PHOTOBIOLOGY OF RNA BACTERIOPHAGES—I. ULTRAVIOLET INACTIVATION AND PHOTOREACTIVATION STUDIES*

Abstract— Biologically active f2-RNA, Obtained from bacteriophage f2, was inactivated by ultraviolet (u.v) light (2537 Å) with a quantum yield of 3.3 ± 0.3 times 10^-3 when assayed in the dark with protoplasts of an F- strain of E. coli k12. Assay under “black light” gave a quantum yield of 2.7 ± 0.5 times 10^-3 which was just enough lower to suggest that 17 per cent photorecovery of the u.v. lesions has taken place. Intact phage f2 was inactivated by u.v. radiation with a quantum yield of 0.7 ± 0.12 times 10^-3, Thus the whole phage is much less sensitive than the free RNA. No evidence of photorecovery was found in u.v.-irradiated RNA phage 7S assayed in its host Pseudomonas aeruginosa.     

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.     

SUPPRESSION OF PHAGE T4 BY CO-INFECTION WITH U.V.-INACTIVATED HOMOLOGOUS PHAGE

Abstract— Unirradiated phage T4v₁ may fail to produce viable progeny in cells which are co-infected with u.v.-irradiated homologous particles. The extent of this effect, called suppression , is positively correlated with the multiplicity of infection of the irradiated phage and with the U.V. dose. The suppression reaches a maximum level at about 30–600 lethal hits. Quantitative evaluation of the results shows that in some complexes one irradiated phage particle is sufficient to suppress an unirradiated phage. Two hypotheses are discussed to explain the results. (a) Lethal u.v.-damages are incorporated into the unirradiated phage genome by genetic recombination; ( b ) Genetic subunits (e.g. cistrons or operons) of the u.v.-irradiated phages produce informationally incorrect messenger RNA molecules, which compete with the correct ones from the unirradiated phage in the protein-synthetizing system. Hypothesis (6) appears to be more adequate to explain the experimental results.     

Liquid-holding effects in U.V.-irradiated phage T3

Abstract— Holding complexes of u.v.-irradiated (254 nm) T3 phage in E. coli B/r cells for several hours at 37°C in buffer, or broth with chloramphenicol, affects the phage survival in at least two different ways: (1) by enhancing excision repair, resulting under certain conditions in liquid-holding recovery (LHR), and (2) by destroying the phage (holding inactivation). LHR is most apparent in buffer containing 20 μg ml^-1 chloramphenicol (CAP). It is expressed by as much as a 10–fold increase in the fraction of complexes that display host-cell reactivation (resulting from excision repair), but the percentage of u.v. lesions repaired within repair-proficient complexes is slightly decreased. LHR is not observed if T3 infects the repair-deficient strain B_s-1. Holding inactivation is readily observed with unirradiated phage complexes in broth containing CAP. The response of irradiated-phage complexes to liquid-holding conditions is more complex: holding inactivation is less effective for irradiated than for unirradiated phage DNA (i.e. the irradiated DNA is to some extent ‘protected’), and processes leading to LHR are superimposed. Thus under certain holding conditions one observes the paradoxical phenomenon that the viable titer of irradiated phage is several times higher than that of unirradiated phage. The nature of holding inactivation is not known, nor is the mechanism by which irradiated DNA is partially protected against it. Holding inactivation does not require protein synthesis; it is rather enhanced at high CAP concentration and seems to be favored by otherwise active cell metabolism. At high CAP concentrations (200–400 μg ml^-1, as compared to 20 μg ml^-1) irradiated-phage complexes show neither LHR nor protection against holding inactivation. Likewise they fail to undergo some step by which the phage DNA becomes insensitive to repair inhibition by caffeine.     

THE ROLE OF HOST-CELL REPAIR IN LIQUID-HOLDING RECOVERY OF U.V.-IRRADIATED ESCHERICHIA COLI

Abstract— The experiments reported give evidence that liquid-holding recovery (LHR) of u.v. irradiated E. coli cells involves basically the same type of dark repair which causes reactivation of phage and which results in much increased survival of the cells themselves [host-cell reactivation (HCR)]. LHR is very small in the two HCR(-) strains B syn^- and B_s-1, but occurs to larger but different extents in the three HCR(+) strains B, B/r, and B/r (Λ). LHR is inhibited if the liquid contains caffeine or acriflavine, both of which are known to inhibit HCR. The results indicate that most of the LHR effect, if not all, occurs during the liquid holding, rather than under growth conditions after liquid holding. It is assumed that the holding itself allows a prolonged time for, and therefore an enhancement of, HCR. It is thus implicit that LHR can be observed only where otherwise HCR of repairable u.v. damage would be incomplete, and that different extents of LHR, as observed in the three HCR(+) strains, reflect different extents of incompleteness of HCR. It is concluded that the repairable u.v. hits which are not fully repaired by HCR are predominantly those concerned with the extra u.v. sensitivity of the strains B and B/r (Λ), relative to B/r.     

STUDIES ON THE INACTIVATION OF TOBACCO MOSAIC VIRUS BY ULTRAVIOLET LIGHT*,‡,§

Abstract— The irradiation of TMV with u.v. light of 2537 Å wavelength results in the binding of protein subunits to the RNA. These bound subunits are stable towards warm sodium dodecyl-sulfate; however, the binding is not covalent since the subunits are removed by 66% acetic acid, guanidine hydrochloride, or phenol. Approximately one protein subunit is bound per lethal biological 'hit'. The virus and the nucleic acid extracted from irradiated virus show virtually identical rates of inactivation.     

Photoreactivation of killing in Streptomyces. II. Kinetics of formation and photolysis of pyrimidine dimers and adducts in S. coelicolor and S. griseus PHR-1

Abstract— A pyrimidine adduct, 6-4‘-[pyrimidine-2’-one] thymine (PO-T)?, observed in DNA hydrolysates of 254-nm ultraviolet (u.v.) irradiated conidia of Streptomyces coelicolor, increases linearly with u.v. dose up to 2 × 10⁵ ergs/mm². Yields of thymine dimer (T○) and uracil-thymine dimer (U○) level off at much lower doses. Initial relative rates of formation of these u.v. photoproducts are: 1:1.3:4.8 for PO-T, T○ and U○, respectively. Similar results were obtained with a Streptomyces griseus mutant, PHR-1. An equation is derived to estimate the ratio of the amount of PO-T to the total amount of thymine-derived photoproducts at low (biological) u.v. doses. The observed PO-T fractions compare well with the calculated values. Rapid photolysis of the precursor of PO-T was observed by post-u. v. treatment at 313 nm of conidia of S. coelicolor and of S. griseus PHR-1. The photolysis was much slower at 365 nm and did not occur at all at 405 nm. Pyrimidine dimers were not appreciably affected by post-u. v. treatment at the above wavelengths in these Streptomyces strains. Both of these strains are phenotypically photoreactivation-deficient, and the present results indicate that they do not possess active photoreactivating enzyme. In earlier papers[3,4,5], the pyrimidine adduct found in acid hydrolysates of DNA was loosely referred to as “uracil-thymine adduct (U-T adduct)”. Such terminology is not strictly correct. The pyrimidine adduct in acid hydrolysates is PO-T (sometimes called P₂B), which could theoretically result from removal of ammonia from a C-T adduct or removal of water from a U-T adduct (see [6]).     

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.     

STUDIES OF THE ROLE OF THE COAT PROTEIN IN THE U.V. PHOTOINACTIVATION OF U(1) AND U(2) STRAINS OF TMV*

Abstract— Two properties of the u.v. inactivation process in the u.v. sensitive U(2) strain have been investigated: (1) The increased binding of protein to RNA induced by irradiation of the virus at 254 nm; (2) The action spectrum for u.v. inactivation of U(2) between 250 nm and 285 nm. The extent of the u.v. induced binding of protein to RNA is similar to that previously found in the resistant U(1) strain, thereby eliminating the possibility that the capacity for this binding phenomenon bears any correlation to the difference in u.v. sensitivities of these two viruses at 254 nm. The results indicate that the radiation induced interaction of protein and RNA in U(1) and U(2) are probably similar. The action spectrum for U(2) resembles the absorption spectrum of the RNA between 250 nm and 285 nm implicating the RNA as the primary absorber leading to inactivation of the virus in this region of the spectrum. Quantum yields calculated for U(2) virus and free TMV-RNA irradiated at 254 nm reveal that the irradiated free RNA may be as much as 1–4 times more sensitive to inactivation at this wavelength than RNA in the intact virus. It is concluded that the coat protein of U(2) probably offers some protection to the enclosed RNA against u.v. damage at 254 nm, therefore, the difference in u.v. sensitivity between U(1) and U(2) TMV at this wavelength is a consequence of a difference in the degree of protection offered by the respective coat proteins to the enclosed RNA.     

Mutagenic effects of near ultraviolet and visible radiant energy on continuous cultures of escherichia coli

Abstract— –The induction of mutation to phage T5 resistance by near ultraviolet (u.v.) and visible light was studied in chemostat cultures of Escherichia coli strains B/r and B/r/1, trp. The visible light mutation rate to phage T5 resistance was independent of growth rate over the range studied. This result is consistent with a photochemical mechanism of mutagenesis. Changeovers, in which a faster growing subpopulation takes over the culture, usually causing the mutant frequency to decline sharply, occur more frequently in chemostat cultures irradiated with visible light than in cultures treated with far u.v. or caffeine. A preliminary action spectrum was obtained with aerated chemostats that revealed effective wavelengths to be between 330 nm and 500 nm. Wavelengths longer than 500 nm were not effective. Wavelengths longer than 340 nm were not mutagenic in anaerobic chemostats. This oxygen requirement for mutagenesis between 340 nm and 500 nm is consistent with a photodynamic mechanism of action. In aerated cultures, wavelengths between 400 nm and 500 nm were as effective as wavelengths between 330 nm and 400 nm. A number of naturally occurring compounds, including riboflavin and vitamin K, are consistent with the data as candidates for the chromophore responsible for near u.v. and visible light mutagenesis.     

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.     

KINETICS OF ENZYMATIC PHOTOREACTIVATION STUDIED WITH PHAGE T1 AND ESCHERZCHZA COLI Bs-1*

Abstract— The kinetics of enzymatic photoreactivation (PR) of u.v.-induced killing was compared among E. coli B_s-1, phage T1 in B_s-1 and phage T1 in irradiated B_s-1. The PR action spectrum showed no substantial difference between PR of B_s-1 and PR of T1 in B_s-1. The PR D₃₇ (i.e. the PR dose required to reactivate all but 37 per cent of the reactivable lethal lesions) was found to decrease linearly with decreasing U.V. dose whether U.V. was given to produce pyrimidine dimers in B_s-1 DNA, which then compete with irradiated T1 DNA for PR enzyme, or to B_s-1 or T1 DNA to produce dimers serving as substrate for the PR enzyme. A generalized Michaelis-Menten formula was used to analyze the data and the following conclusions were drawn. (1) The number of PR enzyme molecules per cell available for PR of T1 DNA inside the B_s-1 host is only a quarter of the number available for PR of the B_s-1 host itself. (2) The Michaelis constant K_m for reaction of host-DNA-damage and PR-enzyme becomes larger when the host damage acts as competitive inhibitor to PR of T1 DNA than when it is the substrate for PR enzyme. (3) PR enzyme retains almost all its initial catalytic efficiency even after about two-hundred rounds of catalytic functioning. Conclusions (1) and (2) suggest that PR enzyme is concentrated within the nuclear area surrounding the host DNA.     

REPAIR OF NEAR (365 nm)- AND FAR (254 nm)-UV DAMAGE TO BACTERIOPHAGE OF ESCHERICHIA COLI

Abstract: Intact bacteriophage have been irradiated at 365 nm or at 254 nm and then analysed for DNA photoproducts or injected into their bacterial host to test susceptibility of the damage to both phage and host-cell mediated repair systems. Both thymine dimers and single-strand breaks are induced in the phage DNA by 365 nm radiation. The dimers appear to be the major lethal lesion (approximately 2 dimers per lethal event) in both repair deficient bacteriophage T4 and bacteriophage λ. after irradiation with either 254 nm or 365 nm radiation. Damage induced in T4 by either wavelength is equally susceptible to x -gene reactivation (repair sector approximately 0.5). v -gene reactivation acts on a larger fraction of the near-UV damage (repair sector of 0.82 at 365 nm as against 0.66 at 254 nm). The host-cell mediated photoreactivation system is only slightly less effective for near-UV damage but host-cell reactivation (as measured by comparing survival of phage λ. on a uvr⁺ and a uvr^- host) is effective against a far smaller sector of near-UV damage (0.35) than far-UV damage (0.85). Weigle-reactivation (far-UV induced) of near-UV damage to phage λ is not observed. The results suggest that unless the near-UV damaged phage DNA is repaired immediately after injection. the lesions rapidly lose their susceptibility to repair with a consequent loss of activity of the phage particles.     

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.     

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.     

Purification of plant viral and satellite double-stranded RNAs on DEAE monoliths

Replicative double-stranded RNA (dsRNA) is useful in preliminary identification of Cucumber mosaic virus and its satellite RNA (satRNA). This plant pathogen complex yields sufficient quantity of the replicative RNA form that can be isolated by chromatography on chemically unmodified graded cellulose powder (CF-11). In this work, much faster and more efficient procedure using DEAE monoliths was developed in which dsRNA was separated from other species in total nucleic acids extract originating from the infected plant tissue. The developed chromatographic method revealed the pathogens' presence in only 15 min, avoiding nucleic acid precipitation and electrophoretic analysis.     

INACTIVATION OF PHAGE BY NEAR-ULTRAVIOLET RADIATION AND HYDROGEN PEROXIDE

A series of phage with different genomes (both single-stranded and double-stranded RNA and DNA) was inactivated with hydrogen peroxide (H₂O₂) in various combinations with far-ultraviolet (FUV) and near-ultraviolet (NUV) radiations. In every case but one (a lipid-coated phage), a sublethal H₂O₂ concentration greatly enhanced killing by NUV but not FUV. Moreover, this NUV/H₂O₂ synergism was oxygen independent and there was little if any host cell reactivation upon NUV plus H₂O₂ inactivation. These results suggest that these phage are inactivated by a common mechanism irrespective of nucleic acid composition, but that some phage genomes may be more vulnerable to NUV/H₂O₂ inactivation than others.     

HOST-CELL REACTIVATION OF NON-LETHAL ULTRAVIOLET-EFFECTS

Abstract— Delay of intracellular growth of u.v.-irradiated bacteriophage T1 and Λ was compared in host-cell reactivating [HCR(+)] and non-host-cell reactivating [HCR(—)] bacterial strains. At a given phage survival level, intracellular growth delay occurs to the same extent in HCR (+) and HCR (-) strains; at a given absolute u.v.-dose, this delay is considerably more expressed in HCR (-) than in HCR (+) strains. Therefore, it does not reflect the time required for the HCR repair of otherwise lethal U.V. lesions. The results rather suggest that U.V. causes, besides lethal lesions, stable photoproducts in the DNA, which are a priori non-lethal, and which are recognized and efficiently eliminated by the HCR repair system. The HCR enzymes likewise act on (non-lethal) u.v.-photoproducts causing prophage induction in lysogenic cells. Consequently, one obtains the maximum induction effect in a lysogenic HCR (-) strain at a much lower u.v.-dose than in the corresponding lysogenic HCR (+) strain. In contrast, u.v.-damage causing loss of the host cell's capacity to support growth of unirradiated phage is not affected by HCR.     

U.V. INDUCED CONFORMATIONAL CHANGES IN TRANSFER RNA

Abstract— The quantum yields for the u.v. inactivation of the amino acid acceptor function of E. coli transfer RNA (for val, phe and lys) and for the loss of its conformation, as a function of exposure, have been determined following irradiation at 280, 265 and 254 nm. Our results suggest that u.v. damage produces a change in the conformation of transfer RNA which in turn inactivates it, and that the anticodon is not the u.v. sensitive site. Calculations indicate that a small number of photoproducts inactivate the transfer RNA.