UHM-ULM Interactions in the RBM39-U2AF65 Splicing-Factor Complex
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research papers UHM–ULM interactions in the RBM39–U2AF65 splicing-factor complex ISSN 2059-7983 Galina A. Stepanyuk,a Pedro Serrano,a,b Eigen Peralta,c Carol L. Farr,a,b,d Herbert L. Axelrod,b,e Michael Geralt,a,b Debanu Das,b,e Hsiu-Ju Chiu,b,e Lukasz Jaroszewski,b,f,g Ashley M. Deacon,b,e Scott A. Lesley,a,b,d Marc-Andre´ Elsliger,a,b Adam Godzik,b,f,g Ian A. Wilson,a,b,h Kurt Wu¨thrich,a,b,h Daniel R. Salomonc and a Received 9 January 2016 James R. Williamson * Accepted 19 January 2016 aDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, bJoint Center for Structural Genomics, http://www.jcsg.org, cDepartment of Molecular and Experimental Medicine, Edited by T. O. Yeates, University of The Scripps Research Institute, La Jolla, CA 92037, USA, dProtein Sciences Department, Genomics Institute of the California, USA Novartis Research Foundation, San Diego, CA 92121, USA, eStanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA, fProgram on Bioinformatics and Systems Biology, Sanford Burnham Keywords: RNA-binding proteins; alternative Prebys Medical Discovery Institute, La Jolla, CA 92037, USA, gCenter for Research in Biological Systems, University of splicing; U2AF homology motif; CAPER ; California, San Diego, La Jolla, CA 92093-0446, USA, and hThe Skaggs Institute for Chemical Biology, The Scripps HCC1; RBM39; RNA-binding protein 39; Research Institute, La Jolla, CA 92037, USA. *Correspondence e-mail: [email protected] U2AF5; UHM; ULM. RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co- PDB references: RBM39-UHM, crystal structure, 3s6e; NMR structure, 2lq5; crystal activator of estrogen receptors and Jun/AP-1, and its function has been structure of complex with U2AF65-ULM, 5cxt associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), Supporting information: this article has which mediate protein–protein interactions through a short tryptophan- supporting information at journals.iucr.org/d 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. 1. Introduction Alternative splicing of pre-mRNA is a prevalent mechanism for increasing the genomic coding capacity by the coordinated removal of introns and differential exon joining to produce different coding mRNAs from the same primary transcript (Black, 2003). Functional alterations of proteins involved in regulating alternative splicing are implicated in immune diseases and cancer development, demonstrating the func- tional importance of controlled alternative splicing (Lynch, 2004; Moore et al., 2010; Venables, 2006; Srebrow & Korn- blihtt, 2006). In higher eukaryotes, spliceosome assembly begins with recognition of the 50 splice site by U1snRNP and binding of U2 auxiliary factor (U2AF) to the polypyrimidine tract (Py-tract) and the 30 splice site. U2AF is required for the stable association of the U2 snRNP with the pre-mRNA # 2016 International Union of Crystallography branch-point sequence during the first ATP-dependent step of Acta Cryst. (2016). D72, 497–511 http://dx.doi.org/10.1107/S2059798316001248 497 research papers the splicing process (Complex A). The U2AF protein complex et al., 1999; Corsini et al., 2007, 2009; Manceau et al., 2006; consists of large (U2AF65) and small (U2AF35) subunits that Fig. 1b). Moreover, the UHM–ULM protein–protein inter- form a stable heterodimer that binds to the AG dinucleotide at action is involved in a number of higher order complexes, the 30 splice site (Merendino et al., 1999; Zorio & Blumenthal, including the constitutive 30 splice site U2AF35–U2A65 1999; Wu et al., 1999). U2AF65 is essential for splicing, and complex (Kielkopf et al., 2001), U2AF65 in complex with binding of U2AF65 alone is sufficient for bending the Py-tract, splicing factor SF1 binding to the Py-tract (Selenko et al., juxtaposing the branch region and the 30 splice site (Kent et al., 2003) and alternative splicing factors SPF45 and RBM39 2003). U2AF35 is dispensable for in vitro pre-mRNAs associated with the ULM of SF3b155 (Corsini et al., 2007; containing strong Py-tracts (Burge et al., 1999), but is required Loerch et al., 2014). In addition, it has been proposed that the for in vitro splicing of a pre-mRNA substrate with a Py-tract U2AF65 subunit might form structurally similar heterodimers that deviates from the consensus (Guth et al., 1999). with a diverse set of UHM proteins with distinct functional U2AF65 contains an N-terminal arginine/serine-rich (RS) activities in a tissue-specific manner. domain followed by two RNA-recognition motifs (RRM) and The UHMs are noncanonical RRMs that have noncon- a third C-terminal noncanonical RRM (Fig. 1a; Mollet et al., sensus residues in the RNP1 and RNP2 RNA-binding motifs 2006; Kielkopf et al., 2004) that mediates protein–protein and instead contain two ULM-recognition motifs: one motif domain interactions and is commonly termed the U2AF consists of an arginine–any amino acid (X)–phenylalanine homology motif (UHM). Besides the association between (R-X-F) element (Kielkopf et al., 2001, 2004; Selenko et al., protein and RNA, specific protein–protein interactions are 2003; Fig. 1c) and the other an extended negatively charged often needed to recruit and coordinate the assembly of spli- -helix A. The ULM consensus sequence therefore includes cing factors at the sites of mRNA processing. UHMs are found two different binding motifs. In the structure of U2AF65- in several other nuclear proteins, such as PUF60, SPF45, UHM complexed with SF1-ULM, the positively charged U2AF35 and RBM39 (Fig. 1a), which are linked to constitu- N-terminal segment of the ULM winds along the negatively tive and alternative splicing through UHM-mediated protein– charged -helix A of U2AF65, while the consensus tryptophan protein interactions to short tryptophan-containing linear docks into a cavity formed by -helices A and B. In UHM ligand motifs (ULMs). A consensus ULM sequence the U2AF35-UHM–U2AF65-ULM structure the primary [(K/R)4–6X0–1W(D/E/N/Q)1–2] is found in several nuclear interface occurs between the R-X-F element of the UHM and proteins, including U2AF65, SF1 and SF3b155 (Page-McCaw the C-terminal region of the ULM sequence, and is driven by Figure 1 UHM and ULM domains in splicing factors. (a) Domain composition and arrangement of nuclear proteins containing UHM domains. (b) Sequence alignment of nuclear splicing factors that contain ULM motifs [(K/R)4–6X0–1W(D/E/N/Q)1–2]. Conserved tryptophans are highlighted in yellow, conservative negatively charged and polar amino acids following the tryptophan are highlighted in red and the N-terminal stretch of positively charged amino acids is highlighted in blue. Potential in vivo phosphorylated sites are indicated in green. (c) Sequence alignment of the UHM domains shown in (a). The conserved amino acids known to be involved in the ‘knob-into-hole’ interaction are highlighted in red, and their homologous substitutions are in light red. RBM39 residues that directly bind to U2AF65-ULM are shown in white on a red background. 498 Stepanyuk et al. UHM–ULM interactions in RBM39–U2AF65 Acta Cryst. (2016). D72, 497–511 research papers reciprocal tryptophan interactions, in which a Trp residue on greatest effect on substrates that have weak or variable 30 one protein occupies a Trp pocket on the other protein. splice sites (Konarska & Query, 2005). The splicing regulator RNA-binding protein 39 (RBM39), also known as polypyrimidine tract-binding protein (PTB1) represses the CAPER or HCC1, exhibits the same domain architecture as excision of an alternatively spliced exon by preventing the 50 U2AF65 and contains both the R-X-F element and a nega- splice-site-dependent assembly of U2AF on the 30 splice site tively charged -helix A characteristic of the UHM. RBM39 (Sharma et al., 2005). However, RBM39 promotes the inclu- is both a splicing factor and a transcriptional co-activator of sion of a pseudoexon in the iron–sulfur cluster-assembly gene AP-1/Jun and estrogen receptors (Imai et al., 1993; Dowhan ISCU by interfering with PTB1 binding and repression et al., 2005). RBM39 function has been linked to a number (Nordin et al., 2012). Thus, it is also possible that variant of cancers and malignant progression (Sillars-Hardebol, complexes with U2AF provide a flexible regulation Carvalho, Tijssen et al., 2012), and the RBM39-interacting mechanism involving tissue-specific splicing choices deter- proteins in particular environments determine the anti- or mined by regulators such as PTB1 or RBM39. pro-oncogenic activity of RBM39. RBM39 expression is up- In this regard, RBM39 mRNA expression displays a distinct regulated in small-cell lung and breast cancers, colorectal tissue-specific pattern in healthy tissues and is abundant in adenomas and carcinomas (Bangur et al., 2002; Mercier et al., immune system-associated cells, as well as lymph-node cells, 2009; Chai et al., 2014; Sillars-Hardebol, Carvalho, Belie¨n et uterus, thyroid and pineal gland cells.