RNA Splicing by the Spliceosome

Wilkinson, Max E.; Charenton, Clément; Nagai, Kiyoshi

doi:10.1146/annurev-biochem-091719-064225

Cited by 484 publications

(437 citation statements)

References 148 publications

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“…The improved resolution of our new Ccomplex map allows a finer analysis of the active site of the spliceosome. The active site is formed by the U6 snRNA, which adopts a triplex conformation to position two catalytic Mg 2+ ions during branching and exon ligation 1,5,6,32 . The spliceosome uses the same configuration of the active site and the same two-metal ion mechanism for catalysis as observed in group II self-splicing introns 5,33 , and recent structural studies support the evolution of the spliceosome from group II introns 34,35 .…”

Section: Resultsmentioning

confidence: 99%

“…The spliceosome produces mRNA by excising introns from pre-mRNAs in two phosphoryl transfer reactionsbranching and exon ligation. The spliceosome assembles de novo on each pre-mRNA through protein and RNA interactions that recognise conserved sequences at exon-intron junctions, called splice sites 1 (Fig. 1a).…”

Section: Introductionmentioning

confidence: 99%

“…1a). The U6 snRNA recognises the 5ʹ-splice site (5ʹ-SS), while the U2 snRNA pairs with the intron around the branch adenosine (brA), forming the branch helix 1,2 . The 5ʹ-exon is stabilised in the active site by pairing with loop I of the U5 snRNA (refs.…”

Section: Introductionmentioning

confidence: 99%

“…1,5,6). This active site is stabilised by binding of the Prp19-associated complex 1,7 (NTC). Branching occurs in the B* complex when the 2ʹ-hydroxyl of the brA attacks the 5ʹ-SS.…”

Section: Introductionmentioning

confidence: 99%

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Structural basis for conformational equilibrium of the catalytic spliceosome

Fica

Galej

Nagai

2020

Preprint

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The catalytic spliceosome exists in equilibrium between the branching (B*/C) and exon ligation (C*/P) conformations. Here we present the electron cryo-microscopy reconstruction of the Saccharomyces cerevisiae C-complex spliceosome at 2.8 Å resolution and identify a novel C-complex intermediate (Ci) that elucidates the molecular basis for this equilibrium. In the Ci conformation, the exon-ligation factors Prp18 and Slu7 are already bound before ATP hydrolysis by Prp16, which destabilises the branching conformation. Biochemical assays suggest these pre-bound factors prime C complex for conversion to C* by Prp16. A complete model of the Prp19-complex (NTC) shows how branching factors Yju2 and Isy1 bind the NTC before branching. Prp16 remodels Yju2 binding after branching, allowing Yju2 to remain associated with the C* complex to promote exon ligation. Our results explain how Prp16 action modulates dynamic binding of step-specific factors to alternatively stabilise the C or C* conformation and establish equilibrium of the catalytic spliceosome.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…1,5,6). This active site is stabilised by binding of the Prp19-associated complex 1,7 (NTC). Branching occurs in the B* complex when the 2ʹ-hydroxyl of the brA attacks the 5ʹ-SS.…”

Section: Introductionmentioning

confidence: 99%

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Structural basis for conformational equilibrium of the catalytic spliceosome

Fica

Galej

Nagai

2020

Preprint

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“…Recruitment of U1 and U2 to pre-mRNA is followed by association of tri-snRNP U4-U6-U5 to form the pre-catalytic B complex. One of the key steps during spliceosome assembly is the recruitment of the NineTeen Complex (NTC, or Prp19 complex, (GO:0000974)) accompanied by the dissociation of U4 and U1, which leads to the activation of the B complex for catalysis of the first trans-esterification reaction ( Figure 7C) (63). Interestingly, while components of U1 and U2 snRNPs (specific proteins for U1 snRNP (GO:0005685) and U2 snRNP (GO:0005686)) are enriched, components of NTC are depleted in the mtl1-1 interactome ( Figure 7C).…”

Section: Mub1 Regulates Exosome Degradation Of the Stress-induced Mrnasmentioning

confidence: 99%

RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response

Birot

Kilchert

Kuś

et al. 2020

Preprint

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ABSTRACTThe nuclear RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given it has multiple roles in RNA regulation. Here we have analysed changes in the poly(A)+ RNA transcriptome and interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. We have identified multiple proteins whose occupancy on RNA is altered in the exosome mutants. We demonstrate that the Zinc-finger protein Mub1 regulates exosome dependent transcripts that encode stress-responsive proteins. Furthermore, we assess impact of the exosome inactivation upon RNA binding of the components of the mRNA processing machineries such as spliceosome and mRNA cleavage polyadenylation complex. We show that mutations in the exosome lead to accumulation of the components of U1 and U2 snRNPs on poly(A)+ RNA and depletion of the components of the activated spliceosome from RNA suggesting that the early stages of spliceosome assembly might provide a critical quality control step. Collectively, our data provide a global view of how RNA metabolism is affected in the exosome-deficient cells and reveal RNA-binding proteins that may act as novel exosome cofactors.

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Catalytic RNA

Kent¹,

Burke²,

Lupták³

2021

Encyclopedia of Life Sciences

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RNA molecules have diverse roles in biological systems. While some code for proteins or act to translate codons to amino acids, others fold into specific shapes that endow them with the ability to catalyse specific chemical transformations. These catalytic RNAs, ribozymes, are responsible for protein synthesis, tRNA processing, self‐splicing of certain introns, self‐scission during rolling circle replication of some single‐stranded RNA viruses and cofactor‐dependent gene regulation in bacteria. Other ribozymes have been evolved in vitro to perform a wide variety of transformations. Two of these, tRNA aminoacylase and RNA polymerase ribozymes, are featured here because molecules with such capabilities are thought to have existed on early Earth, before proteins took over as the dominant biological catalysts. Most of the ribozymes have been shown to perform multiturnover catalysis and thus act as true enzymes, either in their natural, biological form or as engineered constructs. Key Concepts RNA molecules can fold into specific conformations and accelerate chemical transformations, thus acting as catalytic biomacromolecules, ribozymes. Ribozymes can accelerate chemical reactions by many orders of magnitude. Many ribozymes are capable of multiturnover catalysis, acting as enzymes. Protein synthesis templated by mRNA is catalysed by ribosomal RNA. Most ribozymes are phosphoryl transferases. In vitro selected ribozymes have been shown to catalyse a wide variety of reactions. The existence of ribozymes supports the RNA World hypothesis.

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RNA Splicing by the Spliceosome

Cited by 484 publications

References 148 publications

Structural basis for conformational equilibrium of the catalytic spliceosome

Structural basis for conformational equilibrium of the catalytic spliceosome

RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response

Catalytic RNA

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