Isolation and structure determination of the fluorescent base from bovine liver phenylalanine transfer ribonucleic acid

Blobstein, Steven H.; Grünberger, Dezider; Weinstein, I. Bernard; Nakanishi, Koji

doi:10.1021/bi00726a002

Cited by 93 publications

(47 citation statements)

References 22 publications

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“…In fact, OHyW was detected in A. . Peroxywybutosine (o2yW), which has been identified in mammalian tRNA Phe (22,23), was not present in our preparation, similar to a previous report (8). C, biosynthetic pathway of OHyW.…”

Section: Identification Of Tyw5 Responsible For Ohyw Formation-supporting

confidence: 90%

Expanding Role of the Jumonji C Domain as an RNA Hydroxylase

Noma

Ishitani

Kato

et al. 2010

Journal of Biological Chemistry

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JmjC (Jumonji C) domain-containing proteins are known to be an extensive family of Fe(II)/2-oxoglutarate-dependent oxygenases involved in epigenetic regulation of gene expression by catalyzing oxidative demethylation of methylated histones. We report here that a human JmjC protein named Tyw5p (TYW5) unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxywybutosine, in tRNA Phe by catalyzing hydroxylation. The finding provides an insight into the expanding role of JmjC protein as an RNA hydroxylase.The ferrous iron (Fe 2ϩ )-and 2-oxoglutarate (2-OG) 2 -dependent oxygenases are a superfamily of enzymes that catalyze a wide range of reactions, including hydroxylation, demethylation, and oxidative ring closures for a variety of substrates, including metabolites, nucleic acids, and proteins (1). Recent studies have revealed emerging roles of this family of oxygenases involved in histone demethylation, DNA demethylation, protein stabilization, hypoxia sensing, and fatty acid metabolism. Jumonji C (JmjC) domain-containing proteins, an extensive family of Fe(II)/2-OG-dependent oxygenases, play a key role in epigenetic control of gene expression by catalyzing oxidative demethylation of a series of methylated histones, including histone H3 at Arg-2, Lys-4, Lys-9, Lys-27, and Lys-36, and histone H4 at Arg-3 (2-4). In addition, the JmjC protein FIH-1 hydroxylates an Asp residue in HIF-1␣ to regulate hypoxic responses (5). JmjC is an evolutionarily conserved domain widely found in proteins from bacteria, fungi, plants, and animals. There are still many JmjC proteins whose functions remain elusive.Many post-transcriptional modifications required for accurately deciphering the genetic code are found in tRNAs (6). Wybutosine (yW) and hydroxywybutosine (OHyW) (Fig. 1A) are hypermodified guanosines found at position 37 of the phenylalanine tRNA (tRNA Phe ) in yeast and mammals, respectively (Fig. 1B) (7, 8). yW plays a critical role in maintaining the reading frame by stabilizing codon-anticodon pairing (9). The yW synthesis is initiated from N 1 -methylation of G37 (m 1 G) formation catalyzed by Trm5p (Fig. 1C). Further steps of yW synthesis are catalyzed by four enzymes Tyw1p, Tyw2p, Tyw3p, and Tyw4p, which we and other groups identified in yeast ( Fig. 1C) (10 -12). The multistep enzymatic formation of yW from yW-187 can be reconstituted in vitro using recombinant Tyw2p, Tyw3p, and Tyw4p (10). In the last step of yW formation, Tyw4p catalyzes both methylation and methoxycarbonylation of the bulky side chain of yW at a single catalytic site, and in the latter reaction, the methoxycarbonyl group is formed through the fixation of carbon dioxide (13). In mammalian tRNA Phe , the ␤-carbon of the side chain in yW is further hydroxylated to form OhyW (Fig. 1A). The functional role and biogenesis of this additional modification have never been studied. EXPERIMENTAL PROCEDURESStrains, Media and Plasmid-The following Saccharomyces cerevisiae wild-type strain and deletion strains were obtained from EUROSCARF: the BY...

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Section: Identification Of Tyw5 Responsible For Ohyw Formation-supporting

confidence: 90%

Expanding Role of the Jumonji C Domain as an RNA Hydroxylase

Noma

Ishitani

Kato

et al. 2010

Journal of Biological Chemistry

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“…We therefore conclude that this calf liver tRNAPhe contains only peroxy-Y. This result can be explained by the observation of Blomstein et al [7] who found that beef liver tRNAPhe also contains only peroxy-Y. Our result therefore can be due to the fact that the calf liver tRNAPhe purchased from Boehringer-Mannheim may have been extracted from older calves than the calf liver tRNAPhe prepared by Blomstein et al [7] where the maturation of Y into peroxy-Y was not completely achieved.…”

Section: Methodssupporting

confidence: 77%

“…The fluorescent base adjacent to the 3' end of the anticodon was previously found in calf liver tRNAPhe to be a mixture of 9% peroxy-Y base and 10% Y base [7]. With the calf liver tRNAPhe we used in this work, we obtained only one spot which had an RF similar to that described for peroxy-Y.…”

Section: Methodsmentioning

confidence: 55%

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The primary structure of two mammalian tRNAs^Phe: Identity of calf liver and rabbit liver tRNAs^Phe

1974

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“…The chemical nature of these modifications ranges from the simple introduction of methyl groups on one hand to hypermodified nucleosides such as wybutosine (Blobstein et al 1973) or agmatidine (Mandal et al 2010) on the other hand. To date, more than 100 chemically different modifications have been described for tRNA nucleotides (Rozenski et al 1999).…”

Section: Introductionmentioning

confidence: 99%

Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs

Wurm

Griese²,

Bahr³

et al. 2012

RNA

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ABSTRACTtRNAs from all three kingdoms of life contain a variety of modified nucleotides required for their stability, proper folding, and accurate decoding. One prominent example is the eponymous ribothymidine (rT) modification at position 54 in the T-arm of eukaryotic and bacterial tRNAs. In contrast, in most archaea this position is occupied by another hypermodified nucleotide: the isosteric N1-methylated pseudouridine. While the enzyme catalyzing pseudouridine formation at this position is known, the pseudouridine N1-specific methyltransferase responsible for this modification has not yet been experimentally identified. Here, we present biochemical and genetic evidence that the two homologous proteins, Mja_1640 (COG 1901, Pfam DUF358) and Hvo_1989 (Pfam DUF358) from Methanocaldococcus jannaschii and Haloferax volcanii, respectively, are representatives of the methyltransferase responsible for this modification. However, the in-frame deletion of the pseudouridine N1-methyltransferase gene in H. volcanii did not result in a discernable phenotype in line with similar observations for knockouts of other T-arm methylating enzymes.

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Isolation and structure determination of the fluorescent base from bovine liver phenylalanine transfer ribonucleic acid

Cited by 93 publications

References 22 publications

Expanding Role of the Jumonji C Domain as an RNA Hydroxylase

Expanding Role of the Jumonji C Domain as an RNA Hydroxylase

The primary structure of two mammalian tRNAs^Phe: Identity of calf liver and rabbit liver tRNAs^Phe

Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs

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Isolation and structure determination of the fluorescent base from bovine liver phenylalanine transfer ribonucleic acid

Cited by 93 publications

References 22 publications

Expanding Role of the Jumonji C Domain as an RNA Hydroxylase

Expanding Role of the Jumonji C Domain as an RNA Hydroxylase

The primary structure of two mammalian tRNAsPhe: Identity of calf liver and rabbit liver tRNAsPhe

Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs

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The primary structure of two mammalian tRNAs^Phe: Identity of calf liver and rabbit liver tRNAs^Phe