Solution structure of the two RNA recognition motifs of hnRNP A1 using segmental isotope labeling: how the relative orientation between RRMs influences the nucleic acid binding topology

ABSTRACTAbnormalities in nucleic acid processing are associated with the development of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Mutations in Matrin 3 (MATR3), a poorly understood DNA- and RNA-binding protein, cause familial ALS/FTD, and MATR3 pathology is a feature of sporadic disease, suggesting that MATR3 dysfunction is integrally linked to ALS pathogenesis. Using a primary neuron model to assess MATR3-mediated toxicity, we noted that neurons were bidirectionally vulnerable to MATR3 levels, with pathogenic MATR3 mutants displaying enhanced toxicity. MATR3’s zinc finger domains partially modulated toxicity, but elimination of its RNA recognition motifs had no effect on neuronal survival, instead facilitating its self-assembly into liquid-like droplets. In contrast to other RNA-binding proteins associated with ALS, cytoplasmic MATR3 redistribution mitigated neurodegeneration, suggesting that nuclear MATR3 mediates toxicity. Our findings offer a foundation for understanding MATR3-related neurodegeneration and how nucleic acid binding functions, localization, and pathogenic mutations drive sporadic and familial disease.

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Crystal Structure of the N-Terminal RNA Recognition Motif of mRNA Decay Regulator AUF1

BioMed Research International ◽

10.1155/2016/3286191 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Young Jun Choi ◽

Je-Hyun Yoon ◽

Jeong Ho Chang

Keyword(s):

Limited Proteolysis ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Hnrnp A1 ◽

Structural Investigations ◽

Rna Recognition Motifs ◽

Intact Proteins ◽

Rich Domain ◽

Recognition Motifs ◽

Apoptosis And Inflammation

AU-rich element binding/degradation factor 1 (AUF1) plays a role in destabilizing mRNAs by forming complexes with AU-rich elements (ARE) in the 3′-untranslated regions. Multiple AUF1-ARE complexes regulate the translation of encoded products related to the cell cycle, apoptosis, and inflammation. AUF1 contains two tandem RNA recognition motifs (RRM) and a Gln- (Q-) rich domain in their C-terminal region. To observe how the two RRMs are involved in recognizing ARE, we obtained the AUF1-p37 protein covering the two RRMs. However, only N-terminal RRM (RRM1) was crystallized and its structure was determined at 1.7 Å resolution. It appears that the RRM1 and RRM2 separated before crystallization. To demonstrate which factors affect the separate RRM1-2, we performed limited proteolysis using trypsin. The results indicated that the intact proteins were cleaved by unknown proteases that were associated with them prior to crystallization. In comparison with each of the monomers, the conformations of theβ2-β3 loops were highly variable. Furthermore, a comparison with the RRM1-2 structures of HuR and hnRNP A1 revealed that a dimer of RRM1 could be one of the possible conformations of RRM1-2. Our data may provide a guidance for further structural investigations of AUF1 tandem RRM repeat and its mode of ARE binding.

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Gbp1p, a Protein with RNA Recognition Motifs, Binds Single-Stranded Telomeric DNA and Changes Its Binding Specificity upon Dimerization

Molecular and Cellular Biology ◽

10.1128/mcb.19.1.923 ◽

1999 ◽

Vol 19 (1) ◽

pp. 923-933 ◽

Cited By ~ 24

Author(s):

Stephen D. Johnston ◽

Jodi E. Lew ◽

Judith Berman

Keyword(s):

Binding Protein ◽

Telomeric Sequence ◽

Rna Recognition ◽

Nucleic Acid Binding ◽

Telomeric Dna ◽

Rna Recognition Motifs ◽

Telomere Binding Protein ◽

Binding Preference ◽

Lower Protein ◽

Recognition Motifs

ABSTRACT Gbp1p is a putative telomere-binding protein fromChlamydomonas reinhardtii that contains two RNA recognition motifs (RRMs) which are commonly found in heterogeneous nuclear ribonucleoproteins (hnRNPs). Previously we demonstrated that Gbp1p binds single-stranded DNA (ssDNA) containing the Chlamydomonas telomeric sequence but not the RNA containing the cognate sequence. Here we show that at lower protein concentrations Gbp1 can also bind an RNA containing the cognate sequence. We found that mutation of the two RRM motifs of Gbp1p to match the highly conserved region of hnRNP RRMs did not alter the affinity of Gbp1p for either RNA or DNA. The ability of Gbp1p to associate with either of these two nucleic acids is governed by the dimerization state of the protein. Monomeric Gbp1p associates with either ssDNA or RNA, showing a small binding preference for RNA. Dimeric Gbp1p has a strong preference for binding ssDNA and shows little affinity for RNA. To the best of our knowledge, this is the first example of a protein that qualitatively shifts its nucleic acid binding preference upon dimerization. The biological implications of a telomere-binding protein that is regulated by dimerization are discussed.

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Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7

eLife ◽

10.7554/elife.25736 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 24

Author(s):

Irene Beusch ◽

Pierre Barraud ◽

Ahmed Moursy ◽

Antoine Cléry ◽

Frédéric Hai-Trieu Allain

Keyword(s):

Motor Neuron ◽

Rna Binding ◽

Binding Capacity ◽

Survival Motor Neuron ◽

Rna Recognition ◽

Hnrnp A1 ◽

Rna Recognition Motifs ◽

Splicing Silencer ◽

Silencer Elements ◽

Recognition Motifs

HnRNP A1 regulates many alternative splicing events by the recognition of splicing silencer elements. Here, we provide the solution structures of its two RNA recognition motifs (RRMs) in complex with short RNA. In addition, we show by NMR that both RRMs of hnRNP A1 can bind simultaneously to a single bipartite motif of the human intronic splicing silencer ISS-N1, which controls survival of motor neuron exon 7 splicing. RRM2 binds to the upstream motif and RRM1 to the downstream motif. Combining the insights from the structure with in cell splicing assays we show that the architecture and organization of the two RRMs is essential to hnRNP A1 function. The disruption of the inter-RRM interaction or the loss of RNA binding capacity of either RRM impairs splicing repression by hnRNP A1. Furthermore, both binding sites within the ISS-N1 are important for splicing repression and their contributions are cumulative rather than synergistic.

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Decision letter: Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7

10.7554/elife.25736.034 ◽

2017 ◽

Keyword(s):

Motor Neuron ◽

Survival Motor Neuron ◽

Rna Recognition ◽

Hnrnp A1 ◽

Rna Recognition Motifs ◽

Recognition Motifs

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Distinct functions of the closely related tandem RNA-recognition motifs of hnRNP A1

RNA ◽

10.1017/s135583829898089x ◽

1998 ◽

Vol 4 (9) ◽

pp. 1111-1123 ◽

Cited By ~ 30

Author(s):

AKILA MAYEDA ◽

STEPHEN H. MUNROE ◽

RUI-MING XU ◽

ADRIAN R. KRAINER

Keyword(s):

Rna Recognition ◽

Hnrnp A1 ◽

Rna Recognition Motifs ◽

Recognition Motifs

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Matrin 3-dependent neurotoxicity is modified by nucleic acid binding and nucleocytoplasmic localization

eLife ◽

10.7554/elife.35977 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 25

Author(s):

Ahmed M Malik ◽

Roberto A Miguez ◽

Xingli Li ◽

Ye-Shih Ho ◽

Eva L Feldman ◽

...

Keyword(s):

Nucleic Acid ◽

Self Assembly ◽

Rna Binding ◽

Rna Binding Proteins ◽

Nucleic Acid Binding ◽

Rna Recognition Motifs ◽

Matrin 3 ◽

Dna And Rna ◽

Acid Processing ◽

Recognition Motifs

Abnormalities in nucleic acid processing are associated with the development of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Mutations in Matrin 3 (MATR3), a poorly understood DNA- and RNA-binding protein, cause familial ALS/FTD, and MATR3 pathology is a feature of sporadic disease, suggesting that MATR3 dysfunction is integrally linked to ALS pathogenesis. Using a rat primary neuron model to assess MATR3-mediated toxicity, we noted that neurons were bidirectionally vulnerable to MATR3 levels, with pathogenic MATR3 mutants displaying enhanced toxicity. MATR3’s zinc finger domains partially modulated toxicity, but elimination of its RNA recognition motifs had no effect on survival, instead facilitating its self-assembly into liquid-like droplets. In contrast to other RNA-binding proteins associated with ALS, cytoplasmic MATR3 redistribution mitigated neurodegeneration, suggesting that nuclear MATR3 mediates toxicity. Our findings offer a foundation for understanding MATR3-related neurodegeneration and how nucleic acid binding functions, localization, and pathogenic mutations drive sporadic and familial disease.

Download Full-text