INTRAMOLECULAR ENERGY TRANSFER IN NATIVE tRNA AT ROOM TEMPERATURE

Abstract— The odd nucleoside 4-thiouridine, which is present in position 8 of 70% of E. coli tRNAs, possesses unusual spectroscopic properties which make it suitable for intramolecular energy transfer studies. Both its luminescence excitation spectrum and the action spectrum (230–380 nm) for the 8–13 link formation have been established in native E. coli tRNA at room temperature. The spectra are identical and present a new unexpected peak around 260 nm. At this wavelength, they are amplified by a factor of nine as compared with the absorption and excitation spectra of the free nucleoside in aqueous solution.
The origin of this new peak is discussed and it is concluded that energy transfer does occur from the common nucleosides to the 4-thiouridine residue. Using the values of the nucleosides to 4-thiouridine distances inferred from the sets of atomic coordinates obtained on yeast tRNA^phe crystals, a satisfactory account of our finding can be obtained assuming singlet-singlet energy transfer. The efficiency of the mechanism is probably favoured by a good overlap between the emission spectra of the common nucleosides and the absorption spectrum of 4-thiouridine.     

ROLES OF THE RELA+ GENE AND OF 4-THIOURIDINE IN NEAR-ULTRAVIOLET (334 nm) RADIATION INHIBITION OF INDUCED SYNTHESIS OF TRYPTOPHANASE IN ESCHERICHIA COLI B/r

Abstract— Near-ultraviolet radiation (near UV; 300–380 nm) is known to inhibit the induced synthesis of tryptophanase by tryptophan in Escherichia coli , showing an action spectrum similar to that for near-UV-induced growth delay. The present work shows that a rel A mutant of E. coli B/r exhibits 50% as much monochromatic near-UV (334 nm) inhibition of tryptophanase induction as the wild type, and that a mutant lacking 4-thiouridine, an unusual nucleoside in tRNA, exhibits < 10% as much inhibition of tryptophanase induction. These findings indicate that 4-thiouridine is almost the sole chromophore for this effect in E. coli B/r, but that only 50% of the effect operates by a mechanism utilizing the rel A ⁺ gene product; growth delay appears not to be primarily involved.     

Transient reduction in the tRNA 4-thiouridine content induced by ultraviolet A during post-irradiation growth in Enterobacter cloacae

The influence of previous exposure to ultraviolet-A radiation (UVA) was studied on the susceptibility of Enterobacter cloacae to undergo the growth delay effect. Comparison of growth curves corresponding to irradiated and control cells showed that a previous treatment with UVA almost abolished the growth delay effect. UV absorption spectra of tRNA, and reverse phase HPLC analysis of hydrolysed tRNA, demonstrated a low content of 4-thiouridine in E. cloacae cells grown after UVA exposure at low doses. Since 4-thiouridine is the UVA target responsible for initiation of growth delay, this observation explained the influence of previous exposure to UVA on the susceptibility of this organism to undergo growth delay. A similar but weaker alteration was found when Escherichia coli was assayed. The results suggest that, in addition to cross-linking with cytidine residues, the content of 4-thiouridine in tRNA may be modified by UVA by an unknown mechanism.     

REDUCTION BY NEAR-ULTRAVIOLET (334 nm) LIGHT OF E. COLI CAPACITY FOR PHAGE GROWTH DEPENDS UPON THE rel GENE AND 4-THIOURIDINE

Abstract— Near-ultraviolet radiation (near UV; 300–380 nm) has long been known to produce a transient reduction of the capacity of bacteria to support phage growth. The present work shows that, at high fluenœs (40–100 kJ/m²), 85% of 334-nm-induced reduction of capacity in Escherichia coli B/r requires the rel gene; that is, it results from rel -gene activity caused by the near-UV treatment. This rel -gene activity leads to (1) a bacterial growth delay and concomitantly lowered bacterial metabolism, and (2) a parallel delay in phage development, with a considerable depression of burst size. We propose that the observed effects on phage development are a consequence primarily of the lowered bacterial metabolism, but they may also result partly from a direct inhibition of phage DNA synthesis by the rel gene product, these effects together leading to the observed reduction of capacity in a rel ⁺ strain. The remaining 15% of capacity reduction, observed in a rel strain, has an unknown mechanism, but does appear to involve a delay in phage development.
At least 95% of the total capacity reduction observed in the rel ⁺ strain in the range 40–100 kJ/m² requires the presence of 4-thiouridine, an unusual base in E. coli transfer RNA, which is presumably both the chromophore and the target for near-UV-induced capacity reduction.     

The roles of the rel+ gene and of 4-thiouridine in killing and photoprotection of Escherichia coli by near-ultraviolet radiation

Abstract— Photoprotection is a reduction in response to far-UV (190–300. nm) radiation in cells that have been previously exposed to longer wavelengths. It has been proposed that photoprotection operates by means of a growth delay that permits more time for dark repair. Growth delay in Escherichia coli utilizes 4-thiouridine (⁴Srd) in transfer RNA as a chromophore and it requires the rel⁺ gene, which exerts a stringent control upon RNA synthesis. Mutants that were either rel or ⁴Srd^? were isolated from E. coli B, utilizing a near-UV-induced growth-delay selection technique. The rel mutants, which undergo little growth delay after near-UV irradiation, show only 50% as much photoprotection as wild types, while ⁴Srd^? mutants show no photoprotection at all. Thus, photoprotection appears to utilize ⁴Srd as its sole chromophore in E. coli B and B/r, and no more than 50% of photoprotection in these strains can be a result of near-UV-induced growth delay.     

IN VIVO INDUCTION OF 4-THIOURIDINE-CYTIDINE ADDUCTS IN tRNA OF E. COLI B/r BY NEAR-ULTRAVIOLET RADIATION*

Abstract— Near-ultraviolet (near-UV; 320–405 nm) irradiation of Escherichia coli B/r induces the formation in vivo of ⁴Srd-Cyd adducts in transfer RNA, as evidenced by (1) fluorescence spectrum changes of tRNA extracted from irradiated cells and reduced with NaBH₄, (2) thin-layer chromatography on cellulose of hydrolysates of trichloroacetic acid-precipitable extracts of irradiated cells, and (3) comparison of these findings with adduct formation induced by near-UV irradiation of purified mixed tRNA from E. coli. The kinetics of induction of the ⁴Srd-Cyd adduct in vivo, and the near-UV fluences required, provide strong support for our earlier hypothesis that formation of these adducts is responsible for near-UV-induced growth delay in E. coli.     

Inhibition of sulfur incorporation to transfer RNA by ultraviolet-A radiation in Escherichia coli

tRNA sulfurtransferase activity was assayed in Escherichia coli cell extracts obtained from bacterial suspensions exposed to a sub-lethal dose of ultraviolet-A radiation (fluence 148 kJ m(-2)) imparted at a low fluence rate (41 W m(-2)). We found that the irradiation reduced the enzymatic activity to one fourth of the control value, indicating that ultraviolet-A exposure inhibits the synthesis of 4-thiouridine, the most abundant thionucleoside in E. coli tRNA. Changes in the tRNA content of 4-thiouridine and its derived photoproduct 5-(4'-pyrimidin 2'-one) cytosine were studied in bacteria growing under ultraviolet-A irradiation. In these conditions the accumulation of photoproduct was limited, and the kinetics of this process was non-coincident with disappearance of 4-thiouridine. The results, which are compatible with the fact that ultraviolet-A induces an inhibition of the 4-thiouridine synthesis, suggest that the effect of radiation on tRNA modification is relevant to tRNA photo-inactivation in growing bacteria.     

BASE-SPECIFIC DAMAGE INDUCED BY 4-THIOURIDINE PHOTOSENSITIZATION WITH 334-nm RADIATION IN M13 PHAGE DNA

Abstract— Site-specific DNA damage caused by 334-nm radiation in the presence of the rare Escherichia coli base 4-thiouridine was investigated in vitro by detecting the sites of the termination of DNA synthesis with irradiated M13 phage DNA used as a template. Single-strand breakage was also examined. The results indicate that 334-nm radiation at very low fluences in the presence of 4-thiouridine induces termination of strand synthesis at thymine base sites and at the base immediately prior to thymine. Termination at these sites was diminished by treatment with hot piperidine. Strand cleavage by piperidine treatments was observed preferentially at the guanine site, but only after irradiation at much larger fluences. It is hypothesized that at low fluences 4-thiouridine forms photoadducts with thymine that block DNA synthesis, while at high fluences the guanine site is damaged via oxygen species.     

METABOLISM OF tRNAs IN GROWING CELLS OF Escherichia coli ILLUMINATED WITH NEAR-ULTRAVIOLET LIGHT

Abstract— The tRNA metabolism which accompanies illumination of growing E. coli cells has been examined in conditions that led to growth delay. (i) The in vivo formation of the 8–13 link was followed by a fluorimetric procedure and revealed pseudo-first order kinetics very close to those obtained in vim under the same illumination conditions. The yield of 8–13 link appears to be quantitative (± 10%). Comparison of these kinetics with the radiochromatographic data of Blanchetot et al . (1984) suggests the transient formation during illumination of a new RNase-T,-resistant dinucleotide in tRNA distinct from the 8–13 link. (ii) Evidence is provided that under illumination some tRNA molecules lack one or more bases in a specific position in the sequence, thus yielding discrete fragments after aniline treatment. (iii) During the growth lag, uracil incorporation into nucleic acids occurs at an apparent rate between 4–8% of that normally observed during exponential growth. Evidence is provided however that the pyrimidine ribonucleoside triphosphate pools are strongly perturbed after illumination. Comparison of exogenous [³H]uracil incorporation into two strains proficient or deficient in uracil biosynthesis suggests a derepression of the endogenous path after light treatment. In addition, the UTP-to-CTP conversion is inhibited. In spite of preferential incorporation of exogenously labelled uracil in tRNA after illumination, a possible pyrimidine base turnover cannot be proved. These data are compatible with tRNA repair (Blanchetot et al ., 1984) involving a few tRNA species.     

A5–4 PYRIMIDINE-PYRIMIDONE PHOTOPRODUCT PRODUCED FROM MIXTURES OF THYMINE AND 4-THIOURIDINE IRRADIATED WITH 334 nm LIGHT

The nucleoside 4-thiouridine, present in some bacterial tRNA species, is known to be a chromophore and a target for near-UV light-induced growth delay and also mediates both photoprotection and near-UV cell killing in various bacterial strains. To investigate the photoreaction of 4-thiouridine with DNA or its precursors, we irradiated aqueous mixtures of thymine and 4-thiouridine with 334 nm light and then separated photoproducts using two or more stages of reversed-phase high performance liquid chromatography. The two equally abundant major photoproducts were analyzed by UV absorbance spectrophotometry, fast-atom bombardment and electron-impact mass spectrometry, and ¹H- and ¹³C-NMR spectroscopy, and have been identified as two diastereomers of 6-hydroxy-5-[1-(β-D-erythro-pentofuranosyl)-4′-pyrimidin-2′-one]dihydrothymine (o⁶hThy[5-4]Pdo), of molecular weight = 370.32. These two diastereomers, although stable at room temperature or below, are interconvertible by heating (90d?C for 5 min) in aqueous solution. The possible biological significance of this photoproduct is discussed, and an application as a crosslinker for oligonucleotides to selectively block replication is suggested.     

DELAY IN GROWTH AND DIVISION INDUCED BY NEAR ULTRAVIOLET RADIATION IN ESCHERICHIA COLI B AND ITS ROLE IN PHOTOPROTECTION AND LIQUID HOLDING RECOVERY

Abstract. Microscopic observations show that growth delay and division delay occur on nutrient agar after Escherichia coli B has been irradiated at 3341 Å. These effects also occur in nutrient broth.
A near u.v. action spectrum for growth delay in nutrient broth has been obtained. It shows a single peak at 3380 Å and is indistinguishable from the action spectrum for photo-protection from far u.v. (2537 Å) killing in the same organism. Furthermore, photoprotected cells show a much greater growth delay than cells that have not been photoprotected. These, as well as kinetic data, suggest that the essential action of a photoprotection treatment consists in the induction of a growth-division delay. This delay would presumably permit more time for intracellular recovery systems to operate on the far u. v. damage to nucleic acids.
Liquid holding recovery (effected by holding cells in phosphate buffer after far u. v. irradiation) shows complete overlap with photoprotection. It is concluded that photoprotection and liquid holding recovery operate on the same far u. v. damage. As with photoprotection, it is probable that the essential action of a liquid holding treatment is the induction of a growth-division delay.
No photoprotection is observed of intracellular T2 bacteriophage or of E. coli B_s-l (Hill).     

MUTATIONAL INTERACTIONS BETWEEN NEAR-UV RADIATION AND DNA DAMAGING AGENTS IN Escherichia coli: THE ROLE OF NEAR-UV-INDUCED MODIFICATIONS IN GROWTH AND MACROMOLECULAR SYNTHESIS

Abstract— The mutational interactions between near-ultraviolet (near-UV, 334 nm, 365 nm) radiation and DNA damaging agents (far-UV (254 nm) and ethyl-methanesulphonate (EMS)) were studied in strains of Escherichia coli B/r trp thy with different susceptibilities to near-UV-induced growth delay (wild-type, rel and srd ). Far-UV induced reversion to tryptophan independence is reduced while forward mutation to streptomycin is enhanced by prior exposure of the rel+ srd+ strains to near-UV radiation. The observed interactions are reduced ( rel ) or absent ( srd ) in the two mutant strains as are the corresponding growth and macromolecular synthesis delays normally observed after near-UV treatment. Quantitatively, the degree of interaction induced by near-UV pre-treatment correlates closely with the degree of protein synthesis inhibition. We propose a mechanism for the contrasting interactions at the two genetic loci based on the different pathways by which pre-mutagenic lesions may be processed. The primary chromophore for the mutational interactions would appear to be 4-thiouracil-containing transfer RNA.     

ULTRAVIOLET RADIATION INHIBITS BOTH ACCESSORY CELL AND RESPONDER T CELL FUNCTION IN THE PROLIFERATIVE RESPONSE TO HAPTENATED-SELF

Abstract— Photoprotection i. e. the increased resistance of the cells preilluminated with near ultraviolet light (300–380 nm) to the lethal action of 254 nm radiations is observed in wild-type Escherichia coli B cells (which exhibits the Fil phenotype) but requires either an integrated prophage or a rec A mutation to be detected in E. coli K12 strains. Here we have demonstrated that significant photoprotection occurs in an E. coli K12 rec A⁺ cell containing the Ion allele which is responsible for filamentous growth (Fil phenotype) after 254 nm irradiation. The Fil phenotype can be suppressed by the sfi A of sfi B suppressor genes. Since the E. coli K12 rec A⁺ Ion sfi B strain exhibits no more photoprotection, these data support the conclusion that in Ion strains photoprotection is due to the abolition of the 254 nm induced filamentation by the near ultraviolet treatment. In addition, we show here that near ultraviolet illumination of the cells leads to a severe restriction of the bulk protein synthesis, as well as of the inducibility of β-galactosidase and tryptophanase. These effects are observed only in nuv ⁺ cells that contains 4-thiouridine the chromophore responsible for photoprotection. We propose that in Ion (lysogenic) strains, photoprotection is due to prevention of the SOS response. During the growth lag, the low residual level of protein synthesis does not allow the induction of the SOS response and accordingly prevents filamentation (the lytic cycle). Concomitantly the SOS triggering signals are eliminated via DNA repair.     

THE ROLE OF 4-THIOURIDINE IN LETHAL EFFECTS AND IN DNA BACKBONE BREAKAGE CAUSED BY 334 nm ULTRAVIOLET LIGHT IN Escherichia coli

Strains of Escherichia coli that lack 4-thiouridine (⁴Srd) are killed by monochromatic 334 nm UV light (UV) less efficiently than their wild-type parents, which contain ⁴Srd. Oxygen enhancement ratios (OER) at 10% survival are 3.3 for a strain that possesses ⁴Srd, and 2.6 for one that lacks ⁴Srd. Single-strand breaks in DNA caused by 334 nm UV accumulate more than twice as fast in the wild-type strains than in the strains lacking ⁴Srd. The results suggest that ⁴Srd is an important chromophore in some near-UV lethal effects. The results also suggest that the excitation energy from 334 nm UV light may be passed from RNA to DNA, resulting in single-strand breaks.     

Synthesis of 4-thiouridine, 6-thioinosine, and 6-thioguanosine 3',5'-O-bisphosphates as donor molecules for RNA ligation and their application to the synthesis of photoactivatable TMG-capped U1 snRNA fragments

4-Thiouridine, 6-thioguanosine, and 6-thioinosine 3',5'-bisphosphates (9, 20, and 28) were synthesized in good yields by considerably improved methods. In the former two compounds, uridine and 2-N-phenylacetylguanosine were converted via transient O-trimethylsilylation to the corresponding 4- and 6-O-benzenesulfonyl intermediates (2 and 13), which, in turn, were allowed to react with 2-cyanoethanethiol in the presence of N-methylpyrrolidine to give 4-thiouridine (3) and 2-N-phenylacetyl-6-thioguanosine derivatives (14), respectively. In situ dimethoxytritylation of these thionucleoside derivatives gave the 5'-masked products 4 and 15 in high overall yields from 1 and 11. 6-S-(2-Cyanoethyl)-5'-O-(4,4'-dimethoxytrityl)-6-thioinosine (23) was synthesized via substitution of the 5'-O-tritylated 6-chloropurine riboside derivative 22 with 2-cyanoethanethiol. These S-(2-cyanoethyl)thionucleosides were converted to the 2'-O-(tert-butyldimethylsilyl)ribonucleoside 3'-phosphoramidite derivatives 7, 18, and 26 or 3',5'-bisphosphate derivatives 8, 19, and 27. Treatment of 8, 19, and 27 with DBU gave thionucleoside 3',5'-bisphosphate derivatives 9, 20, and 28, which were found to be substrates of T4 RNA ligase. These thionucleoside 3',5'-bisphosphates were examined as donors for ligation with m3(2,2,7) G5'pppAmUmA, i.e., the 5'-terminal tetranucleotide fragment of U1 snRNA, The 4-thiouridine 3',5'-bisphosphate derivative 9 was found to serve as the most active substrate of T4 RNA ligase with a reaction efficiency of 96%.     

4-THIOURIDINE INCORPORATION INTO THE RNA OF MONKEY KIDNEY CELLS (CV-1) TRIGGERS NEAR-UV LIGHT LONG-TERM INHIBITION OF DNA, RNA AND PROTEIN SYNTHESIS

Monkey kidney cells (CV-1) grown for 4 h in the presence of 0.1 m M 4-thiouridine (s⁴Urd) incorporate this photoactivable uridine analog in their RNA. A minor, 5–8%, thiolated RNA fraction can be isolated from bulk RNA by affinity chromatography. This RNA fraction contains 1.5–2.5 s⁴Urd residues per 100 nucleotides and exhibits a broad chain length distribution ranging from 700 to 7000 nucleotides. It is essentially of nuclear origin and amounts to 30% of the RNA synthesized during exposure of cells to s⁴Urd. Under the same s⁴Urd labeling conditions, no thiolated pyrimidine residues have been detected in DNA.
Irradiation with 365 nm light (45 kJ/m²) of the cells immediately after s⁴Urd exposure triggers long-term inhibition of DNA, RNA and protein synthesis accompanied by a linear decline (50% in 2 days) in the total cell mass of cultured cells. In contrast, exposure to s⁴Urd alone results in moderate but reversible inhibitory effects. The available data suggest that s⁴Urd-induced photolesions in newly synthesized RNA such as RNA-RNA cross-links as well as RNA-protein bridges are directly involved in impairment of essential cellular functions.     

Generation of thiyl radicals by the photolysis of 5-iodo-4-thiouridine

The photochemistry of 2',3',5'-tri-O-acetyl-5-iodo-4-thiouridine (3) in deoxygenated 1:1 CH(3)CN-H(2)O pH 5.8 (phosphate buffer) solution has been studied by means of steady-state and nanosecond laser flash photolysis methods. Under steady-state irradiation (lambda > or = 334 nm), the stable photoproducts were iodide ion, 2',3',5'-tri-O-acetyl-4-thiouridine (4), and two disulfides. The disulfides were the symmetrical bis-(2',3',5'-tri-O-acetyl-5-iodo-4-thiouridine) (5) and unsymmetrical 6, which contains both 4-thiouridine and 5-iodo-4-thiouridine residues. The formation of the dehalogenated photoproduct suggests that C(5)-I bond cleavage is a primary photochemical step. Attempts to scavenge the resulting C(5)-centered radical by suitable addends, bis-(N-alpha-acetyl)cystine-bis-N-ethylamide or benzene, were unsuccessful. Analysis of the photoproducts formed under these conditions showed that the S-atom is the reactive center. The photoproduct 4, obtained by irradiation of 3 in CD(3)CN-H(2)O, followed by reversed-phase HPLC isolation using nonlabeled eluents, did not contain deuterium. An analogous experiment performed in CH(3)CN-D(2)O gave deuterated product 4-d with 88% of the deuterium incorporated at C(5). Transient absorption observed upon laser excitation (lambda= 308 nm) of 3 was assigned to the 4-uridinylthiyl radical on the basis of the similarity of this spectrum with that obtained upon laser photolysis of the disulfide: bis-(2',3',5'-tri-O-acetyl-4-thiouridine) 14. On the basis of the results of steady-state and laser photolysis studies, a mechanism of the photochemical reaction of 3 is proposed. The key mechanistic step is a transformation of the C(5)-centered radical formed initially by C(5)-I bond cleavage into a long-lived S-centered radical via a 1,3-hydrogen shift. Theoretical calculations confirmed that the long-lived S-centered radical is the most stable radical derived from the 4-thiouracil residue.     

LUMINESCENCE AND PHOTOCHEMISTRY OF 4-THIOURIDINE IN AQUEOUS SOLUTION

Abstract— In bidistilled water, 4-thiouridine (4TU) exhibits a weak unusual luminescence, the quantum yield of which is 3 × 10^-4 at 25°C. The excitation spectrum corresponds well to the 4TU absorption spectrum. The emission lies at longer wavelengths (Λ_max 550 nm) than the 4TU phosphorescence observed at 77 K (Λ_max, 470–480 nm). From the emission signal obtained after an excitation flash of 3 ns half-width, an "apparent" rate constant for the radiative deactivation process, shorter than 5 × 10⁶ s, can be inferred. The 300 K emission is efficiently quenched by halides and by oxygen: quenching involves a long-lived intermediate (⋍ 200 ns).
Clearly the emissive state X is populated through the S₀-S₁ electronic transition π→π* of 4TU. The nature of X cannot be unambiguously determined: it cannot be an excimer but can be either the 4TU triplet state or another chemical state distinct from the 4TU excited singlet or triplet states.
An interesting finding is that the 300 K emission and the ability of 4TU to photoreact are related: they are quenched with the same efficiency by halide anions. This indicates that quenching occurs at the same long-lived intermediate species , which is either a precursor of the emitter or the emitter itself.     

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.     

A new route to 2'-O-alkyl-2-thiouridine derivatives via 4-O-protection of the uracil base and hybridization properties of oligonucleotides incorporating these modified nucleoside derivatives

Oligonucleotides containing 2-thiouridine (s2U) in place of uridine form stable RNA duplexes with complementary RNAs. Particularly, this modified nucleoside has proved to recognize highly selectively adenosine, the genuine partner, without formation of a mismatched base pair with the guanosine counterpart. In this paper, we describe new methods for the synthesis of 2-thiouridine and various 2'-O-alkyl-2-thiouridine derivatives. Oligoribonucleotides having these modified nucleoside derivatives were synthesized, and their hybridization and structural properties were studied in detail by the 1H NMR analysis of these modified nucleosides and Tm experiments of RNA duplexes with their complementary RNA strands.