Recognition Elements in rRNA for the Tylosin Resistance Methyltransferase RlmAII

Lebars, Isabelle; Husson, Clotilde; Yoshizawa, Satoko; Douthwaite, Stephen; Fourmy, Dominique

doi:10.1016/j.jmb.2007.06.068

Cited by 12 publications

(15 citation statements)

References 42 publications

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“…Solvent suppression for samples in 90/10 H 2 O/D 2 O was achieved using the WATERGATE and ‘Jump and Return’ sequences (31,32). Assignment of TAR–R06 kissing complex, based on analysis of NOESY spectra recorded in H 2 O, has been previously reported (33,34). …”

Section: Methodsmentioning

confidence: 99%

Exploring TAR–RNA aptamer loop–loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance

Lebars

Legrand

Aimé

et al. 2008

Nucleic Acids Research

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In HIV-1, trans-activation of transcription of the viral genome is regulated by an imperfect hairpin, the trans-activating responsive (TAR) RNA element, located at the 5′ untranslated end of all viral transcripts. TAR acts as a binding site for viral and cellular proteins. In an attempt to identify RNA ligands that would interfere with the virus life-cycle by interacting with TAR, an in vitro selection was previously carried out. RNA hairpins that formed kissing-loop dimers with TAR were selected [Ducongé F. and Toulmé JJ (1999) RNA, 5:1605–1614]. We describe here the crystal structure of TAR bound to a high-affinity RNA aptamer. The two hairpins form a kissing complex and interact through six Watson–Crick base pairs. The complex adopts an overall conformation with an inter-helix angle of 28.1°, thus contrasting with previously reported solution and modelling studies. Structural analysis reveals that inter-backbone hydrogen bonds between ribose 2′ hydroxyl and phosphate oxygens at the stem-loop junctions can be formed. Thermal denaturation and surface plasmon resonance experiments with chemically modified 2′-O-methyl incorporated into both hairpins at key positions, clearly demonstrate the involvement of this intermolecular network of hydrogen bonds in complex stability.

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Section: Methodsmentioning

confidence: 99%

Exploring TAR–RNA aptamer loop–loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance

Lebars

Legrand

Aimé

et al. 2008

Nucleic Acids Research

Self Cite

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“…1). 19 RNA recognition by RlmA II appears to be similar to that of the orthologous methyltransferase, RlmA I (formerly RrmA) that is found in several groups of Gram-negative bacteria. RlmA I and RlmA II have a common evolutionary origin that is reflected in their degree of amino acid sequence identity (∼30%).…”

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confidence: 64%

“…Protection from the probes was attained at a 1:1 ratio of RNA:RlmA II , and was not increased measurably by adding more protein to an RNA: RlmA II ratio of 1:3. Our previous NMR and biochemical studies did not resolve the stoichiometry of this complex unambiguously, 19 which we can now define as an interaction between equimolar . Arrows with open circles indicate that RlmA II affords protection from the probes at this nucleotide; filled circles, enhanced nucleotide accessibility (as described for Fig.…”

mentioning

confidence: 82%

“…These effects were overlooked in our previous NMR study of the rRNA-methyltransferase interaction due to the absence of easily detectable imino protons in this region of the RNA. 19 Comparison of the RlmA II footprinting data with those for RlmA I on an identical E. coli 23 S rRNA substrate shows that both methyltransferases interact with the same rRNA region (Table 1). However, while the RlmA I and RlmA II interactions extend Table 1.…”

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confidence: 99%

“…The S. pneumoniae RlmA II also recognizes rRNA from Gram-negative bacteria, and methylates Escherichia coli rRNA at G748 almost as efficiently as the authentic streptococcal substrate. 19 The interaction of RlmA II with E. coli rRNA was footprinted in parallel experiments to reveal how RlmA II contacts might differ from those of RlmA I . For the reason explained above, E. coli rRNA was isolated from an rlmA I -minus strain that lacks the natural N1-methylation at G745.…”

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confidence: 99%

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