Structure of the modified nucleoside Q isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine

Kasai, Hiroshi; Oashi, Z; Harada, Fumio; Nishimura, Susumu; Oppenheimer, Norman J.; Crain, Pamela F.; Liehr, Joachim G.; Minden, D. L. Von; McCloskey, J A

doi:10.1021/bi00690a008

Cited by 217 publications

(102 citation statements)

References 39 publications

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“…Q is characterized by a cyclopentenediol ring appended to 7-aminomethyl-7-deazaguanosine (Kasai et al, 1975;Ohgi et al, 1979). In some mammalian tRNAs, Q is glycosylated with galactose or mannose at the C5 hydroxyl (Okada & Nishimura, 1977).…”

Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme

et al. 2005

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QueF (MW = 19.4 kDa) is a recently characterized nitrile oxidoreductase which catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ 0 ) to 7-aminomethyl-7-deazaguanine, a late step in the biosynthesis of the modified tRNA nucleoside queuosine. Initial crystals of homododecameric Bacillus subtilis QueF diffracted poorly to 8.0 Å . A three-dimensional model based on homology with the tunnel-fold enzyme GTP cyclohydrolase I suggested catalysis at intersubunit interfaces and a potential role for substrate binding in quaternary structure stabilization. Guided by this insight, a second crystal form was grown that was strictly dependent on the presence of preQ 0 . This crystal form diffracted to 2.25 Å resolution.

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Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme

et al. 2005

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“…With few exceptions (such as yeast and mycoplasma), it is widely distributed in most prokaryotic and eukaryotic phyla (4). Q is based on a very unusual 7-deazaguanosine core, which is further modified by addition of a cyclopentendiol ring (5,6). The Q modification has long been known and has been implicated in a number of disparate physiological phenomena, such as eukaryotic cell proliferation and differentiation (7)(8)(9)(10), tyrosine biosynthesis (11), and bacterial virulence (12).…”

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Identification of Four Genes Necessary for Biosynthesis of the Modified Nucleoside Queuosine

Reader

Metzgar

Schimmel

et al. 2004

Journal of Biological Chemistry

134

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Queuosine (Q) is a hypermodified 7-deazaguanosine nucleoside located in the anticodon wobble position of four amino acid-specific tRNAs. In bacteria, Q is produced de novo from GTP via the 7-deazaguanosine precursor preQ 1 (7-aminoethyl 7-deazaguanine) by an uncharacterized pathway. PreQ 1 is subsequently transferred to its specific tRNA by a tRNA-guanine transglycosylase (TGT) and then further modified in situ to produce Q. Here we use comparative genomics to implicate four gene families (best exemplified by the B. subtilis operon ykvJKLM) as candidates in the preQ 1 biosynthetic pathway. Deletions were constructed in genes for each of the four orthologs in Acinetobacter. High pressure liquid chromatography analysis showed the Q nucleoside was absent from the tRNAs of each of four deletion strains. Electrospray ionization mass spectrometry confirmed the absence of Q in each mutant strain. Finally, introduction of the Bacillus subtilis ykvJKLM operon in trans complemented the Q deficiency of the two deletion mutants that were tested. Thus, the products of these four genes (named queC, -D, -E, and -F) are essential for the Q biosynthetic pathway.Nucleoside modification typically occurs in ϳ10% of the nucleosides of a particular tRNA but can involve as many as 25% of the nucleosides for a specific tRNA (1). Over 80 modified nucleosides have been characterized (1), many of which are phylogenetically conserved. The nature of nucleoside modification varies from simple methylation of the base or ribose ring to extensive "hypermodification" of the canonical bases. The latter involves multiple enzymatic steps and can result in substantive structural changes (2). Queuosine (Q) 1 is an example of a highly modified nucleoside located in the anticodon wobble position 34 of tRNAs specific for Tyr, His, Asp, and Asn (3). With few exceptions (such as yeast and mycoplasma), it is widely distributed in most prokaryotic and eukaryotic phyla (4). Q is based on a very unusual 7-deazaguanosine core, which is further modified by addition of a cyclopentendiol ring (5, 6). The Q modification has long been known and has been implicated in a number of disparate physiological phenomena, such as eukaryotic cell proliferation and differentiation (7-10), tyrosine biosynthesis (11), and bacterial virulence (12). However, despite the presence of Q in the tRNA anticodon loop, no definitive role for Q in translation has been established (13).Unlike eukaryotes that import the queuine base, bacteria synthesize Q modification de novo from a GTP starting block (14). The first stage of synthesis gives 7-cyano-7-deazaguanosine (preQ 0 ) that is then further modified into 7-aminoethyl 7-deazaguanine (preQ 1 ) (Fig. 1). The preQ 1 base is subsequently transferred to the appropriate tRNA in a guanine-exchange reaction catalyzed by a tRNA-guanine transglycosylase (TGT) (15). It is then further modified in situ to give Q (16). A second 7-deazaguanosine tRNA modification, archaeosine, is found in all archaeal tRNAs at position 15 of the D-loop (17). Archa...

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“…The labelled tRNA was purified by chromatography on a column (10 x 0.5 cm) of BD-Sephadex in a 0.25-2 M NaCl gradient in acetate buffer, pH 5. tRNA2'" was labelled at the mams2U base with FITC or with IAFl in the manner described for other tRNAs without the use of blocking by N-ethylmaleimide or iodoacetamide. However, the Q base of tRNATy' was labelled with FITC by literature methods [23,33,341 only after blocking of the two s4U bases by one of these reagents.…”

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Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore

Friedrich

Woolley

Steinhäuser

1988

European Journal of Biochemistry

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The procedures developed earlier (Friedrich and Woolley, preceding paper in this journal) for probing electrostatic potential with the fluorescein label were applied to transfer RNA. By using tRNA species that contain chemically reactive bases we were able to label these bases with fluorescein derivatives and thus to 'map' the electrostatic potential around the molecule. Both the electrostatic potential and the fluorescence emission anisotropy data that were obtained at the same time could be understood in terms of the well-known, paradigmatic crystal structure of tRNAPhe. However, within the distribution of the various tRNA species, tRNA,M"' appeared to occupy an extreme position, which suggests a relation between the conformation in solution and the initiation function of this molecule. Comparison with theoretical predictions by others of the electrostatic potential map of tRNA showed agreement in respect of trends, but the values of the potentials measured were orders of magnitude lower than predicted. This we attribute primarily to solvation.We have demonstrated in the preceding paper [l] that the pK, of the fluorescein label can be used as a probe of electrostatic potential; the theoretical basis of this leads to the simple relationship y = -58.2 ApK,, where y is the potential at the position occupied by the fluorophore and ApK, is the shift in pK, of the bound fluorescein compared with a chemically identical fluorescein derivative not bound to a macromolecule. The method was applied to the 16s RNA molecule, with the fluorescein label bound at its 3' end.Here we investigate the electrostatics of the tRNA molecule. This molecule allows a much more detailed investigation, as the various tRNA species contain many chemically modified bases, at known positions, that can react specifically with various derivatives of fluorescein. Since these bases are found at different locations on the molecule, comparisons can be made and an overall picture can be built up. An advantage of tRNA is that it is less easily denatured than the larger RNA molecules and solution structures may readily be compared. Further, the electrostatics of this molecule have been investigated theoretically [2 -71 so that experimental results can be interpreted in more depth.Of the more than 200 tRNA sequences determined to date, no exception to the clover-leaf structure [8,9] has been found. The X-ray structure of tRNAPhe from yeast and that of tRNA,M"' from Escherichia coli are not greatly different [lo, 111 and it is highly probable that the yeast tRNAPhe crystal Correspondence to' P. Woolley, Kemisk Institut, Aarhus Universitet, DK-8000 k h u s , DenmarkAbbreviations. FITC, fluorescein isothiocyanate; FTSC, fluorescein thiosemicarbazide; IAFl, iodacetamidofluorescein; X, 3-(3-amino-3-carboxypropyl)-uridine; Q, (4,5-cis-dihydroxy-l-cyclopenten-3-yl aminomethyl)-7-deazoguanidine; s4U, 4-thiouridine; mams2U, 5-methylaminomethyl-2-thiouridine.

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Structure of the modified nucleoside Q isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine

Cited by 217 publications

References 39 publications

Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme

Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme

Identification of Four Genes Necessary for Biosynthesis of the Modified Nucleoside Queuosine

Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore

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Structure of the modified nucleoside Q isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine

Cited by 217 publications

References 39 publications

Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme

Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme

Identification of Four Genes Necessary for Biosynthesis of the Modified Nucleoside Queuosine

Electrostatic potential of macromolecules measured by pKa shift of a fluorophore

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Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore