Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing

Abstract

The human prototypical SR protein SRSF1 is an oncoprotein that contains two RRMs and plays a pivotal role in RNA metabolism. We determined the structure of the RRM1 bound to RNA and found that the domain binds preferentially to a CN motif (N is for any nucleotide). Based on this solution structure, we engineered a protein containing a single glutamate to asparagine mutation (E87N), which gains the ability to bind to uridines and thereby activates SMN exon7 inclusion, a strategy that is used to cure spinal muscular atrophy. Finally, we revealed that the flexible inter-RRM linker of SRSF1 allows RRM1 to bind RNA on both sides of RRM2 binding site. Besides revealing an unexpected bimodal mode of interaction of SRSF1 with RNA, which will be of interest to design new therapeutic strategies, this study brings a new perspective on the mode of action of SRSF1 in cells.

Two distinct binding modes provide the RNA binding protein RbFox with extraordinary sequence specificity

“…The structural analysis suggests that the different binding modes are accomplished in a switch-like manner: the cognate variant induces one structure while non-cognate variants another. It is possible that additional, but presumably smaller structural differences occur within the non-cognate binding mode, similar to the differences that have been observed for other RBPs bound to multiple different RNAs [27][28][29]31 .…”

“…In other RBPs for which structures with different RNA variants have been reported, structural variations are generally concentrated at the RNA binding sites [27][28][29] , even where relatively large changes are introduced in the protein 28,30 . Our data with RbFox reveal instead that structural rearrangements in the RRM are communicated to a distant surface.…”

“…The use of distinct binding modes by a single RRM to achieve high sequence specificity is, to our knowledge, a novel concept for single protein domains. Distinct binding modes have been reported for proteins with multiple domains, reflecting the differential contributions of each RRM for binding to complex multimodal RNA sites; an important and well understood advantage of their modular structure 29,[33][34][35] . However, these scenarios differ fundamentally from the multiple binding modes of a single RNA binding module shown here.…”

Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly

“…However, the targets of these kinases include a wide variety of proteins and not limited to one or two specific SR proteins (53). Our work provides evidence for intermolecular interactions of SR proteins (23) to be important for recruitment of early spliceosomal components, highlighting potential targets for SR protein-specific therapeutic intervention.…”

“…We then used two 14-mer short RNA oligonucleotides (β-globin 5'SS and Ron ESE, an SRSF1-binding ESE) to determine the stability of the β-globin:SRSF1-RBD:U1 snRNP ternary complex. Both the RNAs bind SRSF1-RBD with near equal efficiency due to the presence GGN and CN (N= any nucleotides) motifs (Cléry et al, 2021). We compared the stability of the ternary complexes with that of the β-globin:U1 snRNP binary complex by a challenge with the 14-nt long β-globin 5′SS RNA.…”