Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition

AbstractRNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo.

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Hel-N1: an autoimmune RNA-binding protein with specificity for 3' uridylate-rich untranslated regions of growth factor mRNAs.

Molecular and Cellular Biology ◽

10.1128/mcb.13.6.3494 ◽

1993 ◽

Vol 13 (6) ◽

pp. 3494-3504 ◽

Cited By ~ 238

Author(s):

T D Levine ◽

F Gao ◽

P H King ◽

L G Andrews ◽

J D Keene

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Selection Procedure ◽

Vital Role ◽

Untranslated Regions ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Binding Studies ◽

Recognition Motifs

We have investigated the RNA binding specificity of Hel-N1, a human neuron-specific RNA-binding protein, which contains three RNA recognition motifs. Hel-N1 is a human homolog of Drosophila melanogaster elav, which plays a vital role in the development of neurons. A random RNA selection procedure revealed that Hel-N1 prefers to bind RNAs containing short stretches of uridylates similar to those found in the 3' untranslated regions (3' UTRs) of oncoprotein and cytokine mRNAs such as c-myc, c-fos, and granulocyte macrophage colony-stimulating factor. Direct binding studies demonstrated that Hel-N1 bound and formed multimers with c-myc 3' UTR mRNA and required, as a minimum, a specific 29-nucleotide stretch containing AUUUG, AUUUA, and GUUUUU. Deletion analysis demonstrated that a fragment of Hel-N1 containing 87 amino acids, encompassing the third RNA recognition motif, forms an RNA binding domain for the c-myc 3' UTR. In addition, Hel-N1 was shown to be reactive with autoantibodies from patients with paraneoplastic encephalomyelitis both before and after binding to c-myc mRNA.

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Mechanism of RNA recognition by a Musashi RNA-binding protein

Current Research in Structural Biology ◽

10.1016/j.crstbi.2021.12.002 ◽

2021 ◽

Author(s):

Jinan Wang ◽

Lan Lan ◽

Xiaoqing Wu ◽

Liang Xu ◽

Yinglong Miao

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Rna Recognition

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Glycine-Rich RNA-Binding Protein 7 interacts with and potentiates effector-induced immunity by Gpa2 and Rx1 based on an intact RNA Recognition Motif

10.1101/2021.05.18.444452 ◽

2021 ◽

Author(s):

Octavina CA Sukarta ◽

Qi Zheng ◽

Erik J Slootweg ◽

Mark Mekken ◽

Melanie Mendel ◽

...

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Potato Virus X ◽

Globodera Pallida ◽

Transcriptional Level ◽

Rna Recognition Motif ◽

Rna Recognition ◽

In Planta ◽

Recognition Motif

The activity of intracellular plant Nucleotide-Binding Leucine-Rich Repeat (NB-LRR) immune receptors is fine-tuned by interactions between the receptors and their partners. Identifying NB-LRR interacting proteins is, therefore, crucial to advance our understanding of how these receptors function. A Co-Immunoprecipitation/Mass-Spectrometry screening was performed in Nicotiana benthamiana to identify host proteins associated with the Gpa2 CC-NB-LRR, which confers resistance against the potato cyst nematode Globodera pallida. A combination of biochemical, cellular, and functional assays was used to assess the role of a candidate interactor in defence. A N. benthamiana homolog of the Glycine-Rich RNA-Binding Protein 7 (NbGRP7) protein was prioritized as a novel Gpa2-interacting protein for further investigations. NbGRP7 also associates in planta with the homologous Rx1 receptor, which confers immunity to Potato Virus X. We show that NbGRP7 positively regulates extreme resistance by Rx1 and cell death by Gpa2. Mutating the NbGRP7 RNA recognition motif compromises its role in Rx1-mediated defence. Strikingly, ectopic NbGRP7 expression impacts the steady-state levels of Rx1, which relies on an intact RNA recognition motif. Combined, our findings illustrate that NbGRP7 is a novel pro-immune component in effector-triggered immunity by regulating Gpa2/Rx1 functioning at a post-transcriptional level.

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Hel-N1: an autoimmune RNA-binding protein with specificity for 3' uridylate-rich untranslated regions of growth factor mRNAs

Molecular and Cellular Biology ◽

10.1128/mcb.13.6.3494-3504.1993 ◽

1993 ◽

Vol 13 (6) ◽

pp. 3494-3504

Author(s):

T D Levine ◽

F Gao ◽

P H King ◽

L G Andrews ◽

J D Keene

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Selection Procedure ◽

Vital Role ◽

Untranslated Regions ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Binding Studies ◽

Recognition Motifs

We have investigated the RNA binding specificity of Hel-N1, a human neuron-specific RNA-binding protein, which contains three RNA recognition motifs. Hel-N1 is a human homolog of Drosophila melanogaster elav, which plays a vital role in the development of neurons. A random RNA selection procedure revealed that Hel-N1 prefers to bind RNAs containing short stretches of uridylates similar to those found in the 3' untranslated regions (3' UTRs) of oncoprotein and cytokine mRNAs such as c-myc, c-fos, and granulocyte macrophage colony-stimulating factor. Direct binding studies demonstrated that Hel-N1 bound and formed multimers with c-myc 3' UTR mRNA and required, as a minimum, a specific 29-nucleotide stretch containing AUUUG, AUUUA, and GUUUUU. Deletion analysis demonstrated that a fragment of Hel-N1 containing 87 amino acids, encompassing the third RNA recognition motif, forms an RNA binding domain for the c-myc 3' UTR. In addition, Hel-N1 was shown to be reactive with autoantibodies from patients with paraneoplastic encephalomyelitis both before and after binding to c-myc mRNA.

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RNA-recognition motif in Matrin-3 mediates neurodegeneration through interaction with hnRNPM

Acta Neuropathologica Communications ◽

10.1186/s40478-020-01021-5 ◽

2020 ◽

Vol 8 (1) ◽

Cited By ~ 2

Author(s):

Nandini Ramesh ◽

Sukhleen Kour ◽

Eric N. Anderson ◽

Dhivyaa Rajasundaram ◽

Udai Bhan Pandey

Keyword(s):

Motor Neurons ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Dependent Manner ◽

Recognition Motif ◽

Matrin 3

Abstract Background Amyotrophic lateral sclerosis (ALS) is an adult-onset, fatal neurodegenerative disease characterized by progressive loss of upper and lower motor neurons. While pathogenic mutations in the DNA/RNA-binding protein Matrin-3 (MATR3) are linked to ALS and distal myopathy, the molecular mechanisms underlying MATR3-mediated neuromuscular degeneration remain unclear. Methods We generated Drosophila lines with transgenic insertion of human MATR3 wildtype, disease-associated variants F115C and S85C, and deletion variants in functional domains, ΔRRM1, ΔRRM2, ΔZNF1 and ΔZNF2. We utilized genetic, behavioral and biochemical tools for comprehensive characterization of our models in vivo and in vitro. Additionally, we employed in silico approaches to find transcriptomic targets of MATR3 and hnRNPM from publicly available eCLIP datasets. Results We found that targeted expression of MATR3 in Drosophila muscles or motor neurons shorten lifespan and produces progressive motor defects, muscle degeneration and atrophy. Strikingly, deletion of its RNA-recognition motif (RRM2) mitigates MATR3 toxicity. We identified rump, the Drosophila homolog of human RNA-binding protein hnRNPM, as a modifier of mutant MATR3 toxicity in vivo. Interestingly, hnRNPM physically and functionally interacts with MATR3 in an RNA-dependent manner in mammalian cells. Furthermore, common RNA targets of MATR3 and hnRNPM converge in biological processes important for neuronal health and survival. Conclusions We propose a model of MATR3-mediated neuromuscular degeneration governed by its RNA-binding domains and modulated by interaction with splicing factor hnRNPM.

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