Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations

Cretu, Constantin; Schmitzová, Jana; Ponce-Salvatierra, Almudena; Dybkov, Olexandr; Laurentiis, Evelina Ines De; Sharma, K. C.; Will, Cindy L.; Urlaub, Henning; Lührmann, Reinhard; Peña, Vladimir

doi:10.1016/j.molcel.2016.08.036

Cited by 209 publications

(340 citation statements)

References 60 publications

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“…S3B), consistent with the interactions between Hsh155p mutant proteins and other SF3B subunits being unaltered, as also found by Cretu et al (2016).…”

Section: Sf3b1-prp5 Interaction In Splicingsupporting

confidence: 88%

“…In recent structures of the spliceosome (Rauhut et al 2016;Yan et al 2016) and of SF3B alone (Cretu et al 2016), the SF3B complex forms a "spring-loaded clamp"-like structure in which Hsh155p/SF3B1 is the "spring" and the BS-U2 duplex is "clamped" between the first and last HEAT domains of Hsh155p/SF3B1 (Supplemental Fig. S4).…”

Section: The Contribution Of Prp5p-hsh155p Interaction To Spliceosomementioning

confidence: 99%

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SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing

et al. 2016

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Mutations in the U2 snRNP component SF3B1 are prominent in myelodysplastic syndromes (MDSs) and other cancers and have been shown recently to alter branch site (BS) or 3 ′ splice site selection in splicing. However, the molecular mechanism of altered splicing is not known. We show here that hsh155 mutant alleles in Saccharomyces cerevisiae, counterparts of SF3B1 mutations frequently found in cancers, specifically change splicing of suboptimal BS pre-mRNA substrates. We found that Hsh155p interacts directly with Prp5p, the first ATPase that acts during spliceosome assembly, and localized the interacting regions to HEAT (Huntingtin, EF3, PP2A, and TOR1) motifs in SF3B1 associated with disease mutations. Furthermore, we show that mutations in these motifs from both human disease and yeast genetic screens alter the physical interaction with Prp5p, alter branch region specification, and phenocopy mutations in Prp5p. These and other data demonstrate that mutations in Hsh155p and Prp5p alter splicing because they change the direct physical interaction between Hsh155p and Prp5p. This altered physical interaction results in altered loading (i.e., "fidelity") of the BS-U2 duplex into the SF3B complex during prespliceosome formation. These results provide a mechanistic framework to explain the consequences of intron recognition and splicing of SF3B1 mutations found in disease.

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“…S3B), consistent with the interactions between Hsh155p mutant proteins and other SF3B subunits being unaltered, as also found by Cretu et al (2016).…”

Section: Sf3b1-prp5 Interaction In Splicingsupporting

confidence: 88%

Section: The Contribution Of Prp5p-hsh155p Interaction To Spliceosomementioning

confidence: 99%

SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing

et al. 2016

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“…We reported the solution structure of Rds3p (van Roon et al 2008), and recently the crystal structure of a core complex of human SF3b was published containing SF3b130 (Rse1p), SF3b155 (Hsh155p), SF3b14b (Rds3p), and SF3b10 (Ysf3p) (Cretu et al 2016). In this structure the HEAT repeats of SF3b155p wrap around a bipartite scaffold comprising SF3b130, SF3b10, and SF3b14b.…”

Section: Introductionmentioning

confidence: 97%

Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain

Roon¹,

Oubridge²,

Obayashi³

et al. 2017

RNA

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Spliceosomal proteins Hsh49p and Cus1p are components of SF3b, which together with SF3a, Msl1p/Lea1p, Sm proteins, and U2 snRNA, form U2 snRNP, which plays a crucial role in pre-mRNA splicing. Hsh49p, comprising two RRMs, forms a heterodimer with Cus1p. We determined the crystal structures of Saccharomyces cerevisiae full-length Hsh49p as well as its RRM1 in complex with a minimal binding region of Cus1p (residues 290-368). The structures show that the Cus1 fragment binds to the α-helical surface of Hsh49p RRM1, opposite the four-stranded β-sheet, leaving the canonical RNA-binding surface available to bind RNA. Hsh49p binds the 5 ′ end region of U2 snRNA via RRM1. Its affinity is increased in complex with Cus1(290-368)p, partly because an extended RNA-binding surface forms across the protein-protein interface. The Hsh49p RRM1-Cus1(290-368)p structure fits well into cryo-EM density of the B act spliceosome, corroborating the biological relevance of our crystal structure.

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“…The discovery of RNA splicing factor mutations has led to intense efforts to understand their biological impact on hematopoiesis, 6-9 their genomic and biochemical effects on RNA splicing, 10-21 their structural effects, 22 and potential means to therapeutically target cells bearing these mutations. 8,[23][24][25] Although there have been major advances in understanding the role of RNA splicing factor mutations in MDS pathogenesis and therapy (as reviewed recently [26][27][28] ), major questions about their biological consequences within cells, requirement in disease initiation vs maintenance, and cell autonomous vs nonautonomous roles remain.…”

Section: Introductionmentioning

confidence: 99%

How do messenger RNA splicing alterations drive myelodysplasia?

Joshi

Halene

Abdel-Wahab

2017

Blood

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Mutations in RNA splicing factors are the single most common class of genetic alterations in myelodysplastic syndrome (MDS) patients. Although much has been learned about how these mutations affect splicing at a global-and transcript-specific level, critical questions about the role of these mutations in MDS development and maintenance remain. Here we present the questions to be addressed in order to understand the unique enrichment of these mutations in MDS. (Blood. 2017; 129(18):2465-2470 IntroductionMyelodysplastic syndromes (MDSs) represent clonal disorders of hematopoietic stem cells (HSCs) whereby hematopoietic cell-intrinsic genetic alterations as well as non-cell autonomous factors contribute to an aberrant HSC that produces morphologically abnormal progeny and has impaired ability to generate mature blood cells. Due to the wide clinical and morphologic heterogeneity of MDS, substantial effort has been placed on characterizing the genetic alterations present in MDS cells in hopes of improving our ability to understand, diagnose, and treat the disease. Extensive targeted mutational analysis of protein coding genes has identified that MDS is characterized by a high frequency of mutations in genes encoding messenger RNA (mRNA) splicing factors as well as epigenetic modifiers.1-3 The discovery of mutations in RNA splicing factors in particular was quite unexpected as these mutations are generally uncommon in cancer yet are present in 50% to 60% of MDS patients. Interestingly, there are clear associations between specific mutated splicing factors and subtypes of MDS, most notably mutations in the RNA splicing factor SF3B1 in .90% of patients with MDS with ring sideroblasts.1,2,4 Moreover, the nature of these mutations is quite conspicuous as they occur as heterozygous point mutations at highly recurrent residues. Finally, within MDS patients, these mutations are almost always mutually exclusive; an MDS patient almost never has .1 RNA splicing factor mutation at the same time [1][2][3] (although rare individuals with mutations in .1 RNA splicing factor have been noted, 5 these occur far less frequently than expected by chance in MDS and it is unclear if both mutations in such cases are present within the same cell and/or how the mutations may impact splicing if coexpressed in the same cell).The discovery of RNA splicing factor mutations has led to intense efforts to understand their biological impact on hematopoiesis, 6-9 their genomic and biochemical effects on RNA splicing, 10-21 their structural effects, 22 and potential means to therapeutically target cells bearing these mutations. 8,[23][24][25] Although there have been major advances in understanding the role of RNA splicing factor mutations in MDS pathogenesis and therapy (as reviewed recently [26][27][28] ), major questions about their biological consequences within cells, requirement in disease initiation vs maintenance, and cell autonomous vs nonautonomous roles remain. In addition, numerous questions about the structural and biochemical effects of...

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Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations

Cited by 209 publications

References 60 publications

SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing

SF3B1/Hsh155 HEAT motif mutations affect interaction with the spliceosomal ATPase Prp5, resulting in altered branch site selectivity in pre-mRNA splicing

Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain

How do messenger RNA splicing alterations drive myelodysplasia?

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