Genetic and molecular characteristics of X-ray-sensitive mutants of Escherichia coli defective in repair synthesis

Identification by immunobinding assay of the polypeptide coded by the DNA polymerase gene of bacteriophage T5 and its amber mutants and the direction of transcription of the gene

We identified by immunobinding assay the polypeptides synthesized as the result of amber mutations in the DNA polymerase gene of bacteriophage T5. Comparison of the size of such polypeptides revealed the order of mutagenic loci of these mutations and the direction of transcription of the gene. Extracts of cells infected with wild-type T5 and with five amber mutants of the polymerase gene (D7, D8, D9, am1, and am6) were prepared, and the proteins were resolved by sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis. After transfer of the proteins to a nitrocellulose sheet, a radioimmunolabeling technique was used to identify the T5 DNA polymerase and its amber mutant polypeptides. Based on the relative sizes of the polypeptides, the transcription of the T5 DNA polymerase gene was determined to proceed in the order D7, D8, am1, D9, and am6. The molecular weights of the DNA polymerase polypeptides coded by D8, am1, D9, am6, and T5+ were 23,000, 45,000, 75,000, 83,000, and 96,000, respectively. The D7-coded polypeptide was not detectable. These data suggest that the carboxyl-terminal region of the enzyme is essential for the polymerase function.

Azaserine: further evidence for DNA damage in Escherichia coli

Azaserine causes DNA damage in stationary-phase cells. In our investigation of this damage, we used strains of Escherichia coli differing in repair capabilities to study azaserine-induced DNA damage, detected as DNA strand breaks by sucrose gradient sedimentation techniques. Reduced sedimentation in alkaline and neutral sucrose gradients indicated the presence of both alkali-labile sites and in situ strand breaks. Azaserine induced DNA single-strand breaks (SSBs) abundantly in all but the recA strain, in which SSBs were greatly reduced. Treatment of purified DNA with azaserine from bacteriophages T4 and PM2 produced no detectable SSBs. Several other studies also failed to detect DNA damage induced directly by azaserine. Increased levels of beta-galactosidase were induced in an E. coli strain possessing a rec::lac fusion, providing further evidence for azaserine induction of the recA gene product. In addition, azaserine induced adaptation against killing but not against mutagenesis in wild-type E. coli strain.

Cloning vectors that yield high levels of single-stranded DNA for rapid DNA sequencing

We have constructed chimeric plasmid vectors with the origin and intergenic region from M13 phage cloned into the PvuII ( pZ145 ) and AhaIII ( pZ150 , pZ152 ) sites of pBR322. In the absence of M13 phage, these plasmids replicate like any other ColE1-derived plasmid and confer both ampicillin and tetracycline resistance (Amp, Tet). Upon infection with M13 phage, the viral origin present on the plasmids permits phage-directed plasmid replication and results in high yields of single-stranded (ss) plasmid DNA in M13-like particles. This ssDNA, which represents only one of the plasmid strands, is useful as a substrate for rapid DNA sequence determination by the dideoxy sequencing method described by Sanger et al. (1977). Since these plasmids contain an intact pBR322, the intergenic region can be transferred onto most pBR322 derivatives to yield ss plasmid DNA without affecting the recipient plasmid for further studies. We also constructed a deletion derivative of pZ145 , plasmid pZ146 , that does not exhibit interference with the growth of the M13 helper, although this plasmid is encapsidated into phage particles. This result confirms the theory that the intergenic region consists of two domains: one domain being a segment involved in phage morphogenesis and the other being a region of functional origin which interferes with M13 replication.

Construction of a plasmid that overproduces the large proteolytic fragment (Klenow fragment) of DNA polymerase I of Escherichia coli

Using currently available gene fusion techniques, we have constructed plasmids that direct the overproduction of the carboxyl-terminal two-thirds of DNA polymerase I, corresponding to the proteolytically derived "Klenow fragment." We have obtained overproduction amounting to several percent of the cellular protein using constructs in which expression is directed either from the lac promoter or from the leftward promoter of phage lambda. The polymerase fragment has been purified to homogeneity from such overproducing strains by a rapid three-stage purification procedure, yielding material capable of carrying out the same reactions (polymerization, 3' labeling, DNA sequence analysis) as the proteolytically derived fragment. The availability of such overproducing strains should greatly facilitate structural and mechanistic studies of DNA polymerase I. Moreover, the techniques we have described for the cloning and expression of a gene fragment should be generally applicable for the study of protein structure and function in other systems.

Genetic characterization of early amber mutations in the Escherichia coli polA gene and purification of the amber peptides

The polA1 mutation of Escherichia coli K12 and two further mutations, resA1 and resA2, characterized in E. coli B have been shown to produce enzymatically active nonsense (amber) peptides. These enzymes can be purified to virtual homogeneity by use of the lambda polA transducing phage system. The peptides are immunologically related and react weakly but specifically with antibody to whole DNA polymerase I. In their purified form the peptides are less heat-labile than the whole enzyme or the Klenow fragment produced by proteolysis. Physiological studies indicate that all three alleles are compatible with a number of different streptomycin resistance mutations (rpsL alleles) in a variety of genetic backgrounds. There is, however, clear evidence for slight amounts of "read-through" of these mutations under these conditions. DNA sequence studies have indicated the exact nucleotides that have been mutated to produce the amber alleles. The resA1 and resA2 alleles appear to be independent isolates of the same mutation both resulting in CAG (Gln) leads to TAG (amber) at amino acid residue 298. The polA1 mutation results in TGC (Trp) leads to TAG (amber) at amino acid residue 342. The significance of these findings is discussed with reference to the structure of the whole enzyme as shown by the DNA sequence data of Joyce et al. (1982) and protein chemistry of Brown et al. (1982).

Role of AP endonuclease in DNA breakage and cell inactivation of Escherichia coli subjected to mild heat (52 degrees C)

The molecular mechanism of DNA injury by mild heat was investigated using matched isogenic mutants of E. coli. On heating at 52 degrees C for 1 h, the number of DNA single-strand breaks (SSBs) detected by the alkaline sucrose gradient sedimentation technique was consistently smaller in mutants NH5016 and BW2001, both deficient in the AP (apurinic/apyrimidinic) endonuclease of exonuclease III, as compared with their wild-type parent AB1157. The greater number of SSBs in the wild type was accompanied by more extensive cell death as compared with the AP-deficient mutants. Heating of endonuclease-free DNA systems, viz., T4 phage and T4 DNA, at 52 degrees C for up to 4 h did not result in any detectable SSB. Apparently, cellular injury by mild heat is self-inflicted through an AP-endonuclease-mediated process and hence depends on the cell's genetic complement of AP endonuclease. Mild heat is believed to activate the nucleolytic attack, and the resultant DNA-strand breaks, if not repaired, will eventually lead to cell death.

Detection of the catalytic activities of DNA polymerases and their associated exonucleases following SDS-polyacrylamide gel electrophoresis

A method is described to detect DNA polymerases and nucleases in homogeneous or crude enzyme preparations after electrophoresis in SDS-polyacrylamide gels(2) containing the appropriate template or substrate. DNA polymerases are electrophoresed in a gel containing gapped calf thymus DNA and after a renaturation treatment, the gel is incubated in a reaction mixture in which one deoxyribonucleoside triphosphate is [alpha-32P]-labelled. Incorporation of radioactivity into DNA is detected at the vicinity of the polymerase band by autoradiography. An associated nuclease activity can be measured after electrophoresis in a gel containing 32P-labelled gapped DNA, when nucleolytic digestion is seen as a clear band in the resulting autoradiogram. The gels can subsequently be stained with Coomassie blue to establish identical molecular weights of polymerase, nuclease and protein bands. Applications of this technique are discussed.

Repair of x-ray-induced deoxyribonucleic acid single-strand breaks in xth mutants of Escherichia coli

An exonuclease III-deficient strain of Escherichia coli K-12, BW2001 (xthA11), was unable to perform rapid repair of X-ray-induced deoxyribonucleic acid single-strand breaks and appeared to have a defect in the priming of the 3'-termini necessary for initiation of repair synthesis at the breaks. This defect cannot be explained solely by the lack of exonuclease III activity, because other xth mutants tested, including a deletion mutant, repaired radiation-induced strand breaks at close to the normal rate.

The effects of the ultraviolet-protecting plasmids pKM101 and R205 on DNA polymerase I activity in Escherichia coli K-12

The mutagenesis- and repair-enhancing plasmids pKM101 and R205 were introduced into a series of Esherichia coli K-12 polA mutants including two temperature-sensitive mutants. Polymerase levels in extracts of these strains were assayed using an activated DNA template. In none of the cases did the presence of the plasmid in the strains change either the initial rate of incorporation of [3H]thymidine triphosphate into acid-soluble material or the subsequent degradation of the template at longer reaction times. Neither did the presence of the plasmids affect the proportion of N-ethylmaleimide-sensitive polymerase activity detected. Previous studies have reported increased polymerase I-like activity of polA mutants of Salmonella typhimurium and Pseudomonas aeruginosa upon introduction of mutagenesis- and repair-enhancing plasmids. Our experiments indicate that, at least, such an increase in polymerase-I-like activity is not an obligatory phenotype associated with these plasmids.

Deoxyribonucleic acid strand breaks during drying of Escherichia coli on a hydorohobic filter membrane

Cells of Escherichia coli mounted on a hydrophobic filter membrane were dried under various vapor pressures. A mutant defective in deoxyribonucleic acid repair (uvrA recA) was more sensitive to drying at a water activity of 0.53 or below than the parent strain but not at a water activity of 0.75 and above. Sucrose gradient studies showed that single- and double-strand breaks of deoxyribonucleic acid occurred at a water activity of 0.53 or below, but no breaks could be observed at a water activity of 0.75 or above. These results were observed in all cells rehydrated with 0.03 M tris (hydroxymethyl) aminomethane-hydrocholoride buffer solution at 0 or 37 degrees C, in the presence or absence of oxygen, with saturated water vapor or with a hypertonic solution followed by a gradual dilution. Freezable water was detected in the cells only at a water activity above 0.75 by differential scanning calorimetry. Removal of unfreezable water of cells in the drying, therfore, might induce deoxyribonucleic acid strand breaks.

Induction of mutations in bacteriophage T7 by gamma-rays: independence of host-repair mechanisms

Amber mutants of bacteriophage T7 are reverted by gamma-rays to pseudo wild-type particles, i.e. particles able to propagate in a suppressorless host. The yield of revertants is much higher when the phage is irradiated in the presence of oxygen than when irradiated anoxically. Under particular gas conditions the efficiency of mutation induction differs by less than a factor of ten among six different amber codons in cistrons 1, 5, 6, 12, 17 and 19. The induction of mutations is not dependent on error-prone repair involving the recA or lexA genes of the host cell. It is estimated that of the damages that may be inflicted by gamma-rays upon an amber codon, fewer than 1 out of 85 results in reversion of the codon to pseudo wild-type.

Exonuclease associated with bacteriophage T5-Induced DNA polymerase

T-5-induced DNA polymerase has been shown to possess a 3' leads to 5'-exonucleolytic activity. The exonuclease acts on both native and denatured DNA, but the apparent rate of degradation of denatured DNA is about five times faster than that for native DNA. The enzyme appears to act only on 3'-OH ends and produces mainly 5'-dNMP's. Like polymerase activity, exonuclease activity shows a pH optimum around 8.6. Mg2+, dithiothreitol, and N-ethylmaleimide had identical effects on both the activities. Nicked DNA was almost totally protected from exonuclease action under synthetic conditions, i.e., in the presence of 4dNTP's. Denatured DNA was partly degraded in the early phase of incubation with 4dNTP's, presumably due to unhybridized tails at the 3'-OH primer ends. However, the exonuclease activity was operative in both cases under synthetic conditions, as evidenced by template-dependent conversion of [3H]dTTP to [3H]dTMP.

Evidence that the gene uvrB is indispensable for a polymerase I deficient strain of Escherichia coli K-12

Conclusive evidence in presented to show that the gene uvrA is dispensable, but the uvrB is indispensable for an Escherichia coli strain carrying gene polA1. We constructed strains E139 (sup-126 polAl uvrB59) and E159 (sup-126 polAl uvrA43) where mutations polAl, uvrB59 and uvrA43 are amber mutations and mutation sup-126 is an amber suppressor mutation effective at 30 degrees C but not at 42 degrees C. At 42 degrees C, strain E139 is inviable but strain E159 viable whereas both are viable at 30 degrees C. Revertants of E139 viable at 42 degrees C occurred spontaneously at a frequency of about 3 X 10(-4). One of the revertants was shown to be caused by suppressor mutation, designated spu, rather than back mutation of the gene uvrB59 or polAl or amber suppressor mutation. Viabilities of the revertants varied from 10(-3) to 1.0 at 42 degrees C compared with those of 30 degrees C. At 42 degrees C, all the revertants with normal viabilities at 42 degrees C were non-filamentous in contrast to the filamentous character of E139. However, strain E159 was viable at 42 degrees C despite its filamentous character. We conclude that the gene uvrB is involved not only in excision repair but also in normal growth in a polA background.

Replication of bacteriophage T4 DNA in vitro. I. Basic properties of the system

A new in vitro system for T4 DNA replication was developed by concentrating cell lysates on cellophane disks. The time course of [3H]dTTP incorporation into DNA by the system was separated into two phases: one was a very rapid incorporation which was terminated within 2 min (phase I reaction), and the other was a slow but continuous incorporation thereafter (phase II reaction). More than half of the phase I reaction product was Escherichia coli DNA, but the phase II reaction was mostly T4 DNA. Phase II reaction required four deoxyribonucleoside triphosphates, ATP, Mg2+, and KCl. 5-Hydroxymethyldeoxycytidine triphosphate was essential for the reaction and not substitutable by dCTP. The presence of KCN or NaN3 in the reaction mixture did not interfere with [3H]dTTP incorporation, but the addition of deoxyribonuclease completely degraded the system. Alkaline sucrose sedimentation analysis of phage II reaction product revealed that phase II reaction proceeded by the discontinuous mode of DNA replication as in vivo. After T4 infection, the activity for phase II reaction appeared in parallel with the activity of T4 phage DNA replication in vivo.

Formaldehyde induced DNA-protein crosslinks in Escherichia Coli

Exposure of Escherichia coli to low doses of formaldehyde induces interstrand cross-links in the cellular DNA, at least 50% of which involve protein "bridges" between the DNA strands. The biological importance of these cross-links is suggested by both the high yield of formation and by the inability of some sensitive repair deficient mutants to completely remove cross-links and bound protein from the DNA during post treatment incubation.

Increased spontaneous reversion of certain frameshift mutations in DNA polymerase I deficient strains of Escherichia coli

A tenfold increase in the spontaneous reversion frequency of two of six lacZ frameshift mutations tested was observed in strains containing the following DNA polymerase I mutations--polA1, polA5, polA6, polAex1, res-3 and resA1. Reconstruction experiments indicated that this increase was not the result of a selective effect. Only a fourfold increase in frameshift mutations was found in strains containing a polA107 mutation. Both the polAex1 and polA107 mutations result in defective 5' to 3' exonuclease activity and do not affect polymerizing activity, but have different effects on frameshift mutation. A polA mutation on the chromosome induced frameshift mutations in a gene on an F episome. None of three auxotrophic mutations studied showed high frequency reversion in the presence of the polA1 or polA6 mutations.

Comparative analysis of deletion and base-change mutabilities of Escherichia coli B strains differing in DNA repair capacity (wild-type, uvrA-, polA-, recA-) by various mutagens

Dose-response curves were compared for deletions [ColBR (resistant to colicin B) mutations being more than 80% deletions] and base changes (reversion of argFam to prototrophy argplus) induced in the same set of E. coli strains (wild-type for DNA repair, uvrA-, polA- and recA-) by N-methyl-N'-nitro-N-nitrosoguanidine (NTG), ethyl methanesulfonate (EMS), hydroxylamine (HA), 4-nitroquinoline I-oxide (4NQO), mitomycin C (MTC, UV and X-rays. All these agents induced deletions as well as base changes in the wild-type strain. Thus chemical mutagenesis differed in E. coli and bacteriophages in vitro, for HA, NTG, EMS and perhaps UV produced only point mutations in phage Tr. The patterns of deletion and base-change mutability in E. coli were surprisingly similar. (I) The recombination less recA- strain was mutable by only three (NTG, EMS, HA) of the seven mutagens for either deletions or base changes. (2) The uvrA- strain, unable to excise pyrimidine dimers, was very highly mutable by 4NQO and UV but immutable by MTC for both deletions and base changes. (3) The polA- strain, defective in DNA polymerase I due to a non-suppressible mutation, was very highly mutable by HA and highly mutable by MTC and 4NQO for both deletions and base changes but was highly mutable only for deletions by UV and X-rays, remaining normally mutable by the other agents for both deletions and base changes despite its high sensitivity to their inactivating action. We conclude that errors in the recA-dependent repair of induced DNA damage (after 4NQO, MTC, UV and X-rays) or errors in replication enhanced by damage to the replication system or to the template strands (after NTG, EMS, and HA) give rise to deletions as well as to base changes. From a comparative analysis of 14 dose-response curves for deletions and base changes, we conclude that the order of mutagenic efficiency relative to killing is (EMS, NTG) greater than (UV, 4NQO) greater than HA greater than (X-rays, MTC), and that X-rays, 4NQO, HA and MTC induce more ColBR deletions than Argplus base changes, whereas UV and EMS induce ColBR deletions and Argplus base changes at nearly equal rates and the specificity of NTG is intermediate between these two types.

Radiation genetics in microorganisms and evolutionary considerations

Recent knowledge of UV-resistance mechanisms in microorganisms is reviewed in perspective, with emphasis on E. coli. Dark-repair genes are classified into "excision" and "tolerance" (ability to produce a normal copy of DNA from damaged DNA). The phenotype of DNA repair is rather common among the microorganisms compared, and yet their molecular mechanisms are not universal. In contrast, DNA photoreactivation is the simplest and the most general among these three repair systems. It is proposed that DNA repair mechanisms evolved in the order: photoreactivation, excision repair, and tolerance repair. The UV protective capacity and light-inducible RNA photoreactivation possessed by some plant viruses are interpreted to be the result of solar UV selection during a rather recent era of evolution.

A conditional lethal mutant of Escherichia coli K12 defective in the 5' leads to 3' exonuclease associated with DNA polymerase I

A mutant strain of E. coli, initially identified by an abnormally high frequency of recombination, has been found to be defective in the 5' --> 3' exonuclease associated with DNA polymerase I, but not in the polymerase activity. This defect is tolerated at 30 degrees , but is lethal at 43 degrees . Like other polymerase I mutants, the strain is unusually sensitive to methyl methanesulfonate and to ultraviolet irradiation; it is also unable to support the growth of phage lambda defective in general recombination, and shows a reduced rate of joining of 10S "Okazaki fragments." These results demonstrate that a functional DNA polymerase I is essential for normal growth and viability in E. coli K12.

Deoxyribonucleic acid breaks in heated Salmonella typhimurium LT-2 after exposure to nutritionally complex media

Minimal medium recovery of heat-treated Salmonella typhimurium LT-2 has been expressed as the reduced viability on trypticase soy agar supplemented with 0.5% yeast extract (TSY) relative to a glucose-salts (M-9) agar. Incubation of S. typhimurium LT-2 in water at 50 C for 15 min did not change the sedimentation patterns of deoxyribonucleic acid (DNA) in alkaline sucrose gradients. The same pattern was obtained if the heated cells were further incubated for 15 min at 37 C in M-9 broth. However, a marked increase in DNA single-strand breakage accompanied by a loss of viability was observed after a similar incubation of heated bacteria in TSY broth. If heated bacteria were incubated in M-9 broth before TSY broth, there was a decrease in the single-strand breakage occurring in the TSY broth. This decrease is believed to be the result of repair of heat-induced damage. We conclude that minimal medium recovery after heat treatment is due to DNA damage caused by sequential exposure to heat and TSY medium, such damage not occurring after sequential exposure to heat and M-9 medium.

Comparison of the resA1 and polA1 mutations in isogenic strains of Escherichia coli K-12

Strains carrying either the polA1 or resA1 mutation are deficient in DNA polymerase I, and the polA1 and resA1 mutations do not complement in merozygotes. The effect of these mutations in otherwise identical genetic backgrounds was studied: after ultraviolet irradiation both strains degrade their DNA more rapidly and more extensively than the wild-type strains. However, after X-ray irradiation the resA1 strain shows little DNA breakdown and repairs its single-strand breaks. In contrast, the polA1 strain degrades its DNA extensively, and single-strand breaks are not repaired. Moreover, the resA1 strain is capable of supporting the growth of a red(-) bacteriophage lambda, whereas the polA1 strain is not.

Radiation-resistant mutants of Salmonella typhimurium LT2: development and characterization

A series of repeated exposures to gamma irradiation with intervening outgrowth of survivors was used to develop radioresistant cultures of Salmonella typhimuium LT2. Stepwise increases in resistance to both ionizing and ultraviolet irradiation were obtained independently of the presence or absence of integrated P22 prophage. Single clonal isolates, representing parent and radioresistant populations, retained the general characteristics of the LT2 parent, including serological properties, phage typing, antibiotic sensitivities, mouse virulence, and most biochemical test reactions. Resistant cells were generally larger and contained 1.8 to 2.1 times more ribonucleic acid and protein than parent cells, but deoxyribonucleic acid (DNA) contents were similar. Heterogeneity in the populations with respect to release of H(2)S, utilization of carbon sources, and growth on minimal medium is considered to be ancillary, rather than causally related, to increased radioresistance. The resistant isolates displayed an increased ability to reactivate gamma-irradiated P22 phage. DNA polymerase I and polynucleotide-joining enzyme activities were elevated in extracts of radioresistant cells relative to parent cells. It is suggested that the observed increases in radioresistance result from a selection of mutations leading to an increased capacity to repair DNA.

Ultraviolet-stimulated DNA synthesis in toluenzied Escherichia coli deficient in DNA polymerase I

Ultraviolet (UV)-stimulated nonconservative DNA synthesis has been observed in E. coli rendered permeable to nucleoside triphosphates by exposure to toluene. This synthesis is detected in toluenized cells in which the background of UV-independent DNA synthesis is reduced by use of dnaB mutants temperature-sensitive for DNA replication and additionally deficient in DNA polymerase I. UV-stimulated nonconservative synthesis is also seen in polA dnaE mutants that are deficient in two of the three known DNA polymerases. The observed UV-stimulated repair-like synthesis requires the presence of the four deoxyribonucleoside triphosphates and ATP. This mode of synthesis appears to differ from the ATP-independent nonconservative DNA synthesis previously reported to occur in toluenized bacteria.

Ultraviolet-sensitive mutator mutU4 of Escherichia coli inviable with polA

Attempts to transduce the ultraviolet-sensitive mutator lesion mutU4 into strains deficient in deoxyribonucleic acid polymerase I (polA) were unsuccessful. Mutator recombinants were found when the polA recipient had first been reverted to Pol(+) by selection for resistance to methyl methanesulfonate. The inviability of the mutU4 polA double mutant was demonstrated by a reduction in the absolute number of transductants when the recipient was polA as compared with Pol(+), and selection was made for markers very close to mutU4. Double mutants containing mutU4 and polA4, which determines a cold-sensitive polymerase, were unable to grow at 24 C, the nonpermissive temperature.