Mapping of the polA Locus of ESCHERICHIA COLI K12: Genetic Fine Structure of the Cistron

The close linkage of the glnA gene with polA was exploited to construct a fine structure map of polA by means of generalized transduction with phage P1. Nine different polA^- alleles were mapped by recombinational crosses. The results indicate a gene order consistent with previous observations (Kelley and Grindley 1976a; Murray and Kelley 1979). Three mutations, polA5, polA6 and polA12 map within the "carboxy-terminal" or "large-fragment" portion of the gene in unambiguous order. Four alleles, known to affect the "aminoterminal" portion of the gene, polA107, polA214, polA480ex and polA4113, appear to be closely linked with certain ambiguities in their exact order. All four of these mutations are known to alter the 5''→3'' exonuclease activity of DNA polymerase I and three of them result in the conditional lethal polA^- phenotype. The polA1 nonsense mutation maps between these two groups in a position consistent with its known effect, production of an amber fragment that includes the 5''→3'' exonuclease. The final allele, resA1, is another nonsense mutation that maps at the extreme "amino-terminus" of the cistron.——A number of control experiments were conducted to determine the effects of polA^- mutations on the P1-mediated recombinational event. These experiments indicated that abortive transduction occurs quite frequently, but the formation of abortive transductants and segregation of unselected transduced markers among daughter progeny is like that observed by other investigators. There was no evidence that any individual polA^- allele behaved in an exceptional fashion during recombination.     

Spontaneous and induced mutability or frameshift strains of Salmonella typhimurium carrying uvrB and polA mutations

Three strains Salmonella typhimurium carrying frameshift mutations affecting the histidine genes (hisC3076, hisD3052 and hisC207) showed increased sensitivity to mutagenesis by ICR-191 (as judged by measuring back mutation to prototrophy), if they were made deficient in excision repair by deleting the uvrB gene. One frameshift strain, hisC3076, also showed increased sensitivity to mutagenesis by ICR-191 when it carried either of two different polA alleles, whereas the hidD305 and hisD207 frameshifts reduced sensitivity to mutagenesis in the presence of these alleles. Studies of spontaneous back mutation to prototrophy revealed siginificant mutator effects of the polA1 mutation on reversion of the hisD3052 frameshift and of the polA3 mutation on reversion of the hisC3076 frameshift. Other smaller mutator effects of the polA alleles on reversion of the his mutations may also be present. In an attempt to explain the complex interactions between different polA alleles and different frameshift mutations, it is tentatively suggested that deletion frameshift may arise mainly during DNA replication, while addition frameshifts may arise mainly during post-replication repair.     

Novel nematode amber suppressors

Nine amber suppressor mutations were isolated in the nematode Caenorhabditis elegans by reverting amber alleles of a sex-determining gene, tra-3. One suppressor maps to a known locus, sup-5 III , but the other eight map to three new loci, sup-21 X (five alleles), sup-22 IV (two alleles) and sup-23 IV (one allele). Amber alleles of tra-3 and of a dumpy gene, dpy-20, were used to measure the efficiency of suppression; the sup-21 and the sup-22 alleles were both shown to be heterogeneous and generally weaker suppressors than sup-5 alleles, which are homogeneous. The spectrum of mutations suppressed by a strong sup-21 allele, e1957, was investigated and compared to the spectra for the amber suppressors sup-5 III and sup-7 X, using amber alleles in 13 assorted genes. Some of the differences between these spectra may be due to limited tissue specificity in sup-21 expression.—Suppression of dpy-20 was used to show that the sex-linked suppressors sup-7 and sup-21 are not dosage compensated in male (XO) relative to hermaphrodite (XX).—Several uses of amber suppressors are critically discussed: for identifying null mutations, for varying levels of gene activity and for detecting maternal mRNA.     

An amber mutation in the gene rpsA for ribosomal protein S1 in Escherichia coli

Summary An amber mutation has been induced in the gene rpsA (which codes fo ribosomal protein S1) of Escherichia coli K-12 strain in the presence of an amber suppressor (supD) and mutations sueA, sueB and sueC that additively enhance the efficiency of suppression. That the amber mutation has occurred in the gene rpsA was confirmed by complementation with a plasmid which carried the wild-type allele of rpsA. The mutation is lethal in the absence of an amber suppressor, indicating that ribosomal protein S1 is indispensable to E. coli.     

Mutations in the mutY gene of Escherichia coli enhance the frequency of targeted G:C → T:A transversions induced by a single 8-oxoguanine residue in single-stranded DNA

Oxidative damage to guanine in DNA results in the formation of 8-oxoguanine, which has been shown to induce G → T transversions targeted to this site. The mutagenicity of this lesion was studied in several mutator strains of Escherichia coli, using single-stranded DNA containing a single 8-oxoguanine residue. The frequencies of targeted G → T transversions increased markedly in mutY strains, while this mutagenic event was not affected in mutM or mutS strains. Introdution of a mutM mutation into a mutY strain caused a somewhat higher frequency of G → T transversions than that in the mutY strain and the effect of a mutS mutation was marginal. We conclude that the mutY gene plays a crucial role in preventing targeted G → T mutations derived from misreplication of the 8-oxoguanine-containing template DNA.     

Isolation and characterization of a temperature-sensitive amber suppressor mutant of Escherichia coli K12

Summary By mutagenizing an E. coli strain carrying an amber suppressor supD ^- (or su _I ⁺), we isolated a mutant whose amber suppressor activity was now temperature-sensitive. The mutant suppressor gene was named sup-126, which was found to be cotransduced with the his gene by phage P1vir at the frequency of ca. 20%. At 30° C it suppresses many amber mutations of E. coli, phage T4, and phage . At 42° C, however, it can suppress none of over 30 amber mutations tested so far. The sup-126 mutation is unambiguous and stable enough to be useful for making production of an amber protein temperature-sensitive.     

Mutations affecting growth of the Escherichia coli cell under a condition of DNA polymerase I-deficiency

Summary We constructed a strain of E. coli K12 carrying polA1 (an amber mutation of the DNA polymerase I gene; De Lucia and Cairns, 1969), and sup-126 (a temperature-sensitive amber suppressor; Nagata and Horiuchi, 1973). DNA polymerizing activity of the enzyme in this strain is virtually undetectable if the cells are grown at 42°C, but if grown at 30°C it is sufficiently present. By mutagenizing this strain, and after appropriate screening, we obtained mutants no longer able to grow at 42°, but able to do so when the normally functioning polA gene is present. One of them, called TS41, was most extensively studied. It acquired a mutation named pdeB41 which was found to be located between ilv and metE on the E. coli linkage map. Its phenotype is pleiotropic. The mutation by itself, i.e., if present in a polA ⁺ cell, does not kill the cell at 42°, but does so as in TS41 when it is reconstructed into a pdeB41 polA1 sup-126 triple mutant by P1 transduction. The mutation by itself renders the cell sensitive to UV, and tolerant to phage deficient in recombination. It is also a mutator.     

Letter to the editor: Characterization of mutations in the tryptophan operon of Escherichia coli by RNA nucleotide sequencing

The nucleotide sequences of operator-proximal tryptophan messenger RNA of Escherichia coli from strains with mutations very early in trpE have been determined. A frameshift mutant, trpE9777fs, has an additional A residue in the region coding for amino acids 4 and 5 of the trpE polypeptide. The other mutant, trpE9914am, exhibits an amber codon corresponding to the codon normally specifying amino acid residue 9 (glutamic acid) of the trpE polypeptide. These results demonstrate that the site of the trpE9777fs mutation precedes that of the trpE9914am mutation by 9 to 15 nucleotides.     

Thermal resistance to photoreactivation of ultraviolet light induced mutations in the lacI gene of E. coli ung

Ultraviolet light (UV) induced mutations in the lacI gene of Escherichia coli are thought to be targeted by DNA photoproducts. A number of reports suggest that both cyclobutyl pyrimidine dimers and pyrimidine (6−4) pyrimidone photoproducts may be involved. To investigate the potential contribution of each of these DNA photoproducts to mutagenesis in the lacI gene, we held UV-irradiated cells at a temperature of 44°C for 75 min and then exposed them to photoreactivating light (PR). This protocol is expected to preferentially deaminate specifically those cytosines that are contained in cyclobutyl dimers and subsequently monomerize the dimers to yield uracils in the DNA. In a strain deficient for uracil-DNA glycosylase (Ung⁻), these uracils would not be removed and a G : C → A : T transition would result at the site of the dimer. This protocol resulted in the enhancement of amber nonsense mutations that result from transitions at potential cytosine-containing dimer sites. The enhanced mutation frequencies resulting from this procedure were used to estimate the probability of dimer formation at the individual sites. A comparison of the dimer distribution with the mutation frequencies following UV alone suggests that both cyclobutyl dimers and (6−4) photoproducts contribute to UV-mutagenesis in the lacI gene. In addition, we conclude that the frequency of mutation at any particular site not only reflects the occurrence of DNA damage, but also the action of metabolic processes that are responsible for DNA repair and mutagenesis.     

Studies on the bacteriophage MS2: XLI. Nature of the azure mutation

Azure (or reverse amber) mutants grow normally on wild-type Escherichia coli but not on host strains harbouring a strong UAG suppressor mutation. Three different bacteriophage MS2 azure mutants obtained by treatment with nitrous acid have been characterized at the nucleotide sequence level. The 3′-end fragment of the ³²P-labelled mutant genomes was isolated by DNA:RNA hybridization and treatment with nuclease S₁, and was analyzed by mini-fingerprinting of the RNA. It is known that the wild-type MS2 polymerase gene ends with a UAG codon, followed seven triplets further by an in-phase UAA triplet. All three azure mutants contained an A → G transition in this UAA second stop codon of the polymerase gene, resulting in a second suppressible UAG (amber) codon. Analysis of revertants demonstrated that the azure mutation can be counteracted either by a true site reversion at the second stop or by the creation of a new stop signal for the polymerase gene, either UAA (ochre) or UGA (opal), before or at the first stop, or beyond the second stop. On the basis of these results, a mechanism for the azure mutation is proposed. Silent mutations (one in the coding region, three in the untranslated 3′-terminal sequence) have also been observed in these phage stocks.     

An amber dna mutant of Escherichia coli K12 affecting DNA ligase

We have isolated an amber mutant (dnaL321) of Escherichia coli K12, which affects DNA ligase and which is lethal unless it is suppressed. DNA is degraded under the restrictive conditions. The mutation also affects the sensitivity of the cell to ultraviolet light irradiation, and the capacity to support the growth of phage λ that is deficient in general recombination. This pleiotropy is considered to be due to a single mutation, and is suppressed by supD^?_Isu+ and by supF^?su_III⁺). The mutation is cotransducible with dapE(2%), and with ptsI(85%), by phage Plvir.     

A new class of mutants in DNA polymerase I that affects gene transposition

A mutant of Escherichia coli strain K12 is defective in transposition of both the transposons Tn5 and Tn10 and the insertion sequences IS1 and IS5. In addition to the defect in transposition, the mutant is also sensitive to methylmethane sulfonate and ultraviolet light, does not grow phage lambda red and is missing the polymerizing activity and the 5′?3′ exonuclease activity of DNA polymerase I, indicating that the mutation is in the structural gene for this enzyme. We have designated the mutant allele as polA34. All of the properties associated with this mutant cotransduce with a marker known to be linked to polA. Furthermore, revertants of the mutant to methylmethane sulfonate resistance also regain the normal transposition frequencies of Tn5, IS1 and IS5. Complementation tests using the diploid polA34/polA show that the sensitivity to methylmethane sulfonate, and the defect in transposition is recessive to the wild-type. Some revertants of polA34 (called polA34 spa) restore resistance to methylmethane sulfonate and u.v. and partially restore the polymerase and 5′?3′ exonuclease activity but do not restore transposition. Thus we conclude that neither the polymerase activity nor the 5′?3′ exonuclease activity are required in transposition, but rather some other property of DNA polymerase I is needed.     

Genetic studies of the lac repressor. IV. Mutagenic specificity in the lacI gene of Escherichia coli.

An extensive set of amber and ochre sites in the lacI gene has been characterized with respect to the base change required to generate the nonsense codon (Miller et al., 1977; Coulondre &; Miller, 1977). These mutations have been used to analyze the forward mutational spectrum of a series of mutagens in Escherichia coli. The sites induced by N′-methyl-N′-nitro-N-nitrosoguanidine, ethyl methanesulfonate, 4-nitroquinoline-1-oxide, and ultraviolet light, were examined, as well as those which arose spontaneously. Sites induced by the G · C → A · T transition were compared with those generated by 2-aminopurine mutagenesis. All together, more than 4000 independent occurrences of amber and ochre mutations were tabulated in order to define the respective mutagenic specificities. With the exception of the A · T → G · C change, all base substitutions lead to the generation of nonsense codons from wild-type. The A · T → G · C transition was monitored in a reversion system, in which the ochre to amber conversion (UAA → UAG) was scored, as well as the UAA → CAA reversion.Both NG³ and EMS were found to be highly specific for the G · C → A · T transition, less than 1% transversions appearing in either case. At between 1% and 5% the level of the G · C → A · T change, NG can stimulate the A · T → G · C transition. EMS stimulates the A · T → G · C transition at a significantly lower rate. NQO is also highly specific for G · C base-pairs, but approximately 10% of the changes found at these sites are transversions. Mutations found spontaneously or after irradiation with ultraviolet light showed none of the specificities found for EMS, NG or NQO. All transversions were detected in both cases. Moreover, a significant number of tandem double base changes were found to be induced by u.v. irradiation. Some of these have been verified directly by protein sequencing. The frequencies of occurrence of amber and ochre mutations arising from the G · C → A · T transition have been compared for different mutagens, revealing several striking hotspots. The implications of these findings with respect to the mechanism of mutagenesis and the application of different mutagens are discussed.     

The role of DNA polymerase I and the rec system in survival of bacteria and bacteriophages damaged by the photodynamic action of acridine orange

Summary The effect of acridine orange (AO)-sensitized photodynamic treatment (PD) was studied in various repair-deficient mutants of Salmonella typhimurium and Escherichia coli. Bacteria of either species carrying mutations in the polA gene and hence deficient in the enzyme DNA polymerase I were significantly more sensitive to PD-killing than polA ⁺ parent bacteria or phenotypically POL⁺ revertants of the polA strains (selected on the basis of resistance to methyl methanesulphonate). It therefore appears that DNA polymerase I plays an important role in cellular recovery from PD treatment. E. coli carrying a mutation in the recA gene was also more sensitive to PD-treatment than its parent strain, as was S. typhimurium carrying a mutation of the recA type. In S. typhimurium the rec mutant was somewhat less sensitive to PD-killing than the pol mutant even although it is much more sensitive to ultraviolet killing. E. coli strains with mutations in the recB and recC genes were intermediate in PD sensitivity between the recA and the parent strain. S. typhimurium and E. coli bacteria with mutations in the polA and recA genes showed reduced ability to host-cell reactivate PD-damaged bacteriophages ES 18 and c1, indicating that the polA ⁺ and recA ⁺ gene products also contribute to repair of bacteriophages damaged by PD treatment. It is suggested that the recombinational repair process is less important for recovery from PD than for recovery from UV, and that the primary contribution of the rec genes to recovery from PD may be in repair of single-strand gaps by repair resynthesis.     

Effects of different alleles of the E. coli K12 polA gene on the replication of non-transferring plasmids

Summary The effects of eight different polA ^-alleles on the replication of six different non-transferring enterobacterial plasmids have been tested. Using phage P1CM transduction, different allelic polA ^- mutations were introduced into E. coli K12 strains carrying one of several antibiotic resistance plasmids. Plasmid stability in the transductants was examined by testing clones for drug resistance after growth under various conditions. From the results, the R factors may be divided into three different classes. One plasmid is only affected by PolA^- conditions which inhibit host cell growth, three plasmids (from the same compatibility group) are unstable under conditions in which the cells are severely deficient in DNA polymerase I and two other plasmids (compatible with each other and with the other four) are immediately lost from such transductants and are unstable in a number of others. Furthermore, the plasmids which are most dependent on DNA polymerase I have been shown to replicate in the presence of chloramphenicol and therefore typify a class of plasmids which includes bacteriocinogenic factors such as ColE1 and CloDF13, resistance determinant RSF1030 and the E. coli 15 minicircular plasmid.     

DNA degradation in an amber mutant of Escherichia coli K12 affecting DNA ligase and viability

Isolation of an amber mutant lig-321 (or dnaL321) if Escherichia coli K12 with a defect in DNA ligase activity was previously reported (Nagata & Horiuchi, 1974). This was the first demonstration that, in E. coli, conditionally lethal nonsense mutants can be isolated selectively. Unlike the hitherto available E. coli K12 DNA ligase-deficient (lig) mutants, the DNA of this mutant is degraded under lethal conditions. This paper describes its further characterization. The DNA degradation was found to be an energy-requiring process, in which endonuclease I did not seem to participate. Kinetic analyses of prelabeled DNA indicated that the parental strands were degraded. The sedimentation profile of prelabeled DNA in an alkaline sucrose gradient showed that the extensive degradation was preceded by a step in which the parental strands were broken into relatively large pieces. At least in the early phase of degradation, which we examined by alkaline sucrose gradient centrifugation of pulse-labeled DNA, synthesis of discontinuous daughter chains (Okazaki fragments, Okazaki et al., 1968) was confirmed. Joining of the nascent chains, however, was completely inhibited. Genetic analyses revealed that the mutant allele is recessive to the wild type. This agrees with in vitro studies in which the mutant crude extract was found not to inhibit DNA ligase activity of the wild type extract. These and other properties of the lig-321 mutant were compared with the other DNA ligase-deficient mutants of E. coli. The role of this enzyme in DNA replication, repair and recombination is discussed.     

Sister Chromatid Exchange Frequencies in Escherichia coli Analyzed by Recombination at the dif Resolvase Site

Sister chromatid exchange (SCE) in Escherichia coli results in the formation of circular dimer chromosomes, which are converted back to monomers by a compensating exchange at the dif resolvase site. Recombination at dif is site specific and can be monitored by utilizing a density label assay that we recently described. To characterize factors affecting SCE frequency, we analyzed dimer resolution at the dif site in a variety of genetic backgrounds and conditions. Recombination at dif was increased by known hyperrecombinogenic mutations such as polA, dut, and uvrD. It was also increased by a fur mutation, which increased oxidative DNA damage. Recombination at dif was eliminated by a recA mutation, reflecting the role of RecA in SCE and virtually all homologous recombination in E. coli. Interestingly, recombination at dif was reduced to approximately half of the wild-type levels by single mutations in either recB or recF, and it was virtually eliminated when both mutations were present. This result demonstrates the importance of both RecBCD and RecF to chromosomal recombination events in wild-type cells.     

A new mutation inEscherichia coli K12,isfA,which is responsible for inhibition of SOS functions

A new mutation inEscherichia coli K12,isfA, is described, which causes inhibition of SOS functions. The mutation, discovered in a ΔpolA ⁺ mutant, is responsible for inhibition of several phenomena related to the SOS response inpolA ⁺ strains: UV- and methyl methanesulfonate-induced mutagenesis, resumption of DNA replication in UV-irradiated cells, cell filamentation, prophage induction and increase in UV sensitivity. TheisfA mutation also significantly reduces UV-induced expression of β-galactosidase fromrecA::lacZ andumuC′::lacZ fusions. The results suggest that theisfA gene product may affect RecA^* coprotease activity and may be involved in the regulation of the termination of the SOS response after completion of DNA repair. TheisfA mutation was localized at 85 min on theE. coli chromosome, and preliminary experiments suggest that it may be dominant to the wild-type allele.