The cooperative binding of TDP-43 to GU-rich RNA repeats antagonizes TDP-43 aggregation

TDP-43 is a nuclear RNA-binding protein that forms neuronal cytoplasmic inclusions in two major neurodegenerative diseases, ALS and FTLD. While the self-assembly of TDP-43 by its structured N-terminal and intrinsically disordered C-terminal domains has been widely studied, the mechanism by which mRNA preserves TDP-43 solubility in the nucleus has not been addressed. Here, we demonstrate that tandem RNA Recognition Motifs of TDP-43 bind to long GU-repeats in a cooperative manner through intermolecular interactions. Moreover, using mutants whose cooperativity is impaired, we found that the cooperative binding of TDP-43 to mRNA may be critical to maintain the solubility of TDP-43 in the nucleus and the miscibility of TDP-43 in cytoplasmic stress granules. We anticipate that the knowledge of a higher order assembly of TDP-43 on mRNA may clarify its role in intron processing and provide a means of interfering with the cytoplasmic aggregation of TDP-43.

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Stress Granule Assembly Is Mediated by Prion-like Aggregation of TIA-1

Molecular Biology of the Cell ◽

10.1091/mbc.e04-08-0715 ◽

2004 ◽

Vol 15 (12) ◽

pp. 5383-5398 ◽

Cited By ~ 594

Author(s):

Natalie Gilks ◽

Nancy Kedersha ◽

Maranatha Ayodele ◽

Lily Shen ◽

Georg Stoecklin ◽

...

Keyword(s):

Rna Binding ◽

Initiation Factor ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Cytoplasmic Inclusions ◽

Eif2α Phosphorylation ◽

Protease Digestion ◽

Response To Stress ◽

Recognition Motifs ◽

High Level

TIA-1 is an RNA binding protein that promotes the assembly of stress granules (SGs), discrete cytoplasmic inclusions into which stalled translation initiation complexes are dynamically recruited in cells subjected to environmental stress. The RNA recognition motifs of TIA-1 are linked to a glutamine-rich prion-related domain (PRD). Truncation mutants lacking the PRD domain do not induce spontaneous SGs and are not recruited to arsenite-induced SGs, whereas the PRD forms aggregates that are recruited to SGs in low-level–expressing cells but prevent SG assembly in high-level–expressing cells. The PRD of TIA-1 exhibits many characteristics of prions: concentration-dependent aggregation that is inhibited by the molecular chaperone heat shock protein (HSP)70; resistance to protease digestion; sequestration of HSP27, HSP40, and HSP70; and induction of HSP70, a feedback regulator of PRD disaggregation. Substitution of the PRD with the aggregation domain of a yeast prion, SUP35-NM, reconstitutes SG assembly, confirming that a prion domain can mediate the assembly of SGs. Mouse embryomic fibroblasts (MEFs) lacking TIA-1 exhibit impaired ability to form SGs, although they exhibit normal phosphorylation of eukaryotic initiation factor (eIF)2α in response to arsenite. Our results reveal that prion-like aggregation of TIA-1 regulates SG formation downstream of eIF2α phosphorylation in response to stress.

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Faculty Opinions recommendation of The N- and C-terminal RNA recognition motifs of splicing factor Prp24 have distinct functions in U6 RNA binding.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1025155.298750 ◽

2005 ◽

Author(s):

Reinhard Lührmann

Keyword(s):

Rna Binding ◽

Splicing Factor ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Recognition Motifs ◽

U6 Rna

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An RNA-binding protein gene (RBP1) of Saccharomyces cerevisiae encodes a putative glucose-repressible protein containing two RNA recognition motifs

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)82440-1 ◽

1993 ◽

Vol 268 (20) ◽

pp. 15080-15087

Author(s):

F.J. Lee ◽

J. Moss

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Binding ◽

Protein Gene ◽

Binding Protein ◽

Rna Binding Protein ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Binding Protein Gene ◽

Recognition Motifs

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Specificity of RNA Binding by CPEB: Requirement for RNA Recognition Motifs and a Novel Zinc Finger

Molecular and Cellular Biology ◽

10.1128/mcb.18.2.685 ◽

1998 ◽

Vol 18 (2) ◽

pp. 685-693 ◽

Cited By ~ 108

Author(s):

Laura E. Hake ◽

Raul Mendez ◽

Joel D. Richter

Keyword(s):

Zinc Finger ◽

Rna Binding ◽

Rna Recognition ◽

Cytoplasmic Polyadenylation ◽

Functional Motif ◽

Rna Recognition Motifs ◽

Amino Terminal ◽

Terminal Amino ◽

Maternal Mrnas ◽

Recognition Motifs

ABSTRACT CPEB is an RNA binding protein that interacts with the maturation-type cytoplasmic polyadenylation element (CPE) (consensus UUUUUAU) to promote polyadenylation and translational activation of maternal mRNAs in Xenopus laevis. CPEB, which is conserved from mammals to invertebrates, is composed of three regions: an amino-terminal portion with no obvious functional motif, two RNA recognition motifs (RRMs), and a cysteine-histidine region that is reminiscent of a zinc finger. In this study, we investigated the physical properties of CPEB required for RNA binding. CPEB can interact with RNA as a monomer, and phosphorylation, which modifies the protein during oocyte maturation, has little effect on RNA binding. Deletion mutations of CPEB have been overexpressed inEscherichia coli and used in a series of RNA gel shift experiments. Although a full-length and a truncated CPEB that lacks 139 amino-terminal amino acids bind CPE-containing RNA avidly, proteins that have had either RRM deleted bind RNA much less efficiently. CPEB that has had the cysteine-histidine region deleted has no detectable capacity to bind RNA. Single alanine substitutions of specific cysteine or histidine residues within this region also abolish RNA binding, pointing to the importance of this highly conserved domain of the protein. Chelation of metal ions by 1,10-phenanthroline inhibits the ability of CPEB to bind RNA; however, RNA binding is restored if the reaction is supplemented with zinc. CPEB also binds other metals such as cobalt and cadmium, but these destroy RNA binding. These data indicate that the RRMs and a zinc finger region of CPEB are essential for RNA binding.

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Structural properties and RNA-binding activities of two RNA recognition motifs of a mouse neural RNA-binding protein, mouse-Musashi-1

Gene ◽

10.1016/s0378-1119(96)00673-7 ◽

1997 ◽

Vol 186 (1) ◽

pp. 21-27 ◽

Cited By ~ 14

Author(s):

Yasuyuki Kurihara ◽

Takashi Nagata ◽

Takao Imai ◽

Ado Hiwatashi ◽

Masataka Horiuchi ◽

...

Keyword(s):

Structural Properties ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Recognition Motifs

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Domain necessary for Drosophila ELAV nuclear localization: function requires nuclear ELAV

Journal of Cell Science ◽

10.1242/jcs.112.24.4501 ◽

1999 ◽

Vol 112 (24) ◽

pp. 4501-4512 ◽

Cited By ~ 1

Author(s):

Y.M. Yannoni ◽

K. White

Keyword(s):

Nuclear Localization ◽

Rna Binding ◽

Rna Binding Proteins ◽

Nuclear Localization Sequence ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Mutant Proteins ◽

Localization Sequence ◽

Recognition Motifs

The neuron specific Drosophila ELAV protein belongs to the ELAV family of RNA binding proteins which are characterized by three highly conserved RNA recognition motifs, an N-terminal domain, and a hinge region between the second and third RNA recognition motifs. Despite their highly conserved RNA recognition motifs the ELAV family members are a group of proteins with diverse posttranscriptional functions including splicing regulation, mRNA stability and translatability and have a variety of subcellular localizations. The role of the ELAV hinge in localization and function was examined using transgenes encoding ELAV hinge deletions, in vivo. Subcellular localization of the hinge mutant proteins revealed that residues between amino acids 333–374 are necessary for nuclear localization. This delineated sequence has no significant homology to classical nuclear localization sequences, but it is similar to the recently characterized nucleocytoplasmic shuttling sequence, the HNS, from a human ELAV family member, HuR. This defined sequence, however, was insufficient for nuclear localization as tested using hinge-GFP fusion proteins. Functional assays revealed that mutant proteins that fail to localize to the nucleus are unable to provide ELAV vital function, but their function is significantly restored when translocated into the nucleus by a heterologous nuclear localization sequence tag.

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AtRBP1, which encodes an RNA-binding protein containing RNA-recognition motifs, regulates root growth in Arabidopsis thaliana

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2015.04.009 ◽

2015 ◽

Vol 92 ◽

pp. 62-70 ◽

Cited By ~ 6

Author(s):

Takuhiro Shida ◽

Ai Fukuda ◽

Tamao Saito ◽

Hidetaka Ito ◽

Atsushi Kato

Keyword(s):

Arabidopsis Thaliana ◽

Root Growth ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Recognition Motifs

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RNA recognition motifs of disease-linked RNA-binding proteins contribute to amyloid formation

Scientific Reports ◽

10.1038/s41598-019-42367-8 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 8

Author(s):

Sashank Agrawal ◽

Pan-Hsien Kuo ◽

Lee-Ya Chu ◽

Bagher Golzarroshan ◽

Monika Jain ◽

...

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Amyloid Formation ◽

Rna Recognition ◽

Rna Recognition Motifs ◽

Recognition Motifs

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A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52.

Molecular and Cellular Biology ◽

10.1128/mcb.17.5.2649 ◽

1997 ◽

Vol 17 (5) ◽

pp. 2649-2657 ◽

Cited By ~ 49

Author(s):

H Shi ◽

B E Hoffman ◽

J T Lis

Keyword(s):

Rna Binding ◽

Rna Recognition ◽

Loop Structure ◽

Hairpin Loop ◽

Structural Element ◽

Rna Sequences ◽

Sr Protein ◽

Rna Recognition Motifs ◽

Splicing Regulators ◽

Recognition Motifs

B52, also known as SRp55, is a member of the Drosophila melanogaster SR protein family, a group of nuclear proteins that are both essential splicing factors and specific splicing regulators. Like most SR proteins, B52 contains two RNA recognition motifs in the N terminus and a C-terminal domain rich in serine-arginine dipeptide repeats. Since B52 is an essential protein and is expected to play a role in splicing a subset of Drosophila pre-mRNAs, its function is likely to be mediated by specific interactions with RNA. To investigate the RNA-binding specificity of B52, we isolated B52-binding RNAs by selection and amplification from a pool of random RNA sequences by using full-length B52 protein as the target. These RNAs contained a conserved consensus motif that constitutes the core of a secondary structural element predicted by energy minimization. Deletion and substitution mutations defined the B52-binding site on these RNAs as a hairpin loop structure covering about 20 nucleotides, which was confirmed by structure-specific enzymatic probing. Finally, we demonstrated that both RNA recognition motifs of B52 are required for RNA binding, while the RS domain is not involved in this interaction.

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