THE EFFECTS OF HOST-CELL REACTIVATION ON ASSAY OF U.V.-IRRADIATED HAEMOPHILUS INFLUENZAE TRANSFORMING DNA

Abstract— The host cell reactivation (HCR) mechanism in Haemophilus influenzae cells is inhibited by sub-microgram concentrations of acriflavine (as is already known to be true for Escherichia coli ). Exposure of these cells to similar concentrations of the drug during bacterial transformation increases the apparent ultraviolet light (u.v.) sensitivity of previously irradiated transforming DNA, indicating a repair of this DNA after uptake by the cells under normal conditions. Repair is inhibited by applying acriflavine at any time up to one hour after competent cells contact the irradiated transforming DNA. The fraction of the u.v. damage repaired by HCR is very different for different genetic markers. Those markers which are most u.v. sensitive when assayed in the absence of acriflavine are most poorly repaired, suggesting that this is the reason for their higher sensitivity. For all markers the fraction of the damage repairable by in vitro photoreactivation is approximately constant, and strongly overlaps the damage repairable by HCR. The degree of HCR achieved can be altered by experimental treatment of the H. influenzae DNA prior to transformation. Thus treatment of irradiated DNA with an enzyme from Micrococcus lysodeikticus –known to attack u.v. damaged, but not undamaged DNA–prevents subsequent intracellular repair of the same u.v. lesions whose repair is inhibited by acriflavine. Similarly, partial replacement of the thymine in transforming DNA by 5-bromouracil (BU) strongly inhibits repair of subsequent u.v. damage. As in bacteriophage, the BU effect is relieved if the u.v. exposure occurs in the presence of cysteamine. It is clear that intracellular repair must be considered in interpreting experiments with u.v.-irradiated transforming DNA.     

VARIATION IN THE PHOTOCHEMICAL REACTIVITY OF THYMINE IN THE DNA OF B. SUBTILIS SPORES, VEGETATIVE CELLS AND SPORES GERMINATED IN CHLORAMPHENICOL*,†

Abstract— The chief photoproduct of thymine produced in u.v. irradiated (2537Å) vegetative cells of B. subtilis is the cyclobutane-type dimer while in spores very little of this dimer is produced (maximum yield 2·6 per cent of thymine) but a new photoproduct is produced in high yield (maximum of 28·4 per cent of thymine). This difference in photochemical response appears to be due, at least in part, to a difference in uydration of the DNA. The photochemistry of thymine in isolated DNA irradiated in solution is similar to that of DNA in irradiated vegetative cells, but differs markedly from that of isolated DNA irradiated dry. The yield of cyclobutane-type thymine dimer is much reduced in isolated DNA irradiated dry but a new photoproduct of thymine. is produced which is chromatographically similar to the spore photoproduct. The yield of this photoproduct, however, is never as great as that obtained in irradiated spores. The photochemistry of the DNA thymine of spores germinated in the presence of chloramphenicol is very similar to that of normal vegetative cells. Except for hydration, the physical state of the DNA is probably not otherwise altered by germination in the presence of chloramphenicol since DNA replication is prevented by the presence of chloramphenicol. These results are also consistent with the hypothesis that the unique photochemistry of spores is due, at least in part, to the hydration state of the DNA. The acid stability of the spore photoproduct is indicated by the fact that it is isolated from irradiated spores after hydrolysis in trifluoroacetic acid at 155°C for 60 min. It still contains the methyl group of thymine as judged by the fact that for a given dose of u.v. the same yield of photoproduct was obtained whether the spores were labeled with thymine-2–C-14 or -methyl-C-14. This photoproduct is stable to reirradiation (2537Å) in solution under condiditions where thymine dimers of the cyclobutane-type are completely converted back to monomeric thymine. On a column of molecular sieve material (Sephadex-G10), the spore photoproduct elutes in a region intermediate between the cyclobutanetype thymine dimers and monomeric thymine. Of the numerous compounds tested by paper chromatography, the spore photoproduct is most similar (but not identical) in several solvents to 5–hydroxyuracil and 5–hydroxymethyluracil. Our data do not allow us to decide if the product is a monomer or a dimer. Although the photochemistry of thymine in the DNA of spores differs markedly from that for vegetative cells, several lines of evidence make it seem doubtful that the enhanced resistance of spores to u.v. relative to that of vegetative cells can be explained solely on the basis of this difference in the photochemistry of DNA thymine.     

CONDITIONS AFFECTING THE EARLY THYMINELESS DEATH OCCURRING AFTER ULTRAVIOLET IRRADIATION OF ESCHERICHIA COLI B3

Abstract— Exposure of the thymine requiring bacterium Escherichia coli strain B3 to ultraviolet light (u.v.) prior to incubation in the absence of thymine shortens the lag period normally observed before the onset of death due to lack of thymine. Culture conditions promoting synthesis of new kinds of enzymes at the time of thymineless challenge after u.v. irradiation enhance this effect. The effect can be reversed either by the addition of thymine or photo-reactivation. Possible mechanisms for these phenomena are discussed.     

SENSITIZED PHOTOINACTIVATION OF BACTERIOPHAGE T4

Abstract— The photoinactivation of an osmotic shock resistant mutant of the bacteriophage T 4 can be sensitized by two cationic derivatives of acetophenone. At least part of the sensitized inactivation appears to be due to the formation of thymine dimers in phage DNA by a mechanism which involves triplet excitation transfer from the sensitizer to thymine in the DNA. The photoreactivable sector of the phage inactivated by sensitized irradiation is about 0.6, almost twice as large as the sector for u.v. irradiated phage.     

CHANGE IN THE BASE COMPOSITION OF MESSENGER RNA OF ESCHERICHIA COLI BY ULTRAVIOLET IRRADIATION AND ITS RECOVERY

Abstract— The base composition of messenger RNA in Escherichia coli B/r and B _8–1 irradiated with ultraviolet (u.v.) light has been examined. The experimental results are as follows: (1) the synthesis of rapidly labeled RNA does not stop in ultraviolet irradiated bacteria. (2) The rapidly labeled RNA in irradiated cells shows a change in base composition corresponding to the formation of pyrimidine dimers in DNA molecules. The mole per cent of adenine component is increased with ultraviolet dose. The ratio of purine/pyrimidine becomes larger and the GC content smaller. (3) The base composition of the rapidly labeled RNA in irradiated bacteria reversed to that in unirradiated cells, when the irradiated cells were reactivated by experimental procedures for photoreactivation or dark reactivation. The reversion in the base composition corresponds well to the decrease in the amount of thymine dimers in DNA molecules. (4) The mechanism of the change in the base composition of rapidly labeled RNA caused by ultraviolet irradiation is discussed.     

RELATIONSHIP BETWEEN SURVIVAL AND THYMINE-DIMER EXCISION IN ULTRAVIOLET-IRRADIATED ESCHERICHIA COLI

Abstract— The influence of amino acid prestarvation on both the resistance to u.v. light and excision of thymine dimers of bacterial strains E. coli B/r hcr ⁺ thy- trp ^-, E. coli B/r hcr ^-thy^- trp ^-, and E, coli 15 T^- 555–7 thy ^- meth ^- trp ^- arg ^- has been studied.
The prestarvation increased the resistance of all the strains but reasonably inhibited excision of thymine dimers. Thus the enhancement of u.v. resistance after amino acid prestarvation was not due to more complete excision of thymine dimers.     

THYMINE DIMERIZATION IN L-STRAIN MAMMALIAN CELLS AFTER IRRADIATION WITH ULTRAVIOLET LIGHT AND THE SEARCH FOR REPAIR MECHANISMS

Abstract— The formation of thymine dimers in the DNA of L -strain mammalian cells after irradiation with ultraviolet light has been demonstrated. The amount of dimer formed rises with the dose of u.v. light.
In the course of post-irradiation incubation the thymine dimers remain in the TCA insoluble fraction and diminish as did the other thymidine-H³ derivatives with increasing incubation time. The dimer is not found in the soluble fraction. Thus, dimer excision (i.e. its liberation into the soluble fraction) as an expression of repair of radiation damage analogous to dark repair in E. coli was not found in these experiments.     

EFFECTS OF SENSITIZED AND UNSENSITIZED LONGWAVE U.V.-IRRADIATION ON THE SOLUTION PROPERTIES OF DNA

Abstract— Two types of photoreactions occur in DNA irradiated in aqueous systems with longwave u.v.-light (Λ > 295 nm), namely, (a) thymine dimerization, and (b) single- and double-strand breakage of the sugar phosphate backbone; these two reactions are unrelated. The presence of acetophenone as a photosensitizer caused an increase in dimerization by a factor of 16, and an increase in single-strand breaks by a factor of 4. The number of thymine dimers per single-strand break is about 100 in the sensitized and 25 in the unsensitized reaction. The alteration of the radius of gyration of DNA molecules is that expected by the degradation observed. At the same time the change in hyperchromicity is very small. Therefore as far as can be detected by these methods of investigation the gross conformation of the DNA double helix is stable against thymine dimerization.     

THE U.V. SENSITIVITY OF BACTERIA: ITS RELATION TO THE DNA REPLICATION CYCLE

Abstract— A striking increase in the shoulder of the u.v. survival curve but no change in the limiting slope is obtained when cultures of Escherichia coli strain TAU complete the DNA replication cycle in the absence of concommitant protein synthesis prior to irradiation. The u.v. sensitivity of protein synthesis or RNA synthesis is not altered significantly by this treatment.
In contrast to the result for strain TAU, there is no significant change in the u.v. survival curve for the u.v. sensitive E. coli B_s-1 when its DNA replication cycle is completed under similar conditions.
Following a period of inhibited protein synthesis there is a delay in the reinitiation of the normal DNA replication cycle when protein synthesis resumes. This delay would allow time for an intracellular repair system to operate before the attempted resumption of normal replication. Strain B_s-1, which is deficient in this repair system, would not be expected to benefit from such a delay, as consistent with the observed results. A model is presented to account for lethality due to attempted DNA replication during a period of repair synthesis. The maximum survival for a given u.v. dose would be predicted for a culture which has completed the normal DNA replication cycle prior to irradiation and which is not permitted to reinitiate the cycle until all possible repair synthesis is completed.     

DEGRADATION OF THE DNA OF ESCHERICHIA COLI K12 REC- (JC1569b) AFTER IRRADIATION WITH ULTRAVIOLET LIGHT*

Abstract— Degradation of the DNA of a rec^- mutant of Escherichia coli K12 (JC1569 b) induced by u.v. light was investigated. The rate of degradation was much larger by growing bacteria than by stationary cells. When growing bacteria were starved for amino acids, their DNA became resistant to irradiation. The mode of u.v.-induced degradation was investigated by comparing the time course of release from the acid-insoluble fraction of the label for two growing cultures; the one was pulse-labeled with ³H-thymidine and the other was pulse-labeled and chased thereafter for 12 min. It was found that the label incorporated into the former culture begins to be lost from the acid-insoluble fraction prior to the loss of the label incorporated into the latter culture. It was concluded that breakdown of the replicating point precedes degradation of the bulk of the DNA. This result suggested that the replicating point is a sensitive site to irradiation and the u.v.-induced degradation of DNA seemed to be influenced by the state of chromosome at the time of irradiation. Experiments of centrifugation of lysed spheroplasts of bacteria uniformly labeled with ³H-thymidine in alkaline sucrose demonstrated that DNA of low molecular weight appeared after irradiation with only 5 ergs/ mm², and that the molecular weight could not be restored by post-irradiation incubation. Considering these results, an hypothesis is proposed concerning the initiation of induced degradation of the DNA of the rec^- mutant.     

Repair replication in Chinese hamster cells after damage from ultraviolet light

Abstract— After irradiation with u.v. light, Chinese hamster cells perform repair replication of their DNA. Small numbers of nucleosides are inserted into DNA, such that when BrUdR is used there is no detectable change in density. Repair replication begins immediately after irradiation, but it decelerates steadily and at least half is complete within 4 hr. Repair replication saturates above 200 ergs/mm² at a level which represents 0.055 per cent replacement of all thymine sites in 4 hr. Repair replication in mammalian cells, in contrast to that in microorganisms, does not appear to replace pyrimidine dimers excised from DNA in acid soluble form, and neither repair nor semiconservative replication discriminates between BrUdR and TdR.     

RECOVERY OF HAEMOPHILUS INFLUENZAE FROM ULTRAVIOLET AND X-RAY DAMAGE

Abstract— Results of experiments on reactivation of ultraviolet (u.v.)-irradiated Haemophilus influenzae and cellular reactivation of u.v.-damaged transforming deoxyribonucleic acid (DNA) and bacteriophage are reported. Liquid-holding recovery (LHR) is small for the u.v.-sensitive mutant BC100 which, relative to the wild type, also has greatly reduced host-cell reactivation (HCR) of u.v.-inactivated phage, and competent cultures show reduced competent cell reactivation (CCR) of u.v.-inactivated transforming DNA. BC100 cells can be transformed with DNA isolated from the wild type strain Rd to a u.v. resistance similar to that of Rd, and irradiation of the DNA reduces the transformation frequency for this marker (uvr). The u.v.-resistant mutant BC200 displays very little LHR under the usual conditions where reactivation occurs after plating. The colony-forming ability (cfa) of irradiated BC200 is greater than that of Rd, but HCR and CCR are the same on this mutant as on the wild type. The major difference between Rd and BC200 is the enhanced u.v. survival of cfa of the latter. It was determined that this difference reflects cell lysis of irradiated Rd and lack of lysis in BC200 cultures. That lysis is closely correlated with damage to the bacterial chromosome is suggested by the finding that the lytic response of Rd (as determined turbidimetrically) can be negated by the liquid-holding procedure, but lysis of BC100 (which lacks comparable DNA-repair ability) can be only partially inhibited by this procedure. LHR occurs when post-plating dark recovery is incomplete, is temperature-sensitive, and occurs unimpeded when post-u.v. protein synthesis is inhibited by chloramphenicol. It is suggested that enzymatically catalyzed reactivation of DNA occurs or is initiated during liquid-holding of u.v.-irradiated H. influenzae Rd and that the necessary enzyme(s) exists prior to appearance of u.v. lesions in the DNA. Results are reported for X-ray inactivation of transforming DNA as assayed on BC100, Rd and BC200 and of the cfa of the three strains.     

DIFFERENTIAL, LETHAL AND MUTAGENIC ACTION OF 254 nm AND 320–400 nm RADIATION ON SEMI-DRIED BACTERIA

Abstract— The effect of culture conditions on the lethal and mutagenic action of 254 nm (u.v.) and 320–400 nm (b.l.) light has been examined. Ten strains of Escherichin coli were used in these investigations. It was found that semi-dehydration in aerosols greatly enhanced the lethal and mutagenic actions of both U.V. and b.l., Mutations induced by U.V. were found to be of a random kind, while those produced by b.l. were specific and of a particular biochemical type depending on the strain of cell and its stage of development. The presence of oxygen during irradiation enhanced b.l. effects but had no effect on U.V. damage while anaerobic growth endowed the cells with added resistance to b.l. and u.v., Stationary phase cells of E. coli B/r were found to be mutated by b.l. specifically at a thymine locus and to be more sensitive than E. coli B to the inhibition by b.l. of respiration. Some mutations induced by b.l. in E. coli B/r were found to hinder the cells ability to carry out the photoreversal of U.V. damage. It is suggested that b.1. affects a specific piece of DNA which is in contact with the cytochrome chain of the cytoplasmic membrane and that this contact point between the cytochrome chain and DNA alters sequentially as the cell proceeds through its life cycle.     

Direct demonstration of the monomerization of thymine-containing dimers in U.V.-irradiated DNA by yeast photoreactivating enzyme and light

Abstract— Ultraviolet-irradiated E. coli DNA (³H-thymine-labelled) was mixed with un-irradiated E. coli DNA (¹⁴C-thymine-labelled) and exposed to light in the presence of purified yeast photoreactivating enzyme. As the ³H-thymine-containing cyclobutane dimers disappeared during the photoreactivation, there was a stoichiometric increase of monomeric ³H-thymine as determined from the ³H/¹⁴C ratio in thymine. This is the first direct demonstration that thymine-containing dimers in u.v.-irradiated DNA are monomerized by yeast photoreactivating enzyme in the presence of light.     

Ultraviolet action spectra in perspective: with special reference to mutation

Abstract— Problems of determining action spectra are considered as well as various types of action spectra for U.V. action upon cell activities. U.V. is an effective mutagenic agent producing point mutations and chromosomal changes. U.V. is readily absorbed by superficial layers of cells in tissues; therefore, special experimental procedures are necessary for induction of mutations in animals or plants. U.V. is, however, suitable for mutagenesis in microorganisms because their cells are small, permitting the radiation to reach the nuclei. Action spectrum studies reveal that u.v. mutagenesis results from absorption of the radiation by nucleic acid. The most prominent alteration in DNA following absorption of u.v. is dimerization of pyrimidines, chiefly thymine. Such a change not only retards DNA replication but results in errors (mutations). U.V. mutagenesis therefore depends upon the conditions before, during and after irradiation. Thus immediate post-treatment with visible and long u.v. light splits pyrimidine dimers, thereby reversing impending u.v. mutagenesis. For cells kept in the dark, conditions which prevent DNA replication by interfering with the metabolism of the cell provide time for dark repair of the DNA lesion and so for reversal of the impending mutation.     

THE INFLUENCE OF NUTRITION ON THE DNA CONTENT OF ESCHERICHZA COLI AND ITS RESPONSE TO ULTRAVIOLET LIGHT

Abstract— The influence of nutrition on the sensitivity of Escherichia coli 15 T- to ultraviolet light (u.v.) and the synthesis of DNA has been studied. Growth in media containing glucose or NH,⁺ has been found to endow cells with a greater resistance to lethal u.v. damage than those grown in media containing succinate or amino acids, respectively. In addition, the sensitivity of the lactose ( lac ) locus of the DNA to mutagenic damage has been found to be altered by changes in the carbon supply but not by changes in the nitrogen source, while the sensitivity of loci controlling amino acid synthesis was altered by changes in the nitrogen source but not in the carbon source. Cells fed with glucose or NH₄⁺ have been found to possess more DNA than cells fed with succinate or amino acids, respectively. The data indicate that the type of carbon and nitrogen supplied to the cells will determine whether or not set regions of the DNA will undergo more than one round of replication. The presence in the cell of identical genetic loci either in duplicate or in multiples, directed by the particular types of carbon and nitrogen supplied, is suggested to be, in part, the reason why an alteration in nutrition is able to influence the sensitivity of bacterial cells to radiation.     

MEASUREMENT OF DNA CROSSLINKS BY S1 NUCLEASE: INDUCTION AND REPAIR IN PSORALEN-PLUS-360 nm LIGHT TREATED ESCHERICHIA COLI

Abstract—DNA crosslinks in Escherichia coli cells. exposed to 4.5',8-trimethylpsoralen plus 360 nm light, were measured using a rapid and sensitive new approach. The assay is based on the specificity of S₁ nuclease from Aspergillus oryzae to single-stranded DNA. Bacterial cells were lysed and the DNA denatured by alkali. Following acid neutralization. crosslinked DNA undergoes spontaneous renaturation and is rendered S₁-nuclease resistant and therefore acid-precipitable. The single-stranded fraction after denaturation by alkali decreases with increasing near UV light exposure in the presence of TMP following first order kinetics. The kinetics were faster when exposure was at 4°C rather than at 20°C. This suggests that excision of crosslinks occurs during exposure at the higher temperature. Indeed. since the rate of DNA crosslinking in a uvr B mutant which is excision-deficient was higher than in wild type bacteria at 4°C, some excision must have occurred even in the cold. DNA from excision-proficient cells incubated at 37°C following exposure to TMP-plus-near UV at 4° showed a greater single stranded fraction than that from non-incubated cells. This indicates repair of DNA crosslinks. which proceeded with a half-time of 8 min at 37°C and was unaffected by substitution of thymine in DNA by 5-bromouracil.     

OVERLAPPING ACTION OF HOSTCELL REACTIVATION AND PHOTOREACTIVATION IN BACTERIA

Abstract— The photoreactivation rate of U.V. irradiated phages is decreased in u.v. irradiated bacteria. In contrast, the normal photoreactivation rate is observed if the irradiated bacteria are photoreactivated before phage infection. The decrease of the photoreactivation ratc is understood as a competing effect of the u.v. lesions in the bacterial nucleic acids for the photoreactivation enzyme. This competitive inhibition can be diminished not only by photoreactivation of the bacteria before phage infection but also by hostcell reactivation of the u.v. lesions in the bacterium. The results provide strong evidence that hostcell reactivation and photoreactivation revert the same u.v. photoproducts in bacterial nucleic acids. The experiments show that the hostcell reactivation enzyme is not induced by phage infection or by irradiation, but is normally present in the bacterial cell.     

A mutant of Escherichia coli K12 exhibiting varying ultraviolet sensitivities depending on the temperature of incubation after irradiation

Abstract— A mutant, URT-43, was isolated from E. coli C600 dar⁺. The mutant has a characteristic feature in that its sensitivity to ultraviolet (u.v.) light is greatly influenced by the temperature at which irradiated bacteria are incubated. On the basis of dose-reduction factor, URT-43 is approximately ten times more sensitive at 42° than at 30°C, even though unirradiated bacteria are not thenno-sensitive, The mutant could not repair u.v.-irradiated bacteriophage Λ_vir in the dark either at 30° or at 42°C, indicating that it is defective in host-cell reactivation. In contrast, the same bacteriophage was reactivated in preirradiated URT-43 if the host-bacteriophage complex was plated at 30° but there was no reactivation at 42°C. Therefore u.v.reactivation was positive at 30° but negative at 42°C. The induction of prophage by URT-43(Λ_h) was achieved by much lower doses of U.V. light than that required for the induction of lysogenic wild type bacteria. Experiments were performed in which irradiated URT-43 was first incubated for various periods in liquid media and plated both at 30° and 42°C. It was found that irradiated bacteria came to be resistant to subsequent plating at 42° only when they were preincubated in the liquid medium containing necessary amino acids and at 30°C. Since this phenomenon was completely inhibited by chloramphenicol, the process seemed to require de novo protein synthesis. An hypothesis was proposed that there are at least two independent dark-repair mechanisms in E. coli; one is responsible for host-cell reactivation and the other is responsible for U.V. reactivation.     

Investigation of protein–protein interactions in living cells by chemical crosslinking and mass spectrometry

The identification of protein–protein interactions within their physiological environment is the key to understanding biological processes at the molecular level. However, the artificial nature of in vitro experiments, with their lack of other cellular components, may obstruct observations of specific cellular processes. In vivo analyses can provide information on the processes within a cell that might not be observed in vitro. Chemical crosslinking combined with mass spectrometric analysis of the covalently connected binding partners allows us to identify interacting proteins and to map their interface regions directly in the cell. In this paper, different in vivo crosslinking strategies for deriving information on protein–protein interactions in their physiological environment are described.