NMR study of nitrogen-15-labeled Escherichia coli valine transfer RNA

Choi, Byung-Seok; Redfield, Alfred G.

doi:10.1021/bi00166a013

Cited by 6 publications

(2 citation statements)

References 27 publications

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“…3C). This characteristic nitrogen chemical shift is indeed in line with those already reported for the N1 of Ψ on earlier works on several tRNAs 14,17,[19][20][21] , and cannot be mistaken for either the N1 of Gs (142-150 ppm) or the N3 of Us, Ts and Ψ (around 157 ppm). Therefore, A. aeolicus tmRNA-TLD expressed in vivo contains both a ribothymidine and a pseudouridine.…”

Section: Identification Of Two Modified Nucleotidessupporting

confidence: 91%

“…A small 1 ms Z-gradient pulse was applied before the reading JR pulse in JR-NOESY spectra recorded at 110, 130, 200 and 400 ms to cancel out spurious transverse magnetization. For shorter mixing times, (20,35,40, 50 and 70 ms), this was achieved using a combination of two small non refocusing Z-gradients. Moreover the first 90° pulse was phase-shifted by 45° so as to avoid the -180 orientation during phase The tRNA-like domain of tmRNA -25 -cycling (Smallcombe, 1993).…”

Section: Enzymatic and Chemical Rna Probingmentioning

confidence: 99%

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The tRNA-like Domains of E.coli and A.aeolicus Transfer–Messenger RNA: Structural and Functional Studies

Gaudin

Nonin‐Lecomte

Tisné

et al. 2003

Journal of Molecular Biology

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Transfer-messenger RNA (tmRNA, 10Sa RNA or ssrA) acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. The understanding at molecular level of this ubiquitous quality control system in eubacteria requires structural information. Here, we describe the purification and structural analysis of a functional fragment of both Aquifex aeolicus and Escherichia coli tmRNA, recapitulating their tRNA-like domain, which were expressed in vivo from synthetic genes. Both recombinant RNA are correctly processed at both 5' and 3' ends and are produced in quantities suitable for structural analysis by NMR and/or X-ray crystallography. The sequence and solution structure of the tRNA-like domains were analysed by various methods including structural mapping with chemical and enzymatic probes and 2D NMR spectroscopy. The minimalist RNAs contain two post-transcriptional base modifications, 5-methyluridine and pseudouridine, as the full-length tmRNA. Both RNAs fold into three stems, a D-analogue, a T-loop and a GAAA tetra-loop. 2D NMR analysis of the imino proton resonances of both RNAs allowed the assignment of the three stems and of a number of tertiary interactions. It shows the existence of interactions between the TPsiC-loop and the D-analogue, exhibiting a number of similarities and also differences with the canonical tRNA fold, indicating that RNA tertiary interactions can be modulated according to the sequence and secondary structure contexts. Furthermore, the E.coli minimalist RNA is aminoacylatable with alanine with a catalytic efficiency an order of magnitude higher than that for full-length tmRNA.

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Section: Identification Of Two Modified Nucleotidessupporting

confidence: 91%

Section: Enzymatic and Chemical Rna Probingmentioning

confidence: 99%

The tRNA-like Domains of E.coli and A.aeolicus Transfer–Messenger RNA: Structural and Functional Studies

Gaudin

Nonin‐Lecomte

Tisné

et al. 2003

Journal of Molecular Biology

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Imino chemical shift assignments of tRNAAsp, tRNAVal and tRNAPhe from Escherichia coli

Yared,

Chagneau,

Barraud

2024

Biomol NMR Assign

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Transfer RNAs (tRNAs) are an essential component of the protein synthesis machinery. In order to accomplish their cellular functions, tRNAs go through a highly controlled biogenesis process leading to the production of correctly folded tRNAs. tRNAs in solution adopt the characteristic L-shape form, a stable tertiary conformation imperative for the cellular stability of tRNAs, their thermotolerance, their interaction with protein and RNA complexes and their activity in the translation process. The introduction of post-transcriptional modifications by modification enzymes, the global conformation of tRNAs, and their cellular stability are highly interconnected. We aim to further investigate this existing link by monitoring the maturation of bacterial tRNAs in E. coli extracts using NMR. Here, we report on the 1H, 15N chemical shift assignment of the imino groups and some amino groups of unmodified and modified E. coli tRNAAsp, tRNAVal and tRNAPhe, which are essential for characterizing their maturation process using NMR spectroscopy.

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A 15N-1H nuclear magnetic resonance study on the interaction between isoleucine tRNA and isoleucyl-tRNA synthetase from Escherichia coli

Niimi¹,

Kawai²,

Takayanagi³

et al. 1993

Biochimie

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NMR study of nitrogen-15-labeled Escherichia coli valine transfer RNA

Cited by 6 publications

References 27 publications

The tRNA-like Domains of E.coli and A.aeolicus Transfer–Messenger RNA: Structural and Functional Studies

The tRNA-like Domains of E.coli and A.aeolicus Transfer–Messenger RNA: Structural and Functional Studies

Imino chemical shift assignments of tRNAAsp, tRNAVal and tRNAPhe from Escherichia coli

A 15N-1H nuclear magnetic resonance study on the interaction between isoleucine tRNA and isoleucyl-tRNA synthetase from Escherichia coli

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