The RNA binding protein FgRbp1 regulates specific pre-mRNA splicing via interacting with U2AF23 in Fusarium

Minhui Wang,Zhonghua Ma,Haixia Wang,Yun Chen,Jianzhao Liu,Won Bo Shim,Tianling Ma

doi:10.1038/s41467-021-22917-3

Minhui Wang, Zhonghua Ma + Show 5 more

Open Access

https://doi.org/10.1038/s41467-021-22917-3

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Abstract

Precursor messenger RNA (pre-mRNA) splicing is an essential and tightly regulated process in eukaryotic cells; however, the regulatory mechanisms for the splicing are not well understood. Here, we characterize a RNA binding protein named FgRbp1 in Fusarium graminearum, a fungal pathogen of cereal crops worldwide. Deletion of FgRbp1 leads to reduced splicing efficiency in 47% of the F. graminearum intron-containing gene transcripts that are involved in various cellular processes including vegetative growth, development, and virulence. The human ortholog RBM42 is able to fully rescue the growth defects of ΔFgRbp1. FgRbp1 binds to the motif CAAGR in its target mRNAs, and interacts with the splicing factor FgU2AF23, a highly conserved protein involved in 3’ splice site recognition, leading to enhanced recruitment of FgU2AF23 to the target mRNAs. This study demonstrates that FgRbp1 is a splicing regulator and regulates the pre-mRNA splicing in a sequence-dependent manner in F. graminearum.

Highlights

Precursor messenger RNA splicing is an essential and tightly regulated process in eukaryotic cells; the regulatory mechanisms for the splicing are not well understood
By RNA immunoprecipitation followed by deep sequencing (RIP-seq), we identified 384 FgRbp[1] binding peaks (P < 0.0005, fold change >1.5), of which 272 peaks were corresponding to 219 protein-coding genes (Supplementary Data 4a), and the remaining peaks were mapped to noncoding RNAs
FgRbp[1] was unable to bind to a scrambled RNA sequence 5’-ACGAA-3’, nor a mutated RNA sequence 5’-GUUCU-3’ with six repeats (Fig. 4c), indicating the binding specificity of FgRbp[1] to the CAAGR motif. These results indicate that the CAAGR motif deposited in the target mRNAs is one of cis-elements for FgRbp[1] and that the RNA recognition motif (RRM) domain is essential for the binding of FgRbp[1] to this cis-element

Summary

Introduction

Precursor messenger RNA (pre-mRNA) splicing is an essential and tightly regulated process in eukaryotic cells; the regulatory mechanisms for the splicing are not well understood. Deletion of FgRbp[1] leads to reduced splicing efficiency in 47% of the F. graminearum intron-containing gene transcripts that are involved in various cellular processes including vegetative growth, development, and virulence. Pre-mRNAs are subject to alternative splicing to generate more than one mature mRNAs from a single gene. Both constitutive and alternative pre-mRNA splicing are catalyzed by a large ribonucleoprotein complex called the spliceosome, which is composed of five core small nuclear ribonucleoprotein (snRNP) particles named U1, U2, U4, U5, and U6, along with many associated protein cofactors[2]. Subsequent remodeling transforms Bact into a catalytically competent B* complex (i.e., catalytically activated spliceosome), which catalyzes the first step of splicing, yielding the C complex. Mutations in U2AF lead to serious diseases, including the Myelodysplasia Syndrome (MDS)[6,7,8]

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