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Finet O, Yague-Sanz C, Marchand F, Hermand D. The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function. RNA Biol 2022; 19:735-750. [PMID: 35638108 PMCID: PMC9176250 DOI: 10.1080/15476286.2022.2078094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The universal dihydrouridine (D) epitranscriptomic mark results from a reduction of uridine by the Dus family of NADPH-dependent reductases and is typically found within the eponym D-loop of tRNAs. Despite its apparent simplicity, D is structurally unique, with the potential to deeply affect the RNA backbone and many, if not all, RNA-connected processes. The first landscape of its occupancy within the tRNAome was reported 20 years ago. Its potential biological significance was highlighted by observations ranging from a strong bias in its ecological distribution to the predictive nature of Dus enzymes overexpression for worse cancer patient outcomes. The exquisite specificity of the Dus enzymes revealed by a structure-function analyses and accumulating clues that the D distribution may expand beyond tRNAs recently led to the development of new high-resolution mapping methods, including Rho-seq that established the presence of D within mRNAs and led to the demonstration of its critical physiological relevance.
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Affiliation(s)
- Olivier Finet
- URPHYM-GEMO, The University of Namur, Namur, Belgium
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Yang BH, Huang JH, Zhou FY, Bao JS, Lao XF, Wu LF, Shen NZ, Wang SJ, Yang ZW, Lu RR, Tu CZ, Wang Y. Studies on nucleic acid chemistry: VII. Synthesis of four oligoribonucleotides of dihydrouridine (D) loop of yeast alanine transfer RNA. ACTA CHIMICA SINICA 2010. [DOI: 10.1002/cjoc.19860040411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
A new ' photofootprinting ' technique, which uses light to detect protein-DNA contacts as well as changes in the structure of DNA at the base pair level, has been developed and used to detect contacts between lac repressor and the lac operator in Escherichia coli cells.
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Horowitz J, Cotten ML, Hardin CC, Gollnick P. Characterization of the fluorodihydrouracil substituent in 5-fluorouracil-containing Escherichia coli transfer RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 741:70-6. [PMID: 6351924 DOI: 10.1016/0167-4781(83)90011-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
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.
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Kinoshita T, Schram KH, McCloskey JA. Preparation of deuterium-labeled nucleosides by platinum-catalyzed exchange and reduction. J Labelled Comp Radiopharm 1982. [DOI: 10.1002/jlcr.2580190407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hariharan PV, Cerutti PA. Formation of products of the 5,6-dihydroxydihydrothymine type by ultraviolet light in HeLa cells. Biochemistry 1977; 16:2791-5. [PMID: 889777 DOI: 10.1021/bi00631a032] [Citation(s) in RCA: 125] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Krajewska E, Shugar D. Pyrimidine nucleoside analogues as inducers of pyrimidine nucleoside catabolizing enzymes in Salmonella typhimurium. Mol Biol Rep 1975; 2:295-301. [PMID: 765767 DOI: 10.1007/bf00357016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Various structural analogues of cytosine and uracil nucleosides were tested as potential inducers of the nucleoside catabolizing (cyt) enzymes in Salmonella typhimurium. Some analogues, e.g. 5'-O-alkyl cytidines and uridines, resistant to catabolic enzymes, were as effective as the natural inducers cytidine and uridine; but etherification of one of the cis 2' or 3'hydroxyls fully abolished activity, pointing to a requirement of an intact ribose cis-glycol system for activity. A uridine analogue in the syn conformation, 6-methyluridine, a good substrate for uridine phosphorylase, was inactive as an inducer. The behavior of various other analogues, in relation to their structure, conformation and substrate properties, indicated the absence of any correlation between inducing activity and substrate susceptibility. The overall findings are consistent with conclusions derived from genetic experiments. The active analogues apparently act via similar pathways, and probably affect the same regulatory mechanism(s) as the natural inducers.
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Westwick WJ, Allsop J, Watts RW. The effect of gold salts on the biosynthesis of uridine nucleotides in human granulocytes. Biochem Pharmacol 1974; 23:153-62. [PMID: 4359459 DOI: 10.1016/0006-2952(74)90321-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Westwick WJ, Allsop J, Watts RW. A study of the effect of some drugs which cause agranulocytosis on the biosynthesis of pyrimidines in human granulocytes. Biochem Pharmacol 1972; 21:1955-66. [PMID: 4649344 DOI: 10.1016/0006-2952(72)90008-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Cavalieri E, Calvin M. Photochemical coupling of benzo(a)pyrene with 1-methylcytosine; photoenhancement of carcinogenicity. Photochem Photobiol 1971; 14:641-53. [PMID: 5121257 DOI: 10.1111/j.1751-1097.1971.tb06202.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Maley F, Maley GF. Tetrahydrodeoxyuridylate: a potent inhibitor of deoxycytidylate deaminase. Arch Biochem Biophys 1971; 144:723-9. [PMID: 4328164 DOI: 10.1016/0003-9861(71)90379-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Santi DV, Brewer CF, Farber D. Studies on the preparation and exchange reactions of 5-deuterated uracils. J Heterocycl Chem 1970. [DOI: 10.1002/jhet.5570070425] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Derivatives of 2,6-dihydroxy-4,5-dihydropyrimidines. Chem Heterocycl Compd (N Y) 1970. [DOI: 10.1007/bf00478401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Magrath DI, Shaw DC. The occurrence and source of beta-alanine in alkaline hydrolysates of sRNA: a sensitive method for the detection and assay of 5,6-dihydrouracil residues in RNA. Biochem Biophys Res Commun 1967; 26:32-7. [PMID: 6030252 DOI: 10.1016/0006-291x(67)90248-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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[11] Synthesis of nucleoside derivatives by conversion from preformed nucleosides. Methods Enzymol 1967. [DOI: 10.1016/s0076-6879(67)12015-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Schein AH, Schein FT. [6] Reduction of pyrimidines. Methods Enzymol 1967. [DOI: 10.1016/s0076-6879(67)12010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Budowsky EI, Drushinina TN, Eliseeva GI, Gabrielyan ND, Kochetkov NK, Novikova MA, Shibaev VN, Zhdanov GL. Synthetic analogues of uridine diphosphate glucose: biochemical and chemical studies. The secondary structure of nucleoside diphosphate sugars. BIOCHIMICA ET BIOPHYSICA ACTA 1966; 122:213-24. [PMID: 5969299 DOI: 10.1016/0926-6593(66)90063-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Lipsett MN. The Isolation of 4-Thiouridylic Acid from the Soluble Ribonucleic Acid of Escherichia coli. J Biol Chem 1965. [DOI: 10.1016/s0021-9258(18)97137-1] [Citation(s) in RCA: 136] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Cheng CC, Lewis LR. Pyrimidines. XIV. Synthesis of 1-substituted 5,6-dihydrocytosines and an improved synthesis of 1-substituted uracils. J Heterocycl Chem 1964. [DOI: 10.1002/jhet.5570010512] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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GROSSMAN L, GREENLEES J. A colorimetric determination of purine and pyrimidine deoxyribonucleosides and their phosphorylated derivatives. Anal Biochem 1961; 2:189-204. [PMID: 13709092 DOI: 10.1016/s0003-2697(61)80001-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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MOKRASCH LC, GRISOLIA S. Contribution of hydrouracil and its derivatives to pyrimidine biosynthesis II. Mechanism studies. ACTA ACUST UNITED AC 1959; 34:165-70. [PMID: 14423319 DOI: 10.1016/0006-3002(59)90244-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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HUMPHREYS GK, GREENBERG DM. Studies on the conversion of deoxyuridylic acid to thymidylic acid by a soluble extract from rat thymus. Arch Biochem Biophys 1958; 78:275-87. [PMID: 13618009 DOI: 10.1016/0003-9861(58)90351-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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MILES HT. Infared spectra and tautomeric structure of nucleosides and nucleotides in D2O solution. II. BIOCHIMICA ET BIOPHYSICA ACTA 1958; 27:46-52. [PMID: 13510250 DOI: 10.1016/0006-3002(58)90291-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cohen SS, Lichtenstein J, Barner HD, Green M. STUDIES ON THE BIOSYNTHESIS OF BACTERIAL AND VIRAL PYRIMIDINES. J Biol Chem 1957. [DOI: 10.1016/s0021-9258(18)70646-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Green M, Barner HD, Cohen SS. STUDIES ON THE BIOSYNTHESIS OF BACTERIAL AND VIRAL PYRIMIDINES. J Biol Chem 1957. [DOI: 10.1016/s0021-9258(18)70647-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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