A structural perspective of RNA recognition by intrinsically disordered proteins

Basu, Sourav; Bahadur, Ranjit Prasad

doi:10.1007/s00018-016-2283-1

Cited by 65 publications

(65 citation statements)

References 98 publications

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“…IDRs are over-represented among RNA-binding domains (Varadi et al, 2015; Castello et al, 2016). Electrostatic interactions between positively-charged amino acids and the negatively-charged RNA backbone are often invoked as a possible mechanism for RNA binding by IDRs (Guo and Shorter, 2015; Basu and Bahadur, 2016). MEG-3 is rich in basic residues, but shows a strong preference for poly-U over poly-C and poly-G, suggesting that non-charged interactions are also involved.…”

Section: Discussionmentioning

confidence: 99%

Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3

Smith

Calidas

Schmidt

et al. 2016

eLife

212

252

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RNA granules are non-membrane bound cellular compartments that contain RNA and RNA binding proteins. The molecular mechanisms that regulate the spatial distribution of RNA granules in cells are poorly understood. During polarization of the C. elegans zygote, germline RNA granules, called P granules, assemble preferentially in the posterior cytoplasm. We present evidence that P granule asymmetry depends on RNA-induced phase separation of the granule scaffold MEG-3. MEG-3 is an intrinsically disordered protein that binds and phase separates with RNA in vitro. In vivo, MEG-3 forms a posterior-rich concentration gradient that is anti-correlated with a gradient in the RNA-binding protein MEX-5. MEX-5 is necessary and sufficient to suppress MEG-3 granule formation in vivo, and suppresses RNA-induced MEG-3 phase separation in vitro. Our findings suggest that MEX-5 interferes with MEG-3’s access to RNA, thus locally suppressing MEG-3 phase separation to drive P granule asymmetry. Regulated access to RNA, combined with RNA-induced phase separation of key scaffolding proteins, may be a general mechanism for controlling the formation of RNA granules in space and time.DOI: http://dx.doi.org/10.7554/eLife.21337.001

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Section: Discussionmentioning

confidence: 99%

Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3

Smith

Calidas

Schmidt

et al. 2016

eLife

212

252

View full text Add to dashboard Cite

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“…The alternating sequence of net charge has also been shown to be an important determinant in phase‐separated droplet formation involving DDX4 RNA‐helicase . A distribution of hydrophobic residues along an IDP sequence is another important property which affects liquid phase separation, due largely to the contribution of aromatic residues to multivalent interactions with RNA and other proteins (e.g., π–π and cation–π), as shown for a number of RNA‐binding IDPs including FUS . Interestingly, while the FUS RRM is prominently hydrophobic, its RBRs display a different level of hydrophobicity depending on the neighboring sequence context (Fig.…”

Section: Lack Of 3d Organization Motivates Sequence‐based Analysismentioning

confidence: 99%

RNA‐protein interactions in an unstructured context

2018

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Despite their importance, our understanding of noncovalent RNA–protein interactions is incomplete. This especially concerns the binding between RNA and unstructured protein regions, a widespread class of such interactions. Here, we review the recent experimental and computational work on RNA–protein interactions in an unstructured context with a particular focus on how such interactions may be shaped by the intrinsic interaction affinities between individual nucleobases and protein side chains. Specifically, we articulate the claim that the universal genetic code reflects the binding specificity between nucleobases and protein side chains and that, in turn, the code may be seen as the Rosetta stone for understanding RNA–protein interactions in general.

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“…S1 A), it is also predicted to be organized mainly as a-helices by secondary structure prediction programs and to adopt a flexible coiled-coil-like structure (12). The IDD is hypothesized to adopt various conformations to enable the protein to interact with several cellular partners (RNA or proteins), a typical behavior for intrinsically disordered proteins (18)(19)(20)(21)(22).…”

Section: Introductionmentioning

confidence: 99%

Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding

Hardouin

Velours

Bou‐Nader

et al. 2018

Biophysical Journal

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Although RNase Y acts as the key enzyme initiating messenger RNA decay in Bacillus subtilis and likely in many other Gram-positive bacteria, its three-dimensional structure remains unknown. An antibody belonging to the rare immunoglobulin G (IgG) 2b lx isotype was raised against a 12-residue conserved peptide from the N-terminal noncatalytic domain of B. subtilis RNase Y (BsRNaseY) that is predicted to be intrinsically disordered. Here, we show that this domain can be produced as a stand-alone protein called Nter-BsRNaseY that undergoes conformational changes between monomeric and dimeric forms. Circular dichroism and size exclusion chromatography coupled with multiangle light scattering or with small angle x-ray scattering indicate that the Nter-BsRNaseY dimer displays an elongated form and a high content of a-helices, in agreement with the existence of a central coiled-coil structure appended with flexible ends, and that the monomeric state of Nter-BsRNaseY is favored upon binding the fragment antigen binding (Fab) of the antibody. The dissociation constants of the IgG/BsRNaseY, IgG/Nter-BsRNaseY, and IgG/peptide complexes indicate that the affinity of the IgG for Nter-BsRNaseY is in the nM range and suggest that the peptide is less accessible in BsRNaseY than in Nter-BsRNaseY. The crystal structure of the Fab in complex with the peptide antigen shows that the peptide adopts an elongated U-shaped conformation in which the unique hydrophobic residue of the peptide, Leu6, is completely buried. The peptide/Fab complex may mimic the interaction of a microdomain of the N-terminal domain of BsRNaseY with one of its cellular partners within the degradosome complex. Altogether, our results suggest that BsRNaseY may become accessible for protein interaction upon dissociation of its N-terminal domain into the monomeric form. FIGURE 1 Characterization of a monoclonal antibody induced against a 12-residue peptide of Nter-BsRNaseY. (A) Sequence alignment of the N-terminal domains of RNases Y from B. subtilis, Staphylococcus aureus, Streptococcus pyogenes, Listeria monocytogenes, Clostridium perfringens, Lactoccus lactis, Borrelia burgdorferi, and Leadbetterella byssophila was performed with Clustal Omega (67) and rendered with ESPript (68). The predicted N-terminal TM helix (residues 6-24) and the inducing peptide (residues 79-90) are indicated. (B) Recognition of BsRNaseY by IgG RY79-90 as detected by immunoblotting (legend continued on next page) Fab Binding Dissociates RNase Y IDD Biophysical Journal 115, 2102-2113, December 4, 2018 2103Protein stoichiometry analysis of the Nter-BsRNaseY/Fab RY79-90 complex (at a 1:2 ratio) was performed by SEC-MALS using the ''UV extinction from RI peak'' method (28) and the protein conjugate method (29) (see Supporting Materials and Methods). In the first method, the UV 280 extinction coefficients of the peaks are extracted from the SEC-MALS data and compared to the predicted extinction coefficients Fab Binding Dissociates RNase Y IDD (C) Structural models of Nter-BsRNaseY. Top: Two at...

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A structural perspective of RNA recognition by intrinsically disordered proteins

Cited by 65 publications

References 98 publications

Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3

Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3

RNA‐protein interactions in an unstructured context

Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding

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