Structural Basis for Recognition of the Intron Branch Site RNA by Splicing Factor 1

Science ◽  
2001 ◽  
Vol 294 (5544) ◽  
pp. 1098-1102 ◽  
Author(s):  
Z. Liu
Keyword(s):  
Splicing Factor ◽  
Structural Basis ◽  
Branch Site ◽  
Splicing Factor 1

scholarly journals Splicing factor 1 modulates dietary restriction and TORC1 pathway longevity in C. elegans

Nature ◽  
2016 ◽  
Vol 541 (7635) ◽  
pp. 102-106 ◽  
Author(s):  
Caroline Heintz ◽  
Thomas K. Doktor ◽  
Anne Lanjuin ◽  
Caroline C. Escoubas ◽  
Yue Zhang ◽  
...  
Keyword(s):  
Dietary Restriction ◽  
Splicing Factor ◽  
C Elegans ◽  
Splicing Factor 1

scholarly journals Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1

2011 ◽  
Vol 16 (5) ◽  
pp. 479-490 ◽  
Author(s):  
Hitomi Tsuiji ◽  
Rei Yoshimoto ◽  
Yuko Hasegawa ◽  
Masaaki Furuno ◽  
Minoru Yoshida ◽  
...  
Keyword(s):  
Splicing Factor ◽  
Noncoding Exon ◽  
Splicing Factor 1

scholarly journals Recognition of RNA Branch Point Sequences by the KH Domain of Splicing Factor 1 (Mammalian Branch Point Binding Protein) in a Splicing Factor Complex

2001 ◽  
Vol 21 (15) ◽  
pp. 5232-5241 ◽  
Author(s):  
Hadas Peled-Zehavi ◽  
J. Andrew Berglund ◽  
Michael Rosbash ◽  
Alan D. Frankel
Keyword(s):  
Branch Point ◽  
Fusion Proteins ◽  
Rna Binding ◽  
Binding Protein ◽  
Splicing Factor ◽  
Splice Sites ◽  
Reporter System ◽  
Kh Domain ◽  
Tat Fusion Proteins ◽  
Splicing Factor 1

ABSTRACT Mammalian splicing factor 1 (SF1; also mammalian branch point binding protein [mBBP]; hereafter SF1/mBBP) specifically recognizes the seven-nucleotide branch point sequence (BPS) located at 3′ splice sites and participates in the assembly of early spliceosomal complexes. SF1/mBBP utilizes a “maxi-K homology” (maxi-KH) domain for recognition of the single-stranded BPS and requires a cooperative interaction with splicing factor U2AF65 bound to an adjacent polypyrimidine tract (PPT) for high-affinity binding. To investigate how the KH domain of SF1/mBBP recognizes the BPS in conjunction with U2AF and possibly other proteins, we constructed a transcriptional reporter system utilizing human immunodeficiency virus type 1 Tat fusion proteins and examined the RNA-binding specificity of the complex using KH domain and RNA-binding site mutants. We first established that SF1/mBBP and U2AF cooperatively assemble in our reporter system at RNA sites composed of the BPS, PPT, and AG dinucleotide found at 3′ splice sites, with endogenous proteins assembled along with the Tat fusions. We next found that the activities of the Tat fusion proteins on different BPS variants correlated well with the known splicing efficiencies of the variants, supporting a model in which the SF1/mBBP-BPS interaction helps determine splicing efficiency prior to the U2 snRNP-BPS interaction. Finally, the likely RNA-binding surface of the maxi-KH domain was identified by mutagenesis and appears similar to that used by “simple” KH domains, involving residues from two putative α helices, a highly conserved loop, and parts of a β sheet. Using a homology model constructed from the cocrystal structure of a Nova KH domain-RNA complex (Lewis et al., Cell 100:323–332, 2000), we propose a plausible arrangement for SF1/mBBP-U2AF complexes assembled at 3′ splice sites.

scholarly journals Structural Basis for Polypyrimidine Tract Recognition by the Essential Pre-mRNA Splicing Factor U2AF65

2006 ◽  
Vol 23 (1) ◽  
pp. 49-59 ◽  
Author(s):  
E. Allen Sickmier ◽  
Katherine E. Frato ◽  
Haihong Shen ◽  
Shanthi R. Paranawithana ◽  
Michael R. Green ◽  
...  
Keyword(s):  
Mrna Splicing ◽  
Splicing Factor ◽  
Structural Basis ◽  
Polypyrimidine Tract

scholarly journals Splicing Factor 1 in the Pocket

Structure ◽  
2003 ◽  
Vol 11 (5) ◽  
pp. 481-482 ◽  
Author(s):  
Gabriele Varani ◽  
Andres Ramos
Keyword(s):  
Splicing Factor ◽  
Splicing Factor 1

The structural basis of Indisulam-mediated recruitment of RBM39 to the DCAF15-DDB1-DDA1 E3 ligase complex

2019 ◽  
Author(s):  
Dirksen E. Bussiere ◽  
Lili Xie ◽  
Honnappa Srinivas ◽  
Wei Shu ◽  
Ashley Burke ◽  
...  
Keyword(s):  
Structural Model ◽  
Complex Structure ◽  
E3 Ligase ◽  
Mrna Splicing ◽  
Splicing Factor ◽  
Structural Basis ◽  
Anti Cancer ◽  
Novel Targets ◽  
Cancer Agent ◽  
Hct116 Cells

AbstractThe anti-cancer agent Indisulam inhibits cell proliferation by causing degradation of RBM39, an essential mRNA splicing factor. Indisulam promotes an interaction between RBM39 and the DCAF15 E3 ligase substrate receptor leading to RBM39 ubiquitination and proteasome-mediated degradation. To delineate the precise mechanism by which Indisulam mediates DCAF15-RBM39 interaction, we solved the DCAF15-DDB1-DDA1-Indisulam-RBM39(RRM2) complex structure to 2.3 Å. DCAF15 has a novel topology which embraces the RBM39(RRM2) domain largely via nonpolar interactions, and Indisulam binds between DCAF15 and RBM39(RRM2) and coordinates additional interactions between the two proteins. Studies with RBM39 point mutants and Indisulam analogs validated the structural model and defined the RBM39 alpha-helical degron motif. The degron is found only in RBM23 and RBM39 and only these proteins were detectably downregulated in Indisulam-treated HCT116 cells. This work further explains how Indisulam induces RBM39 degradation and defines the challenge of harnessing DCAF15 to degrade novel targets.

scholarly journals UHM–ULM interactions in the RBM39–U2AF65 splicing-factor complex

2016 ◽  
Vol 72 (4) ◽  
pp. 497-511 ◽  
Author(s):  
Galina A. Stepanyuk ◽  
Pedro Serrano ◽  
Eigen Peralta ◽  
Carol L. Farr ◽  
Herbert L. Axelrod ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
Splicing Factor ◽  
Structural Basis ◽  
Titration Calorimetry ◽  
Protein Protein Interactions ◽  
Rrm Domain ◽  
Nmr Structures ◽  
Binding Interface ◽  
Cell Extracts

RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein–protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39–U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemical shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35–U2AF65 and RBM39–SF3b155, the RBM39-UHM–U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM–ULM binding interface, providing a rationale for the known specificity of UHM–ULM interactions. This study therefore establishes a structural basis for specific UHM–ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.

scholarly journals A Role for SRp54 during Intron Bridging of Small Introns with Pyrimidine Tracts Upstream of the Branch Point

1998 ◽  
Vol 18 (9) ◽  
pp. 5425-5434 ◽  
Author(s):  
Catharine F. Kennedy ◽  
Angela Krämer ◽  
Susan M. Berget
Keyword(s):  
Binding Site ◽  
Branch Point ◽  
Splice Site ◽  
Early Recognition ◽  
Splicing Factor ◽  
Splicing Factors ◽  
Sr Protein ◽  
U2 Snrnp ◽  
Auxiliary Factor ◽  
Splicing Factor 1

ABSTRACT One of the earliest steps in pre-mRNA recognition involves binding of the splicing factor U2 snRNP auxiliary factor (U2AF or MUD2 inSaccharomyces cerevisiae) to the 3′ splice site region. U2AF interacts with a number of other proteins, including members of the serine/arginine (SR) family of splicing factors as well as splicing factor 1 (SF1 or branch point bridging protein in S. cerevisiae), thereby participating in bridging either exons or introns. In vertebrates, the binding site for U2AF is the pyrimidine tract located between the branch point and 3′ splice site. Many small introns, especially those in nonvertebrates, lack a classical 3′ pyrimidine tract. Here we show that a 59-nucleotide Drosophila melanogaster intron contains C-rich pyrimidine tracts between the 5′ splice site and branch point that are needed for maximal binding of both U1 snRNPs and U2 snRNPs to the 5′ and 3′ splice site, respectively, suggesting that the tracts are the binding site for an intron bridging factor. The tracts are shown to bind both U2AF and the SR protein SRp54 but not SF1. Addition of a strong 3′ pyrimidine tract downstream of the branch point increases binding of SF1, but in this context, the upstream pyrimidine tracts are inhibitory. We suggest that U2AF- and/or SRp54-mediated intron bridging may be an alternative early recognition mode to SF1-directed bridging for small introns, suggesting gene-specific early spliceosome assembly.

scholarly journals A Conserved DrosophilaTransportin-Serine/Arginine-rich (SR) Protein Permits Nuclear Import ofDrosophila SR Protein Splicing Factors and Their Antagonist Repressor Splicing Factor 1

2002 ◽  
Vol 13 (7) ◽  
pp. 2436-2447 ◽  
Author(s):  
Eric Allemand ◽  
Svetlana Dokudovskaya ◽  
Rémy Bordonné ◽  
Jamal Tazi
Keyword(s):  
Nuclear Import ◽  
Direct Interaction ◽  
Sr Proteins ◽  
Splicing Factor ◽  
Nuclear Speckles ◽  
Sr Protein ◽  
Nuclear Factors ◽  
Localization Signal ◽  
Import Receptors ◽  
Splicing Factor 1

Members of the highly conserved serine/arginine-rich (SR) protein family are nuclear factors involved in splicing of metazoan mRNA precursors. In mammals, two nuclear import receptors, transportin (TRN)-SR1 and TRN-SR2, are responsible for targeting SR proteins to the nucleus. Distinctive features in the nuclear localization signal between Drosophila and mammalian SR proteins prompted us to examine the mechanism by whichDrosophila SR proteins and their antagonist repressor splicing factor 1 (RSF1) are imported into nucleus. Herein, we report the identification and characterization of a Drosophilaimportin β-family protein (dTRN-SR), homologous to TRN-SR2, that specifically interacts with both SR proteins and RSF1. dTRN-SR has a broad localization in the cytoplasm and the nucleus, whereas an N-terminal deletion mutant colocalizes with SR proteins in nuclear speckles. Far Western experiments established that the RS domain of SR proteins and the GRS domain of RSF1 are required for the direct interaction with dTRN-SR, an interaction that can be modulated by phosphorylation. Using the yeast model system in which nuclear import of Drosophila SR proteins and RSF1 is impaired, we demonstrate that complementation with dTRN-SR is sufficient to target these proteins to the nucleus. Together, the results imply that the mechanism by which SR proteins are imported to the nucleus is conserved between Drosophila and humans.

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