Identification of 5-fluorocytidine in RNA from Escherichia coli grown in the presence of 5-fluorouracil

Metabolism and mechanism of action of 5-fluorouracil

This is a review on the mechanism of action of FUra. Three main areas are addressed: metabolism, RNA-directed actions of FUra, and DNA-directed actions of FUra. Key words for bibliographic purposes: metabolism, RNA, rRNA, mRNA, tRNA, DNA primase, DNA, thymidylate synthetase, uracil N-glycosylase, FUra, FUrd, FdUrd, FdUMP, RNA splicing, 5,10-methylene tetrahydrofolate, FUTP.

Specific incorporation of 5-fluorocytidine into Escherichia coli RNA

RNAs isolated from Escherichia coli B grown in the presence of 5-fluorouracil have high levels of the analog replacing uridine and uridine-derived modified nucleosides. Cytidine has also been shown to be replaced in these RNAs by 5-fluorocytidine, a metabolic product of 5-fluorouracil, but to a considerably lesser extent. When 5-fluorocytidine is added to cultured of E. coli B little 5-fluorocytidine (0.20 mol%) is incorporated into cellular RNAs because of the active cytosine/cytidine deaminase activities. Addition of the cytidine deaminase inhibitor tetrahydrouridine (70 micrograms/ml) increases 5-fluorocytidine incorporation to about 3 mol% in tRNAs, but does not eliminate 5-fluorouridine incorporation. E. coli mutants lacking cytosine/cytidine deaminase activities are able to more than double the extent of 5-fluorocytidine incorporation into their transfer and ribosomal RNAs, replacing cytidine with no detectable 5-fluorouridine incorporation. Levels of 5-methyluridine, pseudouridine and dihydrouridine in tRNAs are not affected. These fluorocytidine-containing tRNAs show amino acid-accepting activities similar to control tRNAs. Fluorocytidine was found to be quite susceptible to deamination under alkaline conditions. Its conversion to primarily 5-fluorouridine follows pseudo-first-order reaction kinetics with a half-life of 10 h in 0.3 M KOH at 37 degrees C. This instability in alkali probably explains why 5-fluorocytidine was not found earlier in RNAs isolated from cells treated with 5-fluorouridine, since most early RNA hydrolyses were carried out in alkali. It may also explain the mild mutagenic properties observed in some systems following 5-fluorouridine treatment. Initial 19F-NMR measurements in fluorocytidine-containing tRNAs indicate that this modified tRNA may be useful in future structural studies of tRNAs and in probing tRNA-protein complexes.

Characterization of the fluorodihydrouracil substituent in 5-fluorouracil-containing Escherichia coli transfer RNA

The fluorodihydrouridine derivative previously detected in one of two isoaccepting forms of FUra-substituted Escherichia coli tRNAMetf has been further characterized. This substituent is responsible for the 19F resonance observed 15 ppm upfield from free FUra (= 0 ppm) in the high resolution 19F-NMR spectra of FUra-substituted tRNA purified by chromatography on DEAE-cellulose, at pH 8.9, to remove normal tRNA. Similar highfield 19F signals have now been observed in the spectra of two other purified fluorinated E. coli tRNAs, tRNAMetm and tRNAVal1, as well as in unfractionated tRNA, indicating the widespread occurrence of the constituent. Comparison with 19F spectrum of the model compound 5'-deoxy-5-fluoro-5,6-dihydrouridine (dH56FUrd) (delta FUra = -31.4 ppm; JHF = 48 Hz) indicates that the substituent does not contain an intact fluorodihydrouridine ring. dH56FUrd is considerably more alkali labile than 5,6-dihydrouridine (H56Urd). At pH 8.9, where H56Urd is stable, dH56FUrd is degraded to a derivative, presumably a fluoroureidopropionic acid, with a 19F resonance at - 15.7 ppm that nearly coincides with the upfield peak in the spectrum of pH 8.9-treated tRNA. The 19F-NMR spectrum of fluorinated tRNA, not exposed to pH 8.9, exhibits two peaks 31 and 32 ppm upfield of FUra, in place of the 19F signal at - 15 ppm. Hydrolysis of this tRNA with RNAase T2 produces a sharp doublet 33 ppm upfield (JHF = 45 Hz). Similarities of the 19F chemical shift and coupling constant to those of dH56FUrd, allows assignment of the peak at -33 ppm to an intact fluorodihydrouridine residue in the tRNA. Our results demonstrate that FUra residues incorporated into E. coli tRNA at sites normally occupied by dihydrouridine can be recognized by tRNA-modifying enzymes and reduced to fluorodihydrouridine. This substituent is labile at moderately alkaline pH values and undergoes ring-opening during purification of the tRNA.

Nucleoside changes in tRNAs from Bacillus subtilus treated with 5-fluorouracil

Extensive amounts of 5-fluorouridine and lower levels of 5-fluorocytidine are incorporated into tRNAs from Bacillus subtilus grown in the presence of 5-fluorouracil. Nucleoside analyses revealed both pseudouridine and 5-methyl-uridine levels to be reduced more extensively at low levels of analog incorporation than could be accounted for by a stoichiometric replacement, as observed earlier with Escherichia coli.

Incorporation and excision of 5-fluorouracil from deoxyribonucleic acid in Escherichia coli

When Escherichia coli are grown in the presence of 5-fluorouracil, the 5-fluorouracil is incorporated almost exclusively into ribonucleic acid as fluorouridylate. In this study, small but detectable amounts were incorporated into ribonucleic acid as fluorocytidylate and into deoxyribonucleic acid as fluorodeoxyuridylate and fluorodeoxycytidylate. The amount of 5-fluorouracil found in deoxyribonucleic acid as fluorodeoxyuridylate increased 50-fold when the cells were deficient in both deoxyuridine triphosphatase and uracil-deoxyribonucleic acid glycosylase activities. Therefore, the same mechanisms which excluded uracil from deoxyribonucleic acid in vivo also excluded 5-fluorouracil. Even though purified uracil-deoxyribonucleic acid glycosylase excised 5-fluorouracil from deoxyribonucleic acid at only 5% the rate with which it excised uracil, most of the 5-fluorouracil excised from deoxyribonucleic acid in vivo was apparently excised directly by uracil-deoxyribonucleic acid glycosylase rather than by repair initiated by excision of uracil.

Effects of pH on the properties of normal and 5-fluorouracil-containing tRNAs

Transfer RNAs isolated from Escherichia coli B grown in the presence of 5-fluorouracil (FIUra) show variations in their aminoacylation levels when compared with normal samples. Some of these variations result from the more stringent aminoacylation reaction conditions required for FIUra-tRNAs. Increasing the reaction pH from 7 to 9 for example, generally causes a lowering of amino acid acceptance by the analog-containing tRNAs, while leaving control samples largely unchanged. This decreased activity appears to result primarily from fluorouracil ionization, which in turn disrupts intramolecular hydrogen bonding and promotes an overall increase in the molecular dimensions of FIUra-tRNAs at elevated pH values. Sensitivity to pH differes with the amino acid examined, with lysine showing dramatic changes and glutamine and proline being largely unaffected.

Biological consequences of incorporation of 5-fluorocytidine in the RNA of 5-fluorouracil-treated eukaryotic cells

Treatment of HeLa cells with 5-fluoro-[3H]uracil leads to the incorporation into cellular RNA of 5-fluorocytidine to the extent of about 0.2% of the 5-fluorouridine incorporated. In tobacco mosaic virus RNA produced in tobacco leaves this ratio is one order of magnitude lower. Copolymers of cytidylic with 5-fluorocytidylic acids show unchanged template activity with E. coli RNA polymerase, but slightly altered messenger activity in the wheat germ system, compared to poly(C), and it is suggested that some of the biological consequences of 5-fluorouracil treatment of living cells and organisms may be attributed to this mechanism.