Compilation of tRNA sequences and sequences of tRNA genes

Sprinzl, Mathias

doi:10.1093/nar/26.1.148

Cited by 812 publications

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“…The membrane was washed in 6 ϫ standard saline citrate (SSC) (16) at room temperature for 15 min and then in 3ϫ SSC for a total of 60 min at 55°C. The DNA sequences used as specific probes were 5Ј-CCTCCGAC-CGCTCGG-3Ј for tRNA Arg ICG, 5Ј-CCTGAGACCTCT-GCC-3Ј for tRNA Arg CCG, 5Ј-CCTGCGGCCCACGAC-3Ј for tRNA Arg U*CU (U*: 5-methylaminomethyluridine), and 5Ј-AACCTGCAATTAGCCC-3Ј for tRNA Arg CCU (18). The DNA probes for control RNAs, tRNA Tyr , tRNA His , tRNA Asn tRNA Asp , tRNA 2 Gln , tRNA Lys , tRNA Glu , and 16S-rRNA were described previously (13).…”

Section: Methodsmentioning

confidence: 99%

A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops

Tomita

Ogawa

Uozumi

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

156

141

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Colicin D has long been thought to stop protein synthesis in infected Escherichia coli cells by inactivating ribosomes, just like colicin E3. Here, we show that colicin D specifically cleaves tRNAs Arg including four isoaccepting molecules both in vivo and in vitro. The cleavage occurs in vitro between positions 38 and 39 in an anticodon loop with a 2 ,3 -cyclic phosphate end, and is inhibited by a specific immunity protein. Consistent with the cleavage of tRNAs Arg , the RNA fraction of colicin-treated cells significantly reduced the amino acid-accepting activity only for arginine. Furthermore, we generated a single mutation of histidine in the C-terminal possible catalytic domain, which caused the loss of the killing activity in vivo together with the tRNA Arg -cleaving activity both in vivo and in vitro. These findings show that colicin D directly cleaves cytoplasmic tRNAs Arg , which leads to impairment of protein synthesis and cell death. Recently, we found that colicin E5 stops protein synthesis by cleaving the anticodons of specific tRNAs for Tyr, His, Asn, and Asp. Despite these apparently similar actions on tRNAs and cells, colicins D and E5 not only exhibit no sequence homology but also have different molecular mechanisms as to both substrate recognition and catalytic reaction.C olicins are plasmid-encoded proteins that are toxic to Escherichia coli cells that do not have the same plasmid or a cognate Col plasmid (1-5). Most colicins are produced in response to SOS-inducing signals and are secreted into the medium. After binding to cell-surface receptors on sensitive cells, they are translocated across the membrane and then exert their final cytotoxic activities, which are attributable to their C-terminal domains. Two major modes of toxicity are well known; colicins A, B, E1, Ia, Ib, K, and N are ion-channel formers attacking the cytoplasmic membrane, and colicins E2 to E9 are nucleases. In the latter group, E2, E7, E8, and E9 are DNases, and E3 is a special kind of RNase that cleaves 16S rRNA within ribosomes.Colicins E4 to E6 quickly stop amino acid incorporation in treated cells (6), suggesting impairment of protein synthesis analogous in the established case of E3, which specifically cleaves 16S-RNA at the 49th bond from the 3Ј end leading to inactivation of ribosomes (7-9). This is also the case with colicin D, which Timmis and Hedges have characterized as to the physiological response of treated cells (10, 11), although the actual molecular basis of the cytotoxic effect of colicin D, as well as those of E4 to E6, remained to be elucidated. Colicins E4 and E6 proved to be E3-homologs and showed comparable activity toward ribosomes (ref. 12; GenBank accession number X63621; Y. Gunji, M. Ohno, T.O., H.M., and T.U., unpublished data), but colicin E5 exhibits no similarity to E3 in the C-terminal active domain. We recently showed that colicin E5 comprises a third category of nuclease-type colicins, which does not attack ribosomes but specific tRNAs (13). E5 is a novel RNase that cleaves the anticodons...

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Section: Methodsmentioning

confidence: 99%

A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops

Tomita

Ogawa

Uozumi

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

156

141

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“…A potential mercury derivative was obtained by soaking the crystals in 100 mM HEPES/ KOH pH 6.6, 3 mM MgCl 2 , 2 M (NH 4 ) 2 SO 4 , 25% glycerol as a cryoprotecting solution for data collection at low temperatures and 2.5 mM p-hydroxy mercury benzoate. This reagent is expected to react covalently with 4-thiouridine, a modi®ed nucleoside located at position 8 in tRNA fMet (Sprinzl et al, 1998). The mercury derivative of the crystal short communications yielded the best diffraction data collected so far.…”

Section: Crystals Of If2-c±fmet-trna Fmetmentioning

confidence: 99%

Preliminary characterization by X-ray diffraction and Raman spectroscopy of a crystalline complex ofBacillus stearothermophilusinitiation factor 2 C-domain and fMet-tRNA^fMet

Förster

Krafft

Welfle

et al. 1999

Acta Crystallogr D Biol Cryst

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Bacillus stearothermophilus translation initiation factor 2 (IF2) specifically binds initiator fMet‐tRNAfMet and positions it into the ribosomal peptidyl site in the course of the initiation of protein biosynthesis. The isolated C‐terminal domain of IF2 is capable of binding fMet‐tRNAfMet, as shown by RNase A and hydrolysis protection experiments. In the presence of fMet‐tRNAfMet, the IF2 C‐domain yielded orthorhombic crystals of space group I222 (I212121) diffracting to 3.4 Å resolution. The existence of equimolar amounts of tRNA and protein in the crystals was proven by Raman spectroscopy. The observed unit cell suggests the presence of two IF2 C‐domain–fMet‐tRNAfMet complexes per asymmetric unit of the crystal.

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“…More than 80 different RNA modifications have been described (2), 25 of which are found in cytoplasmic tRNAs of the yeast Saccharomyces cerevisiae; these occur at 35 positions, leading to about 11 modifications in an average yeast tRNA (3).…”

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confidence: 99%

The Specificities of Four Yeast Dihydrouridine Synthases for Cytoplasmic tRNAs

Xing

Hiley

Hughes

et al. 2004

Journal of Biological Chemistry

108

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Dihydrouridine is a highly abundant modified nucleoside found widely in tRNAs of eubacteria, eukaryotes, and some archaea. In cytoplasmic tRNA of Saccharomyces cerevisiae, dihydrouridine occurs exclusively at positions 16, 17, 20, 20A, 20B, and 47. Here we show that the known dihydrouridine synthases Dus1p and Dus2p and two previously uncharacterized homologs, Dus3p (encoded by YLR401c) and Dus4p (YLR405w), are required for all of the dihydrouridine modification of cytoplasmic tRNAs in S. cerevisiae. We have mapped the in vivo position specificity of the four Dus proteins, by three complementary approaches: determination of the molar ratio of dihydrouridine in purified tRNAs from different dus mutants; microarray analysis of a large number of tRNAs based on differential hybridization of uridineand dihydrouridine-containing tRNAs to the complementary oligonucleotides; and the development and use of a novel dihydrouridine mapping technique, employing primer extension. We show that each of the four Dus proteins has a distinct position specificity: Dus1p for U 16 and U 17 , Dus2p for U 20 , Dus3p for U 47 , and Dus4p for U 20a and U 20b .A ubiquitous feature of tRNAs is the presence of numerous base and ribose modifications (1). More than 80 different RNA modifications have been described (2), 25 of which are found in cytoplasmic tRNAs of the yeast Saccharomyces cerevisiae; these occur at 35 positions, leading to about 11 modifications in an average yeast tRNA (3).Dihydrouridine is among the most abundant modified nucleosides found in tRNA (3); the 905 dihydrouridines found in the 561 curated tRNAs are second in number only to the 1,234 pseudouridines. Consistent with its abundance, dihydrouridine is found widely in tRNAs of eubacteria and eukaryotes (3), although it is less common in archaebacteria (4). Furthermore, dihydrouridines are found at one or more of multiple different positions in tRNA, the vast majority of which are in the D loop at positions 16, 17, 20, 20a, and 20b and at the base of the variable arm at position 47. Only in six exceptional cases is dihydrouridine found elsewhere, and in these cases it occurs at one of four other positions in the D loop (15, 17a, 19, and 21) and at position 48 in the variable arm. The persistent occurrence of dihydrouridine in these positions in so many different organisms underscores the evolutionary importance of the modification and of the sites of modification.To begin to address the roles of dihydrouridine modifications, an important first step is to decipher the substrate specificity rules for the various modified dihydrouridine residues of tRNA. The yeast S. cerevisiae is highly suitable for this analysis for three reasons. First, yeast tRNAs are modified with dihydrouridine at most of the sites of modification that have been found in characterized tRNAs. Thus, each of the six most common dihydrouridine modification sites are found in multiple yeast cytoplasmic tRNAs (Table I), and two of the five minor dihydrouridine modification sites are found in its sequen...

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Compilation of tRNA sequences and sequences of tRNA genes

Cited by 812 publications

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A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops

A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops

Preliminary characterization by X-ray diffraction and Raman spectroscopy of a crystalline complex ofBacillus stearothermophilusinitiation factor 2 C-domain and fMet-tRNA^fMet

The Specificities of Four Yeast Dihydrouridine Synthases for Cytoplasmic tRNAs

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Compilation of tRNA sequences and sequences of tRNA genes

Cited by 812 publications

References 0 publications

A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops

A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops

Preliminary characterization by X-ray diffraction and Raman spectroscopy of a crystalline complex ofBacillus stearothermophilusinitiation factor 2 C-domain and fMet-tRNAfMet

The Specificities of Four Yeast Dihydrouridine Synthases for Cytoplasmic tRNAs

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Preliminary characterization by X-ray diffraction and Raman spectroscopy of a crystalline complex ofBacillus stearothermophilusinitiation factor 2 C-domain and fMet-tRNA^fMet