A site-specific self-cleavage reaction performed by a novel RNA in neurospora mitochondria

Saville, Barry J.; Collins, Richard A.

doi:10.1016/0092-8674(90)90480-3

Cited by 262 publications

(203 citation statements)

References 62 publications

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“…Several such catalytic motifs exist, including the hammerhead, hairpin, hepatitis delta virus (HDV), the Neurospora Varkud satellite motifs, and the cofactor-dependent glmS ribozyme. [10][11][12][13][14] The HDV family of ribozymes is the topic of this chapter.…”

Section: Introductionmentioning

confidence: 99%

HDV Family of Self-Cleaving Ribozymes

Riccitelli¹,

Lupták²

2013

Progress in Molecular Biology and Translational Science

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Section: Introductionmentioning

confidence: 99%

HDV Family of Self-Cleaving Ribozymes

Riccitelli¹,

Lupták²

2013

Progress in Molecular Biology and Translational Science

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“…1B) defines the substrate domain (Beattie et al 1995). The cleavage site is located within the internal loop of stem-loop I, between nucleotides G620 and A621 (Saville and Collins 1990). Our present understanding is that in order for cleavage to occur, the cleavage site internal loop must dock in a cleft formed by SLII and SLVI to allow its interaction with the active site formed by the A730 loop of SLVI (Sood et al 1998;Lafontaine et al 2001;Collins 2002;Lilley 2004).…”

Section: Introductionmentioning

confidence: 99%

“…Its catalytic activities are metal-dependent phosphodiester bond cleavage and ligation reactions, which both involve 59-OH and 29,39-cyclic phosphate termini Collins 1990, 1991). Although the natural VS ribozyme isolated from the mitochondria of certain strains of Neurospora performs self-cleavage activity (Saville and Collins 1990), VS ribozyme fragments of z100-160 nucleotides (nt) can perform cleavage in trans when incubated with small hairpin substrates in vitro (Guo and Collins 1995).…”

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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“…Representatives of the twister ribozyme class are found in all domains of life, but its biological role has yet to be determined. In addition to twister, the small self-cleaving ribozyme family includes the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), and glmS ribozymes (the glmS ribozyme is upsteam of the the glmS gene that codes for the enzyme that catalyzes glucosamine-6-phosphate production) (1)(2)(3)(4)(5)(6).…”

mentioning

confidence: 99%

Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme

Eiler¹,

Wang²,

Steitz

2014

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

142

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Twister is a recently discovered RNA motif that is estimated to have one of the fastest known catalytic rates of any naturally occurring small self-cleaving ribozyme. We determined the 4.1-Å resolution crystal structure of a twister sequence from an organism that has not been cultured in isolation, and it shows an ordered scissile phosphate and nucleotide 5′ to the cleavage site. A second crystal structure of twister from Orzyza sativa determined at 3.1-Å resolution exhibits a disordered scissile phosphate and nucleotide 5′ to the cleavage site. The core of twister is stabilized by base pairing, a large network of stacking interactions, and two pseudoknots. We observe three nucleotides that appear to mediate catalysis: a guanosine that we propose deprotonates the 2′-hydroxyl of the nucleotide 5′ to the cleavage site and a conserved adenosine. We suggest the adenosine neutralizes the negative charge on a nonbridging phosphate oxygen atom at the cleavage site. The active site also positions the labile linkage for in-line nucleophilic attack, and thus twister appears to simultaneously use three strategies proposed for small self-cleaving ribozymes. The twister crystal structures (i) show its global structure, (ii) demonstrate the significance of the double pseudoknot fold, (iii) provide a possible hypothesis for enhanced catalysis, and (iv) illuminate the roles of all 10 highly conserved nucleotides of twister that participate in the formation of its small and stable catalytic pocket.X-ray crystallography | RNA structure | weak derivative phasing | samarium derivatives | cesium derivatives T he twister RNA motif was identified by bioinformatic searches and then validated biochemically to be a small self-cleaving ribozyme (1). This recently discovered class of ribozymes is called twister because its conserved secondary structure resembles the ancient Egyptian hieroglyph "twisted flax." Representatives of the twister ribozyme class are found in all domains of life, but its biological role has yet to be determined. In addition to twister, the small self-cleaving ribozyme family includes the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), and glmS ribozymes (the glmS ribozyme is upsteam of the the glmS gene that codes for the enzyme that catalyzes glucosamine-6-phosphate production) (1-6).The small self-cleaving ribozyme family can be split into two groups based on whether their active site is formed by an irregular helix (hammerhead, hairpin, and VS) or a double pseudoknot (PK) structure (HDV and glmS) (7). The structures of HDV and glmS are known, whereas twister was predicted from representative sequences to use two PKs to form its active site. It was expected that twister would be smaller in size than either HDV or glmS and more comparable in size and complexity to hammerhead (1).The self-cleavage rate constant of twister is estimated to be as rapid as or slightly more rapid than the hammerhead ribozyme. The estimated rate constants (k obs ) for twister is 1,000 per minute, and the experime...

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A site-specific self-cleavage reaction performed by a novel RNA in neurospora mitochondria

Cited by 262 publications

References 62 publications

HDV Family of Self-Cleaving Ribozymes

HDV Family of Self-Cleaving Ribozymes

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

Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme

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