Visualizing Group II Intron Catalysis through the Stages of Splicing

Marcia, Marco; Pyle, Anna Marie

doi:10.1016/j.cell.2012.09.033

Cited by 160 publications

(327 citation statements)

References 57 publications

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“…This U2–U6 base-paired complex forms the active site of the spliceosome, where the catalytic transesterification reactions of intron excision and exon joining occur (Figure 3). This structure bears remarkable similarity to the domain V region of self-splicing group II introns (13, 77, 78), which also use a lariat 2′–5′ mechanism for group II intron removal. On the basis of the similarity between the U2–U6 snRNA base pairing and the group II domain V structure and mechanism, it was speculated that the spliceosome used RNA-mediated catalysis, much like the ribosome.…”

Section: Biochemistry Of the Spliceosomementioning

confidence: 91%

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

Lee

Rio

2015

Annu. Rev. Biochem.

1,040

958

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Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA–protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA–RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions.

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Section: Biochemistry Of the Spliceosomementioning

confidence: 91%

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

Lee

Rio

2015

Annu. Rev. Biochem.

1,040

958

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“…The discovery and structural characterization of group I 1,2 and group II 3–5 introns have provided unique mechanistic insights into divalent cation-catalyzed phosphodiester bond cleavage reactions. By contrast, structure-function studies on small self-cleaving ribozymes that promote rate-enhanced site-specific phosphodiester bond cleavage, have identified alternate catalytic strategies whereby predominantly nucleobase-specific acid-base catalysis mediates cleavage chemistry 6,7 .…”

mentioning

confidence: 99%

In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme

et al. 2014

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Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-Å crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modeled 2′-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5′ bond. Both an invariant guanosine and a Mg2+ are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently-reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site.

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“…(D) Overlay of the internal loop within the ISL reveals a conserved bulge structure that is shared between the spliceosome and group II self-splicing introns. 12,57,75 This internal-loop region undergoes dynamic motions in activated spliceosomes. 69,70,108 (E) Three stacked base triples are proximal to the enzyme active site and are structurally conserved between the spliceosome and group II introns.…”

Section: Figurementioning

confidence: 99%

Structural Roles of Noncoding RNAs in the Heart of Enzymatic Complexes

Martin

Reiter

2016

Biochemistry

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Over billions of years of evolution, nature has embraced proteins as the major workhorse molecules of the cell. However, nearly every aspect of metabolism is dependent upon how structured RNAs interact with proteins, ligands, and other nucleic acids. Key processes, including telomere maintenance, RNA processing, and protein synthesis, require large RNAs that assemble into elaborate three-dimensional shapes. These RNAs can (i) act as flexible scaffolds for protein subunits, (ii) participate directly in substrate recognition, and (iii) serve as catalytic components. Here, we juxtapose the near atomic level interactions of three ribonucleoprotein complexes: ribonuclease P (involved in 5′ pre-tRNA processing), the spliceosome (responsible for pre-mRNA splicing), and telomerase (an RNA-directed DNA polymerase that extends the ends of chromosomes). The focus of this perspective is profiling the structural and dynamic roles of RNAs at the core of these enzymes, highlighting how large RNAs contribute to molecular recognition and catalysis.

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Visualizing Group II Intron Catalysis through the Stages of Splicing

Cited by 160 publications

References 57 publications

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme

Structural Roles of Noncoding RNAs in the Heart of Enzymatic Complexes

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