A secondary-structure model for the self-cleaving region of Neurospora VS RNA.

Beattie, Tara L.; Olive, Joan E.; Collins, Richard A.

doi:10.1073/pnas.92.10.4686

Cited by 90 publications

(163 citation statements)

References 33 publications

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“…3C; data not shown). C629 is less reactive with DMS only in the two combinations of stem-loops I and V that form kissing complexes, suggesting that a stem-loop I-V complex is necessary and sufficient for the interaction with C629 that protects this base from modification (22,24). Taken together, the mutational and chemical modification analyses indicate that stem-loops I and V interact in trans through a kissing interaction, forming a kissing complex.…”

Section: Stem-loop V Is Sufficient For the Rearrangement Of Stem-loop Imentioning

confidence: 66%

“…The partial protection of C637 could be due to its interaction with A622 in a non-Watson-Crick pair, as observed by NMR in an isolated, model stem-loop I in the unshifted conformation (33). In the presence of magnesium (lane 5), C629 was protected from modification by a yet unknown interaction, as observed (24). Also, C637 was protected from modification, consistent with its pairing with G623 in the shifted conformation of stem-loop I.…”

Section: Chemical Modification Reveals the Kissing Interaction Is Reqmentioning

confidence: 71%

“…H3 Pre self-cleaves in the presence of magnesium; H3⌬k Pre was cleaved in trans by a wild-type VS ribozyme (27). Analysis of D avoids the analysis of a mixed population of Pre and D in the presence of magnesium (24). In addition, D differs from the minimal self-cleaving domain by only one nucleotide at the 5Ј end, the identity of which is unimportant (21).…”

Section: Chemical Modification Reveals the Kissing Interaction Is Reqmentioning

confidence: 99%

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Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

Andersen

Collins

2001

Proc. Natl. Acad. Sci. U.S.A.

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Kissing interactions in RNA are formed when bases between two hairpin loops pair. Intra-and intermolecular kissing interactions are important in forming the tertiary or quaternary structure of many RNAs. Self-cleavage of the wild-type Varkud satellite (VS) ribozyme requires a kissing interaction between the hairpin loops of stemloops I and V. In addition, self-cleavage requires a rearrangement of several base pairs at the base of stem I. We show that the kissing interaction is necessary for the secondary structure rearrangement of wild-type stem-loop I. Surprisingly, isolated stem-loop V in the absence of the rest of the ribozyme is sufficient to rearrange the secondary structure of isolated stem-loop I. In contrast to kissing interactions in other RNAs that are either confined to the loops or culminate in an extended intermolecular duplex, the VS kissing interaction causes changes in intramolecular base pairs within the target stem-loop.R NA kissing interactions, also called loop-loop pseudoknots, occur when the unpaired nucleotides in one hairpin loop base pair with the unpaired nucleotides in another hairpin loop (1). When the hairpin loops are located on separate RNA molecules, their intermolecular interaction is called a kissing complex. These interactions generally form between stem-loops containing extensive complementarity; however, stable complexes have been observed containing only two intermolecular Watson-Crick base pairs (2).Intramolecular kissing interactions are observed in the native structures of a variety of RNAs including Varkud satellite (VS) RNA, tRNA, and group I introns (3-6). These kissing interactions contribute to the assembly and stabilization of their respective RNA structures by joining and orienting helices. Kissing interactions may stabilize both native and nonnative interactions during tertiary folding, which can affect the rate at which the native structure is formed (7). Kissing interactions often form distorted structures that can serve as recognition sites for proteins, RNAs, metal ions, or other ligands (8-10). As a result, kissing interactions contribute to the stability of an RNA structure by affecting both global and local RNA interactions.The transient formation of an intermolecular kissing complex is required for RNA dimerization during the life cycle of retroviruses (11-15), and for the formation of some antisensetarget complexes (16,17). Kissing complexes in which the loop nucleotides are complementary can form stable dimers that contain intermolecular base pairs between the loop nucleotides only. Other stem-loops with more extensive complementarity sometimes form unstable kissing complexes, which are quickly remodeled into stable duplex or cruciform isoforms (18)(19)(20). Secondary structure remodeling involves breaking intramolecular base pairs in each hairpin and using the bases to form intermolecular helices.The VS ribozyme contains a kissing interaction that is required for self-cleavage of the wild-type RNA in vitro (6). This interaction involves Watson-Crick bas...

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Section: Stem-loop V Is Sufficient For the Rearrangement Of Stem-loop Imentioning

confidence: 66%

Section: Chemical Modification Reveals the Kissing Interaction Is Reqmentioning

confidence: 71%

Section: Chemical Modification Reveals the Kissing Interaction Is Reqmentioning

confidence: 99%

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Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

Andersen

Collins

2001

Proc. Natl. Acad. Sci. U.S.A.

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“…It was clear with the identification of cleavage sites in HDV that those sequences would not assume either a hammerhead or a hairpin motif (Kuo et al, 1988b;Sharmeen et al, 1988;Wu et al, 1989). It is evident that HDV and the Neurosporu VS ribozymes assume distinct structures (Beattie et al, 1995;Rastogi et al, 1996).…”

Section: The Self-cleavage Reactionmentioning

confidence: 99%

Self‐Cleaving Ribozymes of Hepatitis Delta Virus RNA

Been

Wickham

1997

European Journal of Biochemistry

147

170

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Hepatitis delta virus (HDV) is a small single-stranded RNA satellite of hepatitis B virus. Although it is a human pathogen, it shares a number of features with a subset of the small plant satellite RNA viruses, including self-cleaving sequences in the genomic and antigenomic sequences of the viral RNA. The selfcleaving sequence is critical to viral replication and is thought to function as a ribozyme in vivo to process the products of rolling-circle replication to unit-length molecules. A divalent cation is required for cleavage and while a structural role is implicated for metal ions, a more direct role for a metal ion in catalysishas not yet been proven. A minimal natural ribozyme sequence with proficient in viiro self-cleavage activity is about 85 nucleotides long and adopts a secondary structure with four paired regions (Pl-P4).The two pairings that define the 5' and 3' boundaries of the ribozyme, PI and P2, form an atypical pseudoknot arrangement. This secondary structure places a number of constraints on the possible tertiary folding of the sequence, which together with chemical probing, photo-cross-linking, mutagenesis and computer-assisted modeling provides clues to the three-dimensional structure. The data are consistent with a model in which the cleavage site, located at the 5' end of PI, is in close proximity to three singlestranded regions, consisting of a hairpin loop at the end of P3 and two sequences joining P1 to P4 and P4 to P2. While the natural forms of the HDV ribozymes appear to be prone to misfolding, biochemical and mutagenesis studies from a number of laboratories has allowed the production of trans-acting ribozymes and smaller more active cis-acting ribozymes, both of which will aid in further mechanistic and structural studies of this RNA.

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“…1A; Beattie et al 1995), tertiary structure models (Hiley and Collins 2001;Lafontaine et al 2002), and NMR structures of individual stem-loops (Michiels et al 2000;Dieckmann 2001, 2004;Hoffmann et al 2003;Campbell and Legault 2005;Campbell et al 2006). The catalytic domain of the VS ribozyme consists of five stem-loop subdomains (SLII-SLVI) (Fig.…”

Section: Introductionmentioning

confidence: 99%

Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

Bouchard¹,

Lacroix‐Labonté²,

Desjardins³

et al. 2008

RNA

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Substrate recognition by the VS ribozyme involves a magnesium-dependent loop/loop interaction between the SLI substrate and the SLV hairpin from the catalytic domain. Recent NMR studies of SLV demonstrated that magnesium ions stabilize a U-turn loop structure and trigger a conformational change for the extruded loop residue U700, suggesting a role for U700 in SLI recognition. Here, we kinetically characterized VS ribozyme mutants to evaluate the contribution of U700 and other SLV loop residues to SLI recognition. To help interpret the kinetic data, we structurally characterized the SLV mutants by NMR spectroscopy and generated a three-dimensional model of the SLI/SLV complex by homology modeling with MC-Sym. We demonstrated that the mutation of U700 by A, C, or G does not significantly affect ribozyme activity, whereas deletion of U700 dramatically impairs this activity. The U700 backbone is likely important for SLI recognition, but does not appear to be required for either the structural integrity of the SLV loop or for direct interactions with SLI. Thus, deletion of U700 may affect other aspects of SLI recognition, such as magnesium ion binding and SLV loop dynamics. As part of our NMR studies, we developed a convenient assay based on detection of unusual 31 P and 15 N N7 chemical shifts to probe the formation of U-turn structures in RNAs. Our model of the SLI/SLV complex, which is compatible with biochemical data, leads us to propose novel interactions at the loop I/loop V interface.

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A secondary-structure model for the self-cleaving region of Neurospora VS RNA.

Cited by 90 publications

References 33 publications

Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

Self‐Cleaving Ribozymes of Hepatitis Delta Virus RNA

Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme

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