Crystal structure of a core spliceosomal protein interface

Schellenberg, M.J.; Edwards, Ross A.; Ritchie, Dustin B.; Kent, Oliver A.; Golas, Monika M.; Stark, Holger; Lührmann, Reinhard; Glover, J. N. Mark; MacMillan, Andrew M.

doi:10.1073/pnas.0508048103

Cited by 74 publications

(126 citation statements)

References 31 publications

Supporting

Mentioning

122

Contrasting

Order By: Relevance

“…Deletion of this region abolished binding of Pml1p to Snu17p 13,15 . RRM extensions, as observed in Snu17p, are already folded in an RRM's free state [34][35][36] or fold upon binding to RNA and protein 32,33,[37][38][39] . For example, two short C-terminal helices of U1A provide an additional RNA interface for the interaction of its RRM domain with RNA 36,40 .…”

Section: Discussionmentioning

confidence: 94%

See 1 more Smart Citation

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Wysoczanski

Schneider

Munari

et al. 2014

Nat Struct Mol Biol

Self Cite

View full text Add to dashboard Cite

1 1 a r t i c l e sSplicing entails the removal of introns from pre-mRNAs to generate exon-only mRNA, which is exported out of the nucleus for translation 1 . The splicing process is driven and controlled by a large and dynamic RNA-protein complex, the spliceosome 1,2 . The composition and structure of the spliceosome undergoes multiple rearrangements during a splicing reaction, in which a set of distinct structural and compositional states, designated as E, A, B act , B* and C complexes, can be defined 1 . As part of this process, small nuclear ribonucleoprotein (snRNP) particles and non-snRNP splice factors are recruited and released 1,2 . Although the organization of snRNP components of the spliceosome has received considerable attention in recent years, very little is known about the assembly, structure and dynamics of non-snRNP multimeric complexes.The non-snRNP RES complex is present in humans and yeast 3,4 . Deletion of RES genes slows splicing and leads to pre-mRNA leakage into the cytoplasm 3-5 . Distinct introns exhibit RES-dependent splicing 5-9 , as do pre-mRNAs encoding proteins functioning in RNA-nucleotide metabolism 8,10 . Components of the RES complex are found in B and C complexes of the spliceosome, in which RES can interact with U2 snRNP 4,11,12 . In yeast, the RES complex is composed of three proteins, snRNP-associated protein 17 (Snu17p, also known as Ist3p), pre-mRNA-leakage protein 1 (Pml1p) and bud siteselection protein 13 (Bud13p) 3,4 . Snu17p and Bud13p have been implicated directly in splicing 3,5,13 , whereas Pml1p has been linked to the retention of unspliced pre-mRNA in the nucleus 3,5 . Caenorhabditis elegans Bud13p is involved in embryogenesis 14 .Sequence analysis has indicated that Snu17p is a 148-residue (17.1-kDa) noncanonical member of the RRM family of proteins with a long C-terminal part, which exhibits low sequence similarity to published RRM structures 4 . Snu17p binds with nanomolar affinity to the 266-residue (30.5-kDa), natively disordered protein Bud13p 15 . The interaction has been postulated to involve a C-terminal UHM-ligand motif (ULM) in Bud13p that interacts with a U2AF-homology motif (UHM) in the RRM domain of Snu17p 13,15,16 . The only other identified domain encompasses a stretch of lysine residues at the N terminus of Bud13p. Binding of the third component, the 204-residue (23.4-kDa) Pml1p, occurs through its 50 N-terminal disordered residues. The remainder of Pml1p folds as a forkhead-associated domain 13,15,17 , which could potentially bind phosphopeptides 17 . Biochemical evidence has suggested that Snu17p acts as the central binding platform, which interacts with disordered parts of Bud13p and Pml1p 13,15,16 . The precise molecular architecture of the RES complex, however, has been elusive, and its RNA binding capabilities have remained unexplored.Here we solved the three-dimensional structure of the core of the RES complex and demonstrated that its assembly is driven by cooperativity that increases the binding affinity of the components of the complex ...

show abstract

Section: Discussionmentioning

confidence: 94%

“…4,16,31), which binds to SF3b155 in the U2 snRNP-associated SF3b complex 32,33 . Comparison of the structure of the RES core complex with that of p14 bound to a SF3b155 peptide shows that c Pml1p interacts with a different site on the RRM domain (Fig.…”

Section: Discussionmentioning

confidence: 99%

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Wysoczanski

Schneider

Munari

et al. 2014

Nat Struct Mol Biol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Because BP 0 potential to form base-pairing interactions with U2 snRNA is generally superior to that of canonical BP, we suggest that U2 snRNP containing SF3B1 MUT has more stringent requirement for BP sequences than U2 snRNP-containing SF3B1 WT . Consistently, the hotspot mutations of SF3B1 target the HEAT repeats of SF3B1, which form helical structures that occlude the binding surface for RNA recognition motif of p14, a component of U2 snRNP that binds the BP 1,26 . The hotspot mutations of SF3B1 in the HEAT repeats occur on the inner surface of the structure and may induce a conformational change in the U2 snRNP complex altering its selectivity for BPs.…”

Section: Discussionmentioning

confidence: 95%

Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage

Alsafadi¹,

Houy²,

Battistella³

et al. 2016

European Journal of Cancer

View full text Add to dashboard Cite

Hotspot mutations in the spliceosome gene SF3B1 are reported in B20% of uveal melanomas. SF3B1 is involved in 3 0 -splice site (3 0 ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1 R625/K666 mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3 0 ss. Modelling the differential junctions in SF3B1 WT and SF3B1 R625/K666 cell lines demonstrates that the deregulated splice pattern strictly depends on SF3B1 status and on the 3'ss-sequence context. SF3B1 WT knockdown or overexpression do not reproduce the SF3B1 R625/K666 splice pattern, qualifying SF3B1 R625/K666 as change-of-function mutants. Mutagenesis of predicted branchpoints reveals that the SF3B1 R625/K666 -promoted splice pattern is a direct result of alternative branchpoint usage. Altogether, this study provides a better understanding of the mechanisms underlying splicing alterations induced by mutant SF3B1 in cancer, and reveals a role for alternative branchpoints in disease.

show abstract

“…The ULM-containing region of SF3b155 adjoins its binding site for p14, an RRM-like U2 snRNP subunit that ultimately contacts the branch point sequence of the pre-mRNA Cass and Berglund 2006;Schellenberg et al 2006;Spadaccini et al 2006). Considering the above data, multiple UHM-containing proteins are likely to simultaneously associate with the SF3b155 IDR alongside the p14 subunit, possibly with positive cooperativity (Fig.…”

Section: Potential Functions Of Multiple Functions Of Multiple Sf3b15mentioning

confidence: 99%

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

Loerch

Kielkopf

2016

RNA

View full text Add to dashboard Cite

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.

show abstract

Crystal structure of a core spliceosomal protein interface

Cited by 74 publications

References 31 publications

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage

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

Contact Info

Product

Resources

About