Structural basis for RNA recognition by the N-terminal tandem RRM domains of human RBM45

Abstract

RBM45 is an RNA-binding protein involved in neural development, whose aggregation is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). However, the mechanisms of RNA-binding and aggregation of RBM45 remain unelucidated. Here, we report the crystal structure of the N-terminal tandem RRM domains of human RBM45 in complex with single-stranded DNA (ssDNA). Our structural and biochemical results revealed that both the RRM1 and RRM2 of RBM45 recognized the GAC sequence of RNA/ssDNA. Two aromatic residues and an arginine residue in each RRM were critical for RNA-binding, and the interdomain linker was also involved in RNA-binding. Two RRMs formed a pair of antiparallel RNA-binding sites, indicating that the N-terminal tandem RRM domains of RBM45 bound separate GAC motifs in one RNA strand or GAC motifs in different RNA strands. Our findings will be helpful in the identification of physiologic targets of RBM45 and provide evidence for understanding the physiologic and pathologic functions of RBM45.

RBM45 is an m6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs

“…This suggests that the C-terminal RBDs of RBM45, comprised of the HOA and RRM3 domains, work cooperatively to recognize m 6 A. This is consistent with a recent study showing that the N-terminal region of RBM45 does not preferentially bind m 6 A ( Chen et al, 2021 ).…”

“…A previous study found that the HNRNPA2B1 protein binds m 6 A, presumably through its RRM domains ( Alarcón et al, 2015 ), but subsequent work suggests that the RRMs in this protein do not bind m 6 A directly ( Wu et al, 2017 ). A recent structural study showed that the N-terminal RRM1 and RRM2 domains of RBM45 do not bind m 6 A ( Chen et al, 2021 ), which is consistent with our data. However, potential roles of the HOA domain or RRM3 in m 6 A recognition were not examined.…”

“…Previous studies have identified RBM45 as a predominantly nuclear RBP enriched in the brain ( Tamada et al, 2002 ; Wang et al, 2020 ; Chen et al, 2021 ), but the RNAs that it binds in cells are unknown. To identify RBM45 target RNAs, we performed cross-linking and immunoprecipitation sequencing (CLIP-seq) in both mHippoE-2 and HEK293T cells expressing mouse or human HA-RBM45, respectively ( Figure S2A ).…”

Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript-1

“…Additionally, hrp1 C1-RRM contains an extra F202 (Figure 2). Because of difficulties in the formation of ordered ssRNA complexes with these RRM motifs, sometimes ssDNA was used in study instead, 39 which provides only limited information about RNA-RRM interactions.…”

Structural insights into a regulatory mechanism of FIR RRM1–FUSE interaction

“…The observation of different binding configurations of nucleotide in FIR RRM1 prompted us to investigate whether the observed 5 0 -end nucleotide binding configuration resembled interactions observed in other RRM-ssDNA/RNA complexes. We randomly chose five structures of other nucleic acid-bound RRM1 motifs, including human RBM45 [22] (PDB ID: 7CSZ), DAZL (azoospermia (DAZ)-like) [23] (PDB ID: 2XS5), hnRNP A1 [8] (PDB ID: 5MPG), U2AF2 [24] (PDB ID: 6XLW), and IMP3 [25] (PDB ID: 6GX6), for royalsocietypublishing.org/journal/rsob Open Biol. 13: 230031…”