RELATIONSHIP BETWEEN SURVIVAL, PHOTOPRODUCT PRODUCTION AND REPAIR CAPACITY IN A VARIANT OF BACILLUS CEREUS

Abstract —As sporulation progresses, there is an increased resistance to UV irradiation of the cells of Bacillus cereus var. alesti. This progressive increase is independent of post-irradiation treatment and appears to be a property of the stage of sporulation. In addition, the proportion of photoproducts formed is different for each stage of sporulation. Cells irradiated at Stage I (axial filament) of sporulation display relatively large amounts of spore photoproduct 'c' and less of photoproduct 'b'. As sporulation proceeds, UV irradiation results in the production of more spore photoproduct 'b' and less 'c', suggesting a progressive change in configuration of the DNA within the sporulating cell. If irradiated early in the process (Stage II), large amounts of cyclobutane-type dimers are also produced which, with the 'spore-specific' photoproducts, may be retained in the resultant spore. Although no excision-repair was detectable during germination of these spores, both vegetative and 'spore-specific' damage is reduced during this period. The 'spore-specific' repair mechanism may be able to remove vegetative damage from germinating spores.     

ESTIMATION OF PHOTOPRODUCT FORMATION IN GERMINATING SPORES OF BACILLUS SUBTILIS

Abstract— Changes in UV sensitivity during spore germination of Bacillus subtilis mutants possessing various defects in DNA repair capacities were analysed in order to estimate the yield of the DNA photoproducts at the transient, UV resistant stage which occurs in the process of germination. It was concluded that the yield of the spore-specific photoproduct (5-thyminyl-5,6-dihydrothymine, TDHT) at the transient stage was only about 3% of that in dormant spores and the yield of the cyclobutane-type pyrimidine dimers at this stage was about 10% (or less) of that in germinated spores.     

CHANGES IN ULTRAVIOLET RESISTANCE AND PHOTOPRODUCT FORMATION AS EARLY EVENTS IN SPORE GERMINATION OF BACILLUS CEREUS T

Abstract— In order to determine the timing of the change in the state of DNA in bacterial spores during the course of germination, L-alanine-induced germination of Bacillus cereus spores was interrupted by 0.3 M CaCl₂ as an inhibitor, and the resulting semi-refractile spores (spores at the end of the first phase of germination) were examined on the UV-resistance and the photoproduct formation.
Upon UV-irradiation, these spores, still having a semi-refractile core as observed under a phase-contrast microscope, gave rise to mainly the cyclobutane-type thymine dimer. It was concluded that change in the state of the spore DNA occurs early in the process of germination, i.e. before the refractility of the core was lost.
It was also found that CaCl₂ markedly prolonged the duration of the transient UV-resistant stage.     

TRANSITORY UV RESISTANCE DURING GERMINATION OF UV-SENSITIVE SPORES PRODUCED BY A MUTANT OF Bacillus cereus 569

Abstract— A mutant of Bacillus cereus 569, isolated by us and designated 2422 is unable to excise cyclobutane-type dimers and spore-specific photoproducts from the DNA of UV-irradiated vegetative cells and dormant spores. The deficiency in the excision repair mechanism was found to be at the post-incision step in the exonuclease-mediated removal of the photoproducts. During germination, the mutant B. cereus 2422 exhibits UV-resistance and an efficient photoproduct removal which is followed by DNA repair synthesis. The data presented indicate the existence of germinative excision repair in B. cereus 569.     

PHOTOPRODUCT FORMATION IN DNA AT LOW TEMPERATURes.

Abstract— The temperature dependence of thy mine photoproduct formation in Escherichia culi DNA dissolved either in water or in a 50 per cent ethylene glycol solution was studied at temperatures between + 25 and — 196°C. At low temperatures, the formation of thymine dimer was strongly inhibited. A dose of 1 × 10⁴ ergs/mm² at 280 nm converted 2 per cent of the thymine to dimer at 25°C as compared with 0.2 per cent at — 196°C. In addition, a new thymine photo-product which was both nonphotoreversible and nonphotoreactivable was found at low temperatures. On the basis of its chromatographic mobility, this new photoproduct was assumed to be the same as that isolated from irradiated spores of Bacillus megaterium . Extensive irradiation at 254 nrn of DNA at — 120°C resulted in a yield of > 23 per cent for the 'spore-type' photoproduct as compared with 6 per cent for the thymine dimer. In poly d(AT), irradiated at low temperature, no spore-type photoproduct was found; this suggests that adjacent thymine residues are necessary for the formation of the spore-type photoproduct.     

PHOTOCHEMISTRY OF THYMIDINE AS A THIN SOLID FILM*

Abstract— –Photochemistry of thymidine in the solid state has been investigated. Four isomers of the cyclobutane-type thymidine dimer, two bimolecular addition products with u.v. absorbance maxima above 300 nm, (the formation of which involves the C=C and C=O groups of adjacent thymine residues) and 5-thyminyl-5.6 dihydrothymine (TDHT) (formed by the addition of a thyminyl radical at the C₅ position of a thymyl radical) were isolated. TDHT was found to be the major photoproduct. The results are compared with those for thymidine irradiated in the frozen state.     

Photochemistry and Photobiology of the Spore Photoproduct: A 50‐Year Journey

Fifty years ago, a new thymine dimer was discovered as the dominant DNA photolesion in UV‐irradiated bacterial spores [Donnellan, J. E. & Setlow R. B. (1965) Science, 149, 308–310], which was later named the spore photoproduct (SP). Formation of SP is due to the unique environment in the spore core that features low hydration levels favoring an A‐DNA conformation, high levels of calcium dipicolinate that acts as a photosensitizer, and DNA saturation with small, acid‐soluble proteins that alters DNA structure and reduces side reactions. In vitro studies reveal that any of these factors alone can promote SP formation; however, SP formation is usually accompanied by the production of other DNA photolesions. Therefore, the nearly exclusive SP formation in spores is due to the combined effects of these three factors. Spore photoproduct photoreaction is proved to occur via a unique H‐atom transfer mechanism between the two involved thymine residues. Successful incorporation of SP into an oligonucleotide has been achieved via organic synthesis, which enables structural studies that reveal minor conformational changes in the SP‐containing DNA. Here, we review the progress on SP photochemistry and photobiology in the past 50 years, which indicates a very rich SP photobiology that may exist beyond endospores.     

SINGLE-STRAND BREAKS IN THE DNA OF THE uvrA AND uvrB STRAINS OF ESCHERICHIA COLI K-12 AFTER ULTRAVIOLET IRRADIATION

Abstract— DNA single-strand breaks were produced in uvrA and uvrB strains of E. coli K-12 after UV (254 nm) irradiation. These breaks appear to be produced both directly by photochemical events, and by a temperature-dependent process. Cyclobutane-type pyrimidine dimers are probably not the photoproducts that lead to the temperature-dependent breaks, since photoreactivation had no detectable effect on the final yield of breaks. The DNA strand breaks appear to be repairable by a process that requires DNA polymerase I and polynucleotide ligase, but not the recA, recB, recF, lexA 101 or uvrD gene products. We hypothesize that these temperature-dependent breaks occur either as a result of breakdown of a thermolabile photoproduct, or as the initial endonucleolytic event of a uvrA , uvrB -independent excision repair process that acts on a UV photoproduct other than the cyclobutane-type pyrimidine dimer.     

Action spectra for survival and spore photoproduct formation of Bacillus subtilis irradiated with short-wavelength (200-300 nm) UV at atmospheric pressure and in vacuo.

Spores of Bacillus subtilis are approximately ten times less likely to survive UV light irradiation in a vacuum than under atmospheric conditions. Photoproduct formation was studied in spores irradiated under ultrahigh vacuum (UHV) conditions and in spores irradiated at atmospheric pressure. In addition to the "spore photoproduct" 5-thyminyl-5,6-dihydrothymine (TDHT), which is produced in response to irradiation at atmospheric pressure, two additional photoproducts, known as the cis-syn and trans-syn isomers of thymine dimer, are produced on irradiation in vacuo. The spectral efficiencies for photoproduct formation in spores are reduced under vacuum conditions compared with atmospheric conditions by a factor of 2-6, depending on the wavelength. Because formation of TDHT does not increase after irradiation in vacuo, TDHT cannot be responsible for the observed vacuum effect. Vacuum specific photoproducts may cause a synergistic response of spores to the simultaneous action of UV light and UHV. An increased quantum efficiency, destruction of repair systems and formation of irreparable lesions are postulated for the enhanced sensitivity of B. subtilis spores to UV radiation in vacuo.     

PHOTOCHEMICAL REACTIONS OF THYMINE, URACIL, URIDINE, CYTOSINE AND BROMOURACIL IN FROZEN SOLUTION AND IN DRIED FILMS*

Abstract— The photochemistry of uracil, uridine, cytosine, thymine and broinouracil has been investigated in frozen aqueous solution and in dried films. Essentially the same photoproducts were obtained in the two conditions; however, the yield of photoproducts was considerably greater in frozen solution. Uracil forms a dimer which can exist in two forms. Some kinetic data are presented for the interconversion of these two forms, The mixed dimer of thymine and uracil can also exist in two forms. Uridine forms only one acid stable photoproduct and does not appear to form mixed photoproducts under the conditions used. Two new photoproducts of thymine other than the dimer are described. Cytosine was at first considered to be completely inert hut using more sensitive detecting equipment it has recently been found to form uracil dinier as a result of dinierization and deamination. The most remarkable response was shown by bromouracil. When irradiated by itself it formed no photoproducts but when irradiated in the presence of uracil, uridine, cytosine or NaOH it formed many photoproducts. Most of these products were devoid of bromide, but two still contained bromine. One of these has been identified as the mixed dimer of uracil and bromouracil while the other has been tentatively identified as the dimer of bromouracil. Dimers of thymine or bromouracil were not formed by X-rays.     

Effects of the binding of alpha/beta-type small, acid-soluble spore proteins on the photochemistry of DNA in spores of Bacillus subtilis and in vitro

The main lesion produced in DNA by UV-C irradiation of spores of Bacillus subtilis is 5-thyminyl-5,6-dihydrothymine (spore photoproduct [SP]). In contrast, cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) pyrimidone photoproducts (6-4PP) are the main photolesions in other cell types. The novel photochemistry of spore DNA is accounted for in part by its reduced hydration, but largely by the saturation of spore DNA with alpha/beta-type small, acid-soluble spore proteins (SASP). Using high-performance liquid chromatography-mass spectrometry analysis of the photoproducts, we showed that in wild-type B. subtilis spores (1) UV-C irradiation generates almost exclusively SP with little if any CPD and 6-4PP; (2) the SP generated is approximately 99% of the intrastrand derivative, but approximately 1% is in the interstrand form; and (3) there is no detectable formation of the SP analog between adjacent C and T residues. UV-C irradiation of spores lacking the majority of their alpha/beta-type SASP gave less SP than with wild-type spores and significant levels of CPD and 6-4PP. The binding of an alpha/beta-type SASP to isolated DNA either in dry films or in aqueous solution led to a large decrease in the yield of CPD and 6-4PP, and a concomitant increase in the yield of SP, although levels of interstrand photoproducts were extremely low.     

THE PHOTOREACTIVITY OF PYRIMIDINE-PURINE SEQUENCES IN SOME DEOXYDINUCLEOSIDE MONOPHOSPHATES AND ALTERNATING DNA COPOLYMERS

Abstract— A reversed-phase HPLC system has been developed which separates the common nucleo-bases from the 6-methylimidazo[4,5- b ]pyridin-5-one (6-MIP) produced on acid hydrolysis of a thymine-adenine photoadduct (TA*) that is formed between adjacent thymine and adenine bases in UV-irradiated polydeoxyribonucleotides. By measuring the relative amounts of adenine and 6-MIP in acid hydrolysates, this system has been used to investigate how polynucleotide conformation affects the yield of TA* in poly(dA-dT) irradiated at 254 nm. The photoreactivity of other pyrimidine-purine sequences has been examined with the deoxydinucleoside monophosphates d(TpI) and d(m⁵CpA) and with the alternating DNA copolymers poly(dA-dU), poly(dI-dC), poly(dG-dC) and poly(dA-dC).poly(dG-dT). Samples were irradiated at 254 nm in aqueous solution and in ice, and at wavelengths >290 nm with acetone as photosensitizer. A photoproduct resembling TA*, and giving 6-MIP on acid hydrolysis, was isolated from d(TpI) irradiated at 254 nm in solution or in ice; d(m⁵CpA) was comparatively unreactive. Acid hydrolysates of the irradiated DNA copolymers were screened by HPLC and by TLC and paper electrophoresis, for the presence of imidazo[4,5- b ]pyridin-5-one, 6-MIP, or other species attributable to specific photoproduct formation. By this criterion, however, none of the copolymers showed evidence of significant photoreactivity in either their single- or double-stranded conformational states. The formation of mixed pyrimidine-purine photoadducts in DNA is therefore probably restricted to T-A doublets.     

PHOTOCHEMISTRY OF 4-THIOURIDINE AND THYMINE

Abstract— When thymine is irradiated in aqueous solution with monochromatic 334-nm UV radiation in the presence of 4-thiouridine a photoproduct of thymine is formed, as shown by thin-layer chromatography and autoradiography. The quantum yield for the formation of thymine photoproduct (θ=0.017) is greater than that for cytosine photoproduct formation (θ= 0.0015). The identity of the photoproduct is not known: one possibility is the formation of an adduct between the sensitizer and the base yielding a pyrimidine-pyrimidone type of photoproduct.     

EFFECT OF DIPICOLINIC ACID ON THE ULTRAVIOLET RADIATION RESISTANCE OF BACILLUS CEREUS SPORES

Abstract— The ultraviolet radiation (UV) resistance of B. cereus spores was shown to depend on their content of dipicolinic acid (DPA). Wild-type spores with decreasing amounts of DPA exhibited increased UV resistance. Similarly, spores devoid of DPA (DPA-minus), produced by a mutant strain of B. cereus unable to synthesize DPA, were more resistant to UV than mutant spores (DPA-plus) produced in the presence of exogenously supplied DPA. Resistance of both the wild type and mutant strains to ionizing radiation, however, was unaffected by DPA content. Comparison of the resistance of DPA-minus and DPA-plus mutant spores to UV of various wavelengths showed that the greater sensitivity of the latter DPA-plus spores appeared at wavelengths corresponding to the region of the first molecular absorption band of the calcium chelate of DPA. In the wild type and mutant, thymine photoproducts were produced at a greater rate and to a greater extent in spores with high levels of DPA than in spores with low DPA.
The data indicate that DPA transfers energy to DN A in vivo , which leads to the conclusion that DPA occurs in the spore protoplast.     

KINETICS OF THE ULTRAVIOLET-INDUCED DIMERIZATION OF THYMINE IN FROZEN SOLUTIONS*

Abstract— It is known that thymine forms dimers when aqueous solutions are irradiated with ultraviolet light while in the frozen state, but does not form dimers when solutions are irradiated in the liquid state. The eutectic point of aqueous thymine solutions was found to be. —0.02°C. Since the irradiation of frozen solutions is always carried out at lower temperatures, the dimerization must be occurring in the solid state. Activation energies and quantum yields for dimer formation were determined by irradiating 1–mm layers of thymine solution at —5°C to — 707deg;C for various lengths of time. As expected, the activation energy was zero. After measuring the amount of radiation scattered by samples of ice, the extreme values for the quantum yield were found to be 0.73 and 4.08. The lower limit assumed that all the scattered light was absorbed by thymine; the upper limit assumed that none was absorbed. Since the theoretical maximum quantum yield is 2, the best estimate of the quantum yield is considered to be between 1 and 2.     

EFFECT OF THYMINE DIMER INTRODUCTION IN A 21 BASE PAIR OLIGONUCLEOTIDE

Abstract— It is well known that the pyrimidine dimers are the main damage produced by UV radiation on the DNA structure. However, while studies on the photoproduct structure have been carried out extensively, uncertainties still exist on the implication that a single damaging event has on the overall conformation. In particular, the extension of the damage influence on the polynucleotide chain is a matter of debate. This problem is especially important to understanding some steps of the repair mechanisms. In this study we performed a chemical-physical characterization of 21 base pair oligonucleotides containing a single thymine dimer in one strand. Thermodynamic parameters were determined by means of thermal denaturation experiments, and static fluorescence measurements were performed to unequivocally define the primary structure-conformation relationship in this specific case. We used hydroxyl radicals, produced by means of γ-irradiation of the sample solution, to detect fine structure changes. Our data show that the introduction of a single thymine dimer might cause only a slight distortion of the helix geometry, as judged by the evaluation of the enthalpic and the entropic terms and by the small changes observed in the binding of ethidium bromide to DNA. The modifications in the sugar phosphate backbone subsequent to the damaging event are especially evident, near the thymine dimer, toward the 5'-end direction in the strand containing the dimer.     

Photoinduced DNA Lesions in Dormant Bacteria: The Peculiar Route Leading to Spore Photoproducts Characterized by Multiscale Molecular Dynamics**

Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions, such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproducts in spores are not cyclobutane pyrimidine dimers, but rather the so-called spore photoproducts. This noncanonical photochemistry results from the dry state of DNA and its binding to small, acid-soluble proteins that drastically modify the structure and photoreactivity of the nucleic acid. Herein, multiscale molecular dynamics simulations, including extended classical molecular dynamics and quantum mechanics/molecular mechanics based dynamics, are used to elucidate the coupling of electronic and structural factors that lead to this photochemical outcome. In particular, the well-described impact of the peculiar DNA environment found in spores on the favored formation of the spore photoproduct, given the small free energy barrier found for this path, is rationalized. Meanwhile, the specific organization of spore DNA precludes the photochemical path that leads to cyclobutane pyrimidine dimer formation.     

Repair of the main UV-induced thymine dimeric lesions within Arabidopsis thaliana DNA: evidence for the major involvement of photoreactivation pathways.

The UV-B induced formation of thymine cis-syn cyclobutane dimer and related (6-4) photoproduct was monitored within DNA of cultured cells and plants of Arabidopsis thaliana. This was achieved using a sensitive and accurate HPLC-tandem mass spectrometry assay. It was found that the cyclobutane pyrimidine dimer was formed in a ninefold higher yield than the (6-4) photoproduct. The removal of the lesions was then studied by incubating irradiated cells either in the darkness, under visible light or upon exposure to UV-A radiation. Dark repair of both cyclobutane dimers and (6-4) photoproducts was found to be very ineffective. In contrast, a rapid decrease in the level of photoproducts was observed when UV-B-irradiated cells were exposed to UV-A and, to a lesser extent, to visible light. The removal of (6-4) adducts was found to occur more efficiently. These results strongly suggest that repair of UV-induced photolesions in plants is mainly mediated by photolyases.     

WAVELENGTH DEPENDENCE (150–290 nm) OF THE FORMATION OF THE CYCLOBUTANE DIMER AND THE (6–4) PHOTOPRODUCT OF THYMINE

The action cross sections for the formation of the cyclobutane dimer and the (6-4) photoproduct of thymine as well as the absorption cross sections of thymine were determined in the wavelength region between 150 and 290 nm. Thymine films sublimed on glass plates were irradiated by monochromatic photons in a vacuum; the induced photoproducts were quantitatively analyzed by high-performance liquid chromatography (HPLC). Under our conditions, two major peaks appeared on the HPLC chromatograms of irradiated samples. The two peaks were identified as being the cis-syn cyclobutane dimer and the (6-4) photoproduct, based on their HPLC retention times, absorption spectra in the effluent, and photochemical reactivity. The fractions of the two photoproducts increased linearly with the fluence at low fluences over the entire wavelength range. Their action cross sections were determined by the slopes of the linear fluence response curve at 10 nm intervals between 150 and 290 nm. The two action spectra showed a similar wavelength dependence and had a maximum at 270 nm as well as two minor peaks at 180 and 220 nm, at which wavelengths the peaks of the absorption spectrum of thymine sublimed on a CaF2 crystal plate appeared. The quantum yields had relatively constant values of around 0.008 for the dimer and 0.013 for the (6-4) photoproduct above 200 nm, decreasing to 0.003 and 0.006, respectively, at 150 nm as the wavelength became shorter.     

OLIGONUCLEOTIDE PHOTOPRODUCTS FORMED BY PHOTOLYSIS OF POLYRIBOBROMOURIDYLIC ACID

Abstract— Polyribobromouridylic acid was irradiated with 313 nm light at an exposure of ˜ 190 pE/cm*. Oligonucleotides found after RNase hydrolysis of the photolysed poly-rBrU were isolated by DEAE-cellulose chromatography and partially characterized. The dmucleo-tide fraction, found in highest amounts, was not susceptible to hydrolysis by KOH or snake venom phosphodiesterase and may contain a coupled photoproduct. The properties of the dinucleotide were not those of a molecule containing a cyclobutane-type dimer, but were compatible with the properties of a coupled product similar to 5–5'-diuracil. The trinucleotide fraction probably consisted of more than one component. One component may contain a dimeric photoproduct. The tetranucleotide material was sensitive to cleavage into fragments by KOH, and could consist of adjacent photoproducts of the types found in the di- and trinucleotide fractions. The photoproducts formed over a range of lower doses of light were found to have properties similar to those found at high doses.