Intrinsically disordered regions of Tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA

The RNA binding protein Tristetraprolin (TTP) is a potent activator of mRNA decay, specifically for transcripts bearing AU-rich elements (AREs) in their 3'-untranslated regions. TTP functions as a mediator for mRNA decay by interacting with the decay machinery and recruiting it to the target ARE-mRNA. In this study, we report a weak, but direct interaction between TTP and the human decapping enzyme DCP2, which impacts the stability of ARE-transcripts. The TTP-DCP2 interaction is unusual as it involves intrinsically disordered regions (IDRs) of both binding partners. We show that the IDR of DCP2 has a propensity for oligomerization and liquid-liquid phase separation (LLPS) in vitro. Binding of TTP to DCP2 leads to its partitioning into phase-separated droplets formed by DCP2, suggesting that molecular crowding might facilitate the weak interaction between the two proteins and enable assembly of a decapping-competent mRNA-protein complex on TTP-bound transcripts in cells. Our studies underline the role of weak interactions in the cellular interaction network and their contribution towards cellular functionality.

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Ebola Virus VP30 Is an RNA Binding Protein

Journal of Virology ◽

10.1128/jvi.02523-06 ◽

2007 ◽

Vol 81 (17) ◽

pp. 8967-8976 ◽

Cited By ~ 44

Author(s):

Sinu P. John ◽

Tan Wang ◽

Scott Steffen ◽

Sonia Longhi ◽

Connie S. Schmaljohn ◽

...

Keyword(s):

Binding Affinity ◽

Ebola Virus ◽

Rna Binding ◽

Transcriptional Start Site ◽

Direct Interaction ◽

Binding Activity ◽

Stem Loop ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions

ABSTRACT The Ebola virus (EBOV) genome encodes for several proteins that are necessary and sufficient for replication and transcription of the viral RNAs in vitro; NP, VP30, VP35, and L. VP30 acts in trans with an RNA secondary structure upstream of the first transcriptional start site to modulate transcription. Using a bioinformatics approach, we identified a region within the N terminus of VP30 with sequence features that typify intrinsically disordered regions and a putative RNA binding site. To experimentally assess the ability of VP30 to directly interact with the viral RNA, we purified recombinant EBOV VP30 to >90% homogeneity and assessed RNA binding by UV cross-linking and filter-binding assays. VP30 is a strongly acidophilic protein; RNA binding became stronger as pH was decreased. Zn2+, but not Mg2+, enhanced activity. Enhancement of transcription by VP30 requires a RNA stem-loop located within nucleotides 54 to 80 of the leader region. VP30 showed low binding affinity to the predicted stem-loop alone or to double-stranded RNA but showed a good binding affinity for the stem-loop when placed in the context of upstream and downstream sequences. To map the region responsible for interacting with RNA, we constructed, purified, and assayed a series of N-terminal deletion mutations of VP30 for RNA binding. The key amino acids supporting RNA binding activity map to residues 26 to 40, a region rich in arginine. Thus, we show for the first time the direct interaction of EBOV VP30 with RNA and the importance of the N-terminal region for binding RNA.

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Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation

Nature Communications ◽

10.1038/s41467-021-21035-4 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 3

Author(s):

Vikas A. Tillu ◽

James Rae ◽

Ya Gao ◽

Nicholas Ariotti ◽

Matthias Floetenmeyer ◽

...

Keyword(s):

Electrostatic Interactions ◽

Membrane Lipid ◽

Membrane Curvature ◽

Caveolin 1 ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Solution Generation ◽

Endosomal System ◽

Disordered Regions

AbstractCaveolae are spherically shaped nanodomains of the plasma membrane, generated by cooperative assembly of caveolin and cavin proteins. Cavins are cytosolic peripheral membrane proteins with negatively charged intrinsically disordered regions that flank positively charged α-helical regions. Here, we show that the three disordered domains of Cavin1 are essential for caveola formation and dynamic trafficking of caveolae. Electrostatic interactions between disordered regions and α-helical regions promote liquid-liquid phase separation behaviour of Cavin1 in vitro, assembly of Cavin1 oligomers in solution, generation of membrane curvature, association with caveolin-1, and Cavin1 recruitment to caveolae in cells. Removal of the first disordered region causes irreversible gel formation in vitro and results in aberrant caveola trafficking through the endosomal system. We propose a model for caveola assembly whereby fuzzy electrostatic interactions between Cavin1 and caveolin-1 proteins, combined with membrane lipid interactions, are required to generate membrane curvature and a metastable caveola coat.

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Matrin3: Disorder and ALS Pathogenesis

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.794646 ◽

2022 ◽

Vol 8 ◽

Author(s):

Ahmed Salem ◽

Carter J. Wilson ◽

Benjamin S. Rutledge ◽

Allison Dilliott ◽

Sali Farhan ◽

...

Keyword(s):

Nuclear Export ◽

Binding Proteins ◽

Rna Binding ◽

Nuclear Dna ◽

Neurodegenerative Disorder ◽

Rna Binding Proteins ◽

Binding Protein ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Disordered Regions

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons in the brain and spinal cord. ALS is associated with protein misfolding and inclusion formation involving RNA-binding proteins, including TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS). The 125-kDa Matrin3 is a highly conserved nuclear DNA/RNA-binding protein that is implicated in many cellular processes, including binding and stabilizing mRNA, regulating mRNA nuclear export, modulating alternative splicing, and managing chromosomal distribution. Mutations in MATR3, the gene encoding Matrin3, have been identified as causal in familial ALS (fALS). Matrin3 lacks a prion-like domain that characterizes many other ALS-associated RNA-binding proteins, including TDP-43 and FUS, however, our bioinformatics analyses and preliminary studies document that Matrin3 contains long intrinsically disordered regions that may facilitate promiscuous interactions with many proteins and may contribute to its misfolding. In addition, these disordered regions in Matrin3 undergo numerous post-translational modifications, including phosphorylation, ubiquitination and acetylation that modulate the function and misfolding of the protein. Here we discuss the disordered nature of Matrin3 and review the factors that may promote its misfolding and aggregation, two elements that might explain its role in ALS pathogenesis.

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Interactions between the Intrinsically Disordered Regions of hnRNP-A2 and TDP-43 Accelerate TDP-43′s Conformational Transition

International Journal of Molecular Sciences ◽

10.3390/ijms21165930 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5930

Author(s):

Wan-Chin Chiang ◽

Ming-Hsuan Lee ◽

Tsai-Chen Chen ◽

Jie-rong Huang

Keyword(s):

Intrinsically Disordered Proteins ◽

Rna Binding ◽

Conformational Transition ◽

Rna Binding Proteins ◽

Sequence Similarity ◽

Disordered Proteins ◽

General Mechanism ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Disordered Regions

Most biological functions involve protein–protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more than half eukaryotic proteins contain IDRs. RNA-binding proteins (RBPs) are a large family whose members almost all have IDRs in addition to RNA binding domains. These IDRs, having low sequence similarity, interact, but structural details on these interactions are still lacking. Here, using the IDRs of two RBPs (hnRNA-A2 and TDP-43) as a model, we demonstrate that the rate at which TDP-43′s IDR undergoes the neurodegenerative disease related α-helix-to-β-sheet transition increases in relation to the amount of hnRNP-A2′s IDR that is present. There are more than 1500 RBPs in human cells and most of them have IDRs. RBPs often join the same complexes to regulate genes. In addition to the structured RNA-recognition motifs, our study demonstrates a general mechanism through which RBPs may regulate each other’s functions through their IDRs.

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Presence and utility of intrinsically disordered regions in kinases

Molecular BioSystems ◽

10.1039/c4mb00224e ◽

2014 ◽

Vol 10 (11) ◽

pp. 2876-2888 ◽

Cited By ~ 18

Author(s):

Jaymin J. Kathiriya ◽

Ravi Ramesh Pathak ◽

Eric Clayman ◽

Bin Xue ◽

Vladimir N. Uversky ◽

...

Keyword(s):

Interaction Network ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Human Kinome ◽

Disordered Regions

We reveal presence of intrinsically disordered regions in human kinome and build a kinase–kinase interaction network identifying a novel SRC–SMAD relationship.

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An in vitro reconstituted U1 snRNP allows the study of the disordered regions of the particle and the interactions with proteins and ligands

Nucleic Acids Research ◽

10.1093/nar/gkab135 ◽

2021 ◽

Author(s):

Sébastien Campagne ◽

Tebbe de Vries ◽

Florian Malard ◽

Pavel Afanasyev ◽

Georg Dorn ◽

...

Keyword(s):

Nmr Spectroscopy ◽

Molecular Mechanisms ◽

Low Complexity ◽

Stem Loop ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

U1 Snrnp ◽

Splicing Regulator ◽

Disordered Regions

Abstract U1 small nuclear ribonucleoparticle (U1 snRNP) plays a central role during RNA processing. Previous structures of U1 snRNP revealed how the ribonucleoparticle is organized and recognizes the pre-mRNA substrate at the exon–intron junction. As with many other ribonucleoparticles involved in RNA metabolism, U1 snRNP contains extensions made of low complexity sequences. Here, we developed a protocol to reconstitute U1 snRNP in vitro using mostly full-length components in order to perform liquid-state NMR spectroscopy. The accuracy of the reconstitution was validated by probing the shape and structure of the particle by SANS and cryo-EM. Using an NMR spectroscopy-based approach, we probed, for the first time, the U1 snRNP tails at atomic detail and our results confirm their high degree of flexibility. We also monitored the labile interaction between the splicing factor PTBP1 and U1 snRNP and validated the U1 snRNA stem loop 4 as a binding site for the splicing regulator on the ribonucleoparticle. Altogether, we developed a method to probe the intrinsically disordered regions of U1 snRNP and map the interactions controlling splicing regulation. This approach could be used to get insights into the molecular mechanisms of alternative splicing and screen for potential RNA therapeutics.

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Distinct RNA polymerase transcripts direct the assembly of phase-separated DBC1 nuclear bodies in different cell lines

Molecular Biology of the Cell ◽

10.1091/mbc.e21-02-0081 ◽

2021 ◽

pp. mbc.E21-02-0081

Author(s):

Taro Mannen ◽

Masato Goto ◽

Takuya Yoshizawa ◽

Akio Yamashita ◽

Tetsuro Hirose ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Binding ◽

Nuclear Body ◽

Nuclear Bodies ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Binding Domains ◽

Additional Protein ◽

Protein Components

The mammalian cell nucleus is a highly organized organelle that contains membrane-less structures referred to as nuclear bodies (NBs). Some NBs carry specific RNA types that play architectural roles in their formation. Here, we show two types of RNase-sensitive DBC1-containing NBs: DBC1 nuclear body (DNB) in HCT116 cells and Sam68 nuclear body (SNB) in HeLa cells that exhibit phase-separated features and are constructed using RNA polymerase I or II transcripts in a cell type-specific manner. We identified additional protein components present in DNB by immunoprecipitation-mass spectrometry, some of which (DBC1 and HNRNPL) are required for DNB formation. The rescue experiment using the truncated HNRNPL mutants revealed that two RNA-binding domains and intrinsically disordered regions of HNRNPL play significant roles in DNB formation. All these domains of HNRNPL promote in vitro droplet formation, suggesting the need for multivalent interactions between HNRNPL and RNA as well as proteins in DNB formation.

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Dynamic interaction network involving the conserved intrinsically disordered regions in human eIF5

Biophysical Chemistry ◽

10.1016/j.bpc.2021.106740 ◽

2021 ◽

pp. 106740

Author(s):

Eleanor Elise Paul ◽

Kay Ying Lin ◽

Nathan Gamble ◽

Amy Wei-Lun Tsai ◽

Simon H.K. Swan ◽

...

Keyword(s):

Interaction Network ◽

Dynamic Interaction ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Disordered Regions

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Role of “dual-personality” fragments in HEV adaptation—analysis of Y-domain region

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00238-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Zoya Shafat ◽

Anwar Ahmed ◽

Mohammad K. Parvez ◽

Shama Parveen

Keyword(s):

Molecular Recognition ◽

Functional Annotation ◽

Rna Binding ◽

Intrinsic Disorder ◽

Hepatitis E ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Wide Range ◽

Disordered Regions

Abstract Background Hepatitis E is a liver disease caused by the pathogen hepatitis E virus (HEV). The largest polyprotein open reading frame 1 (ORF1) contains a nonstructural Y-domain region (YDR) whose activity in HEV adaptation remains uncharted. The specific role of disordered regions in several nonstructural proteins has been demonstrated to participate in the multiplication and multiple regulatory functions of the viruses. Thus, intrinsic disorder of YDR including its structural and functional annotation was comprehensively studied by exploiting computational methodologies to delineate its role in viral adaptation. Results Based on our findings, it was evident that YDR contains significantly higher levels of ordered regions with less prevalence of disordered residues. Sequence-based analysis of YDR revealed it as a “dual personality” (DP) protein due to the presence of both structured and unstructured (intrinsically disordered) regions. The evolution of YDR was shaped by pressures that lead towards predominance of both disordered and regularly folded amino acids (Ala, Arg, Gly, Ile, Leu, Phe, Pro, Ser, Tyr, Val). Additionally, the predominance of characteristic DP residues (Thr, Arg, Gly, and Pro) further showed the order as well as disorder characteristic possessed by YDR. The intrinsic disorder propensity analysis of YDR revealed it as a moderately disordered protein. All the YDR sequences consisted of molecular recognition features (MoRFs), i.e., intrinsic disorder-based protein–protein interaction (PPI) sites, in addition to several nucleotide-binding sites. Thus, the presence of molecular recognition (PPI, RNA binding, and DNA binding) signifies the YDR’s interaction with specific partners, host membranes leading to further viral infection. The presence of various disordered-based phosphorylation sites further signifies the role of YDR in various biological processes. Furthermore, functional annotation of YDR revealed it as a multifunctional-associated protein, due to its susceptibility in binding to a wide range of ligands and involvement in various catalytic activities. Conclusions As DP are targets for regulation, thus, YDR contributes to cellular signaling processes through PPIs. As YDR is incompletely understood, therefore, our data on disorder-based function could help in better understanding its associated functions. Collectively, our novel data from this comprehensive investigation is the first attempt to delineate YDR role in the regulation and pathogenesis of HEV.

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Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

International Journal of Molecular Sciences ◽

10.3390/ijms21072289 ◽

2020 ◽

Vol 21 (7) ◽

pp. 2289 ◽

Cited By ~ 2

Author(s):

Tsai-Chen Chen ◽

Jie-rong Huang

Keyword(s):

Nmr Spectroscopy ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Structural Heterogeneity ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Self Association ◽

As Stress ◽

Disordered Regions

RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular condensates, such as stress and RNA granules, but dysregulated assembly can be pathological. Because of their structural heterogeneity, IDRs are best studied by NMR spectroscopy. In this study, we used NMR spectroscopy to investigate the structural propensity and self-association of the IDR of the RBP Musashi-1. We identified two transient α-helical regions (residues ~208–218 and ~270–284 in the IDR, the latter with a polyalanine tract). Strong NMR line broadening in these regions and circular dichroism and micrography data suggest that the two α-helical elements and the hydrophobic residues in between may contribute to the formation of oligomers found in stress granules and implicated in Alzheimer’s disease. Bioinformatics analysis suggests that polyalanine stretches in the IDRs of RBPs may have evolved to promote RBP assembly.

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