All ETDs from UAB

Advisory Committee Chair

Jun Zhang

Advisory Committee Members

Champion Deivanayagam

Hui-Ting Lee

Todd Jason Green

William Placzek

Document Type

Dissertation

Date of Award

2023

Degree Name by School

Doctor of Philosophy (PhD) College of Arts and Sciences

Abstract

SRSF1 is a prototypical SR protein and its interactions with single stranded RNA (ssRNA) are crucial in mRNA splicing. Its RNA-binding specificity is governed by the RNA-binding Domain (RBD), which contains two RNA Recognition Motifs (RRMs) tethered by a flexible linker. Its C-terminal unstructured Serine-Arginine-rich (RS) domain has been believed to bind RNA non-specifically so far. Although SRSF1 is known to bind a variety of RNA containing its RRM-cognate motifs, its interactions with such RNA have been poorly characterized. Therefore, we explore how SRSF1 achieves a broad RNA-binding specificity ranging from ssRNA to G-quadruplex (GQ) RNA. According to our Fluorescence Polarization (FP) assays and nuclear magnetic resonance (NMR) results, SRSF1’s RRMs possess similar RNA-binding sites in their isolated and tandem forms. Our NMR relaxation data reveals the high flexibility of the RRM1/RRM2 linker which allows the RBD to bind divergent ssRNA regardless of the relative location of the bipartite RNA motifs and the length of the RNA spacer in between them. Our Xplor-NIH simulations depict the RNA spacer forming loop structures that entropically disfavor RNA-binding of the RBD in the presence of long RNA spacers and downstream RRM1-cognate motif. Moreover, we conducted the first extensive analysis of how SRSF1 binds an RNA GQ called actin-related protein 2 (ARPC2). We discover that SRSF1 requires both the RBD and RS tail which act synergistically to bind the GQ tightly. FP assay data illustrate that the RBD binds the GQ via its ssRNA-binding sites, and that the isolated RS tail preferentially binds guanine-rich RNA regardless of the secondary structure. By employing Circular Dichroism (CD) spectroscopy and ensemble Fluorescence Resonance Energy Transfer (FRET), we discovered that the RS tail is the main contributor to the GQ unfolding driven by SRSF1. Further, arginine residues govern the GQ unfolding triggered by the RS tail which is hindered upon phosphorylation of serine residues. Our in vivo studies demonstrate that SRSF1 mitigates the translation inhibition driven by the RNA GQ. Overall, these findings provide an insight into SRSF1’s hidden RNA-binding landscape and uncover its novel functions in mRNA splicing and translation.

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