Structure of an AAGU Tetraloop and its Contribution to Substrate Selection by yeast RNase III

Gaudin, Cyril; Ghazal, Ghada; Yoshizawa, Satoko; Elela, Sherif Abou; Fourmy, Dominique

doi:10.1016/j.jmb.2006.08.029

Cited by 17 publications

(25 citation statements)

References 46 publications

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“…This finding is in agreement with the recently determined solution structure of the A1-hairpin that shows a different conformation from that exhibited by G2-hairpins. 38 Consistent with this, chemical footprinting and chemical interference assays indicated that Rnt1p binds A1 and G2-substrates using different sets of nucleotides (Figure 4). Cleavage and binding assays showed that the N-term of Rnt1p plays an important role in the selection of A1-hairpins.…”

Section: Discussionsupporting

confidence: 71%

“…Rnt1p cleaves RNA hairpins capped with A1-loops despite the fact that the second nucleotide of the loop is in an anti conformation. 38 It is also unlikely that the sequence of the nucleotide in the second position itself blocks cleavage because the dsRBD of Rnt1p does not directly interact with this position 15 and here we show that changing the sequence of the entire tetraloop does not inhibit cleavage ( Figure 1(b)). Indeed, A1-hairpins were moderately cleaved by Rnt1p (Figure 2(a)), whereas ACAA was not (B. Lamontagne and S.A. E., unpublished observation).…”

Section: Discussionmentioning

confidence: 57%

“…This means that AAGU and not ACAA tetraloops contain features that allow it to be cleaved even in the absence of guanosine in the second position. We propose that the structure at the 3′ end of A1-loops, which is very different from that found in G2 ( Figure 1) and ACAA hairpins, 38 allows it to be recognized by Rnt1p despite the structural changes in the second position of the tetraloop.…”

Section: Discussionmentioning

confidence: 63%

“…Consistently, comparison between the solution structure of the A1 and G2-hairpins show that the two loops differ in the conformation of the second and fourth nucleotides of the loop. 38 This clearly shows that Rnt1p recognition of the A1-substrates is not due to similarity between the two structures. Indeed, hairpins capped with ACAA tetraloops assumes a similar conformation to that of G2 and A1-hairpins but is not cleaved by Rnt1p.…”

Section: Discussionmentioning

confidence: 87%

“…Indeed, hairpins capped with ACAA tetraloops assumes a similar conformation to that of G2 and A1-hairpins but is not cleaved by Rnt1p. 20,21,38 The difference between ACAA and AGNN tetraloops is that the cytosine in the second position of the ACAA tetraloop is in anti glycosidic torsion angle instead of the syn conformation adopted by the AGNN guanosine. 21 These changes in conformation by itself are sufficient to block Rnt1p cleavage of the canonical G2 but not A1-substrates.…”

Section: Discussionmentioning

confidence: 99%

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Characterization of the Reactivity Determinants of a Novel Hairpin Substrate of Yeast RNase III

Ghazal

Elela

2006

Journal of Molecular Biology

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Section: Discussionsupporting

confidence: 71%

Section: Discussionmentioning

confidence: 57%

Section: Discussionmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 99%

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Characterization of the Reactivity Determinants of a Novel Hairpin Substrate of Yeast RNase III

Ghazal

Elela

2006

Journal of Molecular Biology

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Comparison of preribosomal RNA processing pathways in yeast, plant and human cells – focus on coordinated action of endo‐ and exoribonucleases

2017

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Edited by Michael IbbaProper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo-and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans.Keywords: endoribonuclease; exoribonuclease; pre-rRNA processing; ribosome biogenesis; RNA quality control; RNA trimming Ribosome biosynthesis is a multistep process that includes several tightly controlled events -ribosomal DNA (rDNA) transcription, processing of rRNA precursors into mature molecules, accompanied by binding of ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs), and the final assembly of all Abbreviations CD, catalytic domain; dsRBD, double-stranded RNA-binding domain; ETS, external transcribed spacer; ITS, internal transcribed spacer; LSU, large ribosome subunit (60S); miRNA, microRNA; mRNA, messenger RNA; MRP RNA, noncoding RNA component of the RNase MRP; mTOR, mammalian target of rapamycin; nt(s), nucleotide(s); PIN domain, PilT N-terminal domain; Pol I/II/III, RNA polymerase I/II/III; prerRNA, ribosomal RNA precursor; RBF, ribosome biogenesis factor; RMRP, RNase MRP (mitochondrial RNA processing ribonuclease); RNase, ribonuclease; RNB domain, RNase II domain; RNP, ribonucleoprotein; RP, ribosomal protein; rRNA, ribosomal RNA; siRNA, short interfering RNA; snoRNA, small nucleolar RNA; snoRNP, small nucleolar ribonucleoprotein; snRNA, small nuclear RNA; SSU, small ribosome subunit (40S); TRAMP4 or TRAMP5, Trf4/Air/Mtr4 or Trf5/Air/Mtr4 polyadenylation complex; tRNA, transfer RNA.

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Protein–RNA footprinting: an evolving tool

Fourmy

Yoshizawa

2012

WIREs RNA

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As more RNA molecules with important cellular functions are discovered, there is a strong need to characterize their structures, functions, and interactions. Chemical and enzymatic footprinting methods are used to map RNA secondary and tertiary structure, to monitor ligand interactions and conformational changes, and in the study of protein-RNA interactions. These methods provide data at single-nucleotide resolution that nicely complements the structural information available from X-ray diffraction, nuclear magnetic resonance spectroscopy (NMR), or cryo-electron microscopy. Footprinting methods also complement the dynamic information derived from single-molecule Förster resonance energy transfer. RNA footprinting tools have been used for decades, but we have recently seen spectacular advances, for instance, the use in combination with massive parallel sequencing techniques. Large libraries of RNA molecules (small or large in size) can now be probed in high-throughput manner when RNA footprinting methods are combined with fluorescent probe technologies and automation. In this article, after a brief historical overview, we summarize recent advances in RNA-protein footprinting methodologies that now integrate tools for massive parallel analysis.

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Structure of an AAGU Tetraloop and its Contribution to Substrate Selection by yeast RNase III

Cited by 17 publications

References 46 publications

Characterization of the Reactivity Determinants of a Novel Hairpin Substrate of Yeast RNase III

Characterization of the Reactivity Determinants of a Novel Hairpin Substrate of Yeast RNase III

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells – focus on coordinated action of endo‐ and exoribonucleases

Protein–RNA footprinting: an evolving tool

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