Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA

Iwata‐Reuyl, Dirk

doi:10.1016/s0045-2068(02)00513-8

Cited by 127 publications

(148 citation statements)

References 87 publications

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“…The Q modification is known to be important for translational fidelity (Bienz and Kubli 1981;Meier et al 1985;Urbonavičius et al 2001). Q biosynthesis starts with GTP and proceeds through the intermediate preQ 0 (7-cyano-7-deazaguanine) and preQ 1 (7-aminomethyl-7-deazaguanine) in a series of enzymatic steps (Kuchino et al 1976;Okada et al 1978;Iwata-Reuyl 2003;Gaur and Varshney 2005;Van Lanen et al 2005). PreQ 1 is preferentially exchanged for a specific guanine in tRNA (Noguchi et al 1982), and the remaining biosynthetic steps take place in situ (Okada et al 1979;Slany et al 1993).…”

Section: Introductionmentioning

confidence: 99%

Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria

Meyer¹,

Roth²,

Chervin³

et al. 2008

RNA

105

155

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Bioinformatics searches of eubacterial genomes have yielded many riboswitch candidates where the identity of the ligand is not immediately obvious on examination of associated genes. One of these motifs is found exclusively in the family Streptococcaceae within the 59 untranslated regions (UTRs) of genes encoding the hypothetical membrane protein classified as COG4708 or DUF988. While the function of this protein class is unproven, a riboswitch binding the queuosine biosynthetic intermediate pre-queuosine 1 (preQ 1 ) has been identified in the 59 UTR of homologous genes in many Firmicute species of bacteria outside of Streptococcaceae. Here we show that a representative of the COG4708 RNA motif from Streptococcus pneumoniae R6 also binds preQ 1 . Furthermore, representatives of this RNA have structural and molecular recognition characteristics that are distinct from those of the previously described preQ 1 riboswitch class. PreQ 1 is the second metabolite for which two or more distinct classes of natural aptamers exist, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. Additionally, the association of preQ 1 binding RNAs with most genes encoding proteins classified as COG4708 strongly suggests that these proteins function as transporters for preQ 1 or another queuosine biosynthetic intermediate.

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Section: Introductionmentioning

confidence: 99%

Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria

Meyer¹,

Roth²,

Chervin³

et al. 2008

RNA

105

155

View full text Add to dashboard Cite

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“…113 Q is synthesized by bacteria, and eukaryotes acquire Q either as a nutrient or from the intestinal flora as quenine, the free base form of Q, which is then directly inserted into the pertinent tRNAs through substitution of the base quenine. 114 Interestingly, the E. coli tRNA Tyr contains pseudouridine at position 35, the second position of the anticodon and adjacent to Q, ms 2 i 6 A at position 37, and Ψ at position 39. Loss of Ψ at the rarely modified position 35 compromises translational fidelity in vitro , implying that some ASLs need even more than three modified nucleosides for accurate function.…”

Section: The Modified Wobble Hypothesis and Decoding At Position 34mentioning

confidence: 99%

Celebrating wobble decoding: Half a century and still much is new

et al. 2017

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A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.

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“…(Morris & Elliott, 2001). In contrast to prokaryotes and eukaryotes, archaea contain a hypermodified nucleoside structurally similar to queuosine termed archaeosine (Iwata-Reuyl, 2003). Only prokaryotes can synthesize Q de novo, while eukaryotic organisms rely on Q produced by intestinal flora (Kuchino et al, 1976).…”

Section: Introductionmentioning

confidence: 99%

Crystallization and preliminary X-ray characterization of queD fromBacillus subtilis, an enzyme involved in queuosine biosynthesis

Cicmil

Shi

2008

Acta Cryst Sect F

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QueD (previously named ykvK) is one of several enzymes involved in the biosynthesis of the hypermodified nucleoside queuosine. Queuosine is incorporated into tRNA at position 34 of four tRNAs: tRNA His , tRNA Asp , tRNA Asn and tRNA Tyr . The crystallization and preliminary X-ray crystallographic studies of queD are described here. The recombinant protein from Bacillus subtilis was overproduced in Escherichia coli and crystallized using the hanging-drop vapor-diffusion method from 25% PEG 600, 100 mM NaCl and sodium citrate buffer pH 5.5 at 291 K. The crystals diffract to 3.6 Å resolution and belong to the cubic space group F4 1 32, with unit-cell parameter a = 240.88 Å .

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Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA

Cited by 127 publications

References 87 publications

Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria

Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria

Celebrating wobble decoding: Half a century and still much is new

Crystallization and preliminary X-ray characterization of queD fromBacillus subtilis, an enzyme involved in queuosine biosynthesis

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Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA

Cited by 127 publications

References 87 publications

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

Celebrating wobble decoding: Half a century and still much is new

Crystallization and preliminary X-ray characterization of queD fromBacillus subtilis, an enzyme involved in queuosine biosynthesis

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Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria

Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria