Cryo-EM structure of the spliceosome immediately after branching

Galej, Wojciech P.; Wilkinson, Max E.; Fica, Sebastian M.; Oubridge, Chris; Newman, Andrew; Nagai, Kiyoshi

doi:10.1038/nature19316

Cited by 226 publications

(449 citation statements)

References 81 publications

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“…Structures of RRM-containing ribonucleoproteins and seminal spliceosome complexes (Yan et al 2015;Galej et al 2016;Rauhut et al 2016;Wan et al 2016a,b;Yan et al 2016) demonstrate that the RRM fold serves as a platform for multiprotein assemblies with RNA. One of the first RRM structures revealed distinct α-helical and β-sheet surfaces of the U2B ′′ RRM bound to the U2A ′ protein and the U2 small nuclear (sn) RNA (Price et al 1998).…”

Section: Introductionmentioning

confidence: 99%

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

Loerch

Kielkopf

2016

RNA

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U2AF homology motifs (UHM) that recognize U2AF ligand motifs (ULM) are an emerging family of protein-protein interaction modules. UHM-ULM interactions recur in pre-mRNA splicing factors including U2AF1 and SF3b1, which are frequently mutated in myelodysplastic syndromes. The core topology of the UHM resembles an RNA recognition motif and is often mistakenly classified within this large family. Here, we unmask the charade and review recent discoveries of UHM-ULM modules for protein-protein interactions. Diverse polypeptide extensions and selective phosphorylation of UHM and ULM family members offer new molecular mechanisms for the assembly of specific partners in the early-stage spliceosome.

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Section: Introductionmentioning

confidence: 99%

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

Loerch

Kielkopf

2016

RNA

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“…NTR-and Jab1-based regulation during splicing Very recently, cryo-EM structures of yeast spliceosomal B act complexes, 100,101 of 2 states of the yeast spliceosome after step 1 (C complex) 102,103 and of a post-catalytic intron-lariat spliceosome 81 have been determined. These structures together with previous functional analyses support a picture, in which Brr2 aids in recruiting and possibly regulating other spliceosome remodeling enzymes, during which Brr2 itself is apparently inhibited by different combinations of NTR-and Jab1-based mechanisms.…”

Section: Brr2 Regulation During Splicingmentioning

confidence: 99%

“…In one structure of a yeast post-step 1 spliceosome, 102 Brr2 uses the HLH domain of its NC to directly interact with the DEAH/RHA helicase Prp16 (Fig. 5B).…”

Section: Brr2 Regulation During Splicingmentioning

confidence: 99%

“…Views of (A) a yeast spliceosomal B act complex (PDB ID 5GM6) 100 and (B) a yeast spliceosomal C complex (PDB ID 5LJ5). 102 Brr2 and proteins interacting with the Brr2 NTR, and the Prp2 and Prp16 helicases are highlighted by colors. NTR, magenta; NC, dark gray; CC, beige; Jab1, gold; SF3B1, dark teal; Prp2, red; Prp16, dark red.…”

Section: Brr2 Regulation During Splicingmentioning

confidence: 99%

“…As the RH domain can interact with the NTR of Brr2 14 as well as with U4/U6 87 and can dramatically change its position during splicing, [100][101][102][103] it may intermittently contact U4/U6 during priming of a pre-catalytic spliceosome for Brr2-mediated activation, thus guiding the core of Brr2 to its entry site on U4 snRNA. Interestingly, the Prp8 Jab1 domain resembles corresponding domains in deubiquitinating enzymes.…”

Section: Brr2 Regulation During Splicingmentioning

confidence: 99%

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Functions and regulation of the Brr2 RNA helicase during splicing

2016

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Pre-mRNA splicing entails the stepwise assembly of an inactive spliceosome, its catalytic activation, splicing catalysis and spliceosome disassembly. Transitions in this reaction cycle are accompanied by compositional and conformational rearrangements of the underlying RNA-protein interaction networks, which are driven and controlled by 8 conserved superfamily 2 RNA helicases. The Ski2-like helicase, Brr2, provides the key remodeling activity during spliceosome activation and is additionally implicated in the catalytic and disassembly phases of splicing, indicating that Brr2 needs to be tightly regulated during splicing. Recent structural and functional analyses have begun to unravel how Brr2 regulation is established via multiple layers of intra-and inter-molecular mechanisms. Brr2 has an unusual structure, including a long N-terminal region and a catalytically inactive C-terminal helicase cassette, which can auto-inhibit and auto-activate the enzyme, respectively. Both elements are essential, also serve as protein-protein interaction devices and the N-terminal region is required for stable Brr2 association with the tri-snRNP, tri-snRNP stability and retention of U5 and U6 snRNAs during spliceosome activation in vivo. Furthermore, a C-terminal region of the Prp8 protein, comprising consecutive RNase H-like and Jab1/MPN-like domains, can both up-and downregulate Brr2 activity. Biochemical studies revealed an intricate cross-talk among the various cis-and transregulatory mechanisms. Comparison of isolated Brr2 to electron cryo-microscopic structures of yeast and human U4/U6 U5 tri-snRNPs and spliceosomes indicates how some of the regulatory elements exert their functions during splicing. The various modulatory mechanisms acting on Brr2 might be exploited to enhance splicing fidelity and to regulate alternative splicing. KEYWORDSPre-mRNA splicing; regulation of pre-mRNA splicing; remodeling of RNAprotein complexes; RNA helicase structure, function and regulation; spliceosome catalytic activation

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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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Cryo-EM structure of the spliceosome immediately after branching

Cited by 226 publications

References 81 publications

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

Functions and regulation of the Brr2 RNA helicase during splicing

Catalytic RNA

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