of activity on CMC were respectively 6.4 and 30°C. The enzyme was active on CMC, barley -glucan, and lichenan but would not hydrolyze laminarin and exhibited no exoglucanase-type activity, suggesting that it is an endo-(1,4)--d-glucanase.     

Inefficient mismatch repair: genetic defects and down regulation

The mismatch repair system is involved in the maintenance of genomic integrity by editing DNA replication and recombination. However, although most mutations are neutral or deleterious, a mutator phenotype due to an inefficient mismatch repair may generate advantageous variants and may therefore be selected for. We review the evidence for inefficient mismatch repair due either to genetic defects in mismatch repair genes or to physiological conditions. Among natural isolates ofEscherichia coli andSalmonella enterica, about 1% are mutator bacteria, mostly deficient in mismatch repair (most of them defective in themutS gene). Characterization of mutators derived from laboratory strains led also to the isolation of mismatch repair mutants in which the most frequently found defects are inmutL andmutS. The correlation of the size of the antimutator genes with the frequency of their defective alleles amongE. coli andSalmonella strains reveals thatmutU mutants are underrepresented. Analysis of the progeny of a defined M13 phage heteroduplex DNA transfected intoE. coli cells shows that mismatch repair efficiency progressively decreases from the end of the exponential growth in K-12 and is variable among natural isolates. Implications of this defective mismatch repair activity for evolution and tumorigenesis will be discussed.