scholarly journals Emergence of order in condensates composed of multi-valent, multi-domain proteins

2021 ◽  
Author(s):  
Srivastav Ranganathan ◽  
Eugene Shakhnovich
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Orientational Order ◽  
Structural Diversity ◽  
Coarse Grained ◽  
Post Translational Modifications ◽  
First Order Transition ◽  
Dynamics Simulations ◽  
Common Architecture ◽  
Folded Rna

Many RNA-binding proteins (RBPs) that assemble into membraneless organelles, have a common architecture including disordered prion-like domain (PLD) and folded RNA-binding domain (RBD). An enrichment of PLD within the condensed phase gives rise to formation, on longer time scales, amyloid-like fibrils (aging). In this study, we employ coarse-grained Langevin dynamics simulations to explore the physical basis for the structural diversity in condensed phases of multi-domain RBPs. We discovered a highly cooperative first order transition between disordered (liquid-like) structures and an ordered (solid-like) phase whereby chains of PLD organize in fibrils with high nematic orientational order. Cooperativity of this liquid-solid transition makes fibril formation highly malleable to mutations or post-translational modifications. An interplay between homo-domain (PLD-PLD) and hetero-domain (PLD-RBD) interactions results in variety of structures with distinct spatial architectures. Our results provide a mechanistic understanding of how multi-domain RBPs could form assemblies with distinct structural and, potentially, material properties.

scholarly journals Polycomb complexes in X chromosome inactivation

2017 ◽  
Vol 372 (1733) ◽  
pp. 20170021 ◽  
Author(s):  
Neil Brockdorff
Keyword(s):  
X Chromosome ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Histone H2a ◽  
Post Translational Modifications ◽  
Link Type ◽  
Polycomb Proteins ◽  
Inactive X Chromosome

Identifying the critical RNA binding proteins (RBPs) that elicit Xist mediated silencing has been a key goal in X inactivation research. Early studies implicated the Polycomb proteins, a family of factors linked to one of two major multiprotein complexes, PRC1 and PRC2 (Wang 2001 Nat. Genet. 28 , 371–375 ( doi:10.1038/ng574 ); Silva 2003 Dev. Cell 4 , 481–495 ( doi:10.1016/S1534-5807(03)00068-6 ); de Napoles 2004 Dev. Cell 7 , 663–676 ( doi:10.1016/j.devcel.2004.10.005 ); Plath 2003 Science 300 , 131–135 ( doi:10.1126/science.1084274 )). PRC1 and PRC2 complexes catalyse specific histone post-translational modifications (PTMs), ubiquitylation of histone H2A at position lysine 119 (H2AK119u1) and methylation of histone H3 at position lysine 27 (H3K27me3), respectively, and accordingly, these modifications are highly enriched over the length of the inactive X chromosome (Xi). A key study proposed that PRC2 subunits bind directly to Xist RNA A-repeat element, a region located at the 5′ end of the transcript known to be required for Xist mediated silencing (Zhao 2008 Science 322 , 750–756 ( doi:10.1126/science.1163045 )). Subsequent recruitment of PRC1 was assumed to occur via recognition of PRC2 mediated H3K27me3 by the CBX subunit of PRC1, as has been shown to be the case at other Polycomb target loci (Cao 2002 Science 298 , 1039–1043 ( doi:10.1126/science.1076997 )). More recently, several reports have questioned aspects of the prevailing view, both in relation to the mechanism for Polycomb recruitment by Xist RNA and the contribution of the Polycomb pathway to Xist mediated silencing. In this article I provide an overview of our recent progress towards resolving these discrepancies. This article is part of the themed issue ‘X-chromosome inactivation: a tribute to Mary Lyon’.

scholarly journals Sequence dependent co-phase separation of RNA-protein mixtures elucidated using molecular simulations

2020 ◽  
Author(s):  
Roshan Mammen Regy ◽  
Gregory L. Dignon ◽  
Wenwei Zheng ◽  
Young Chan Kim ◽  
Jeetain Mittal
Keyword(s):  
Phase Separation ◽  
Intrinsically Disordered Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Experimental Studies ◽  
Coarse Grained ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Modelling Framework

ABSTRACTRibonucleoprotein (RNP) granules are membraneless organelles (MLOs) which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA play a key role in modulating protein phase separation. There is currently a dearth of modelling techniques which allow one to delve deeper into how RNA plays its role as a modulator/promoter of LLPS in cells using computational methods. Here we present a coarse-grained RNA model developed to fill this gap, which together with our recently developed HPS model for protein LLPS, allows us to capture the factors driving RNA-protein co-phase separation. We explore the capabilities of the modelling framework with the LAF-1 RGG/RNA system which has been well studied in experiments and also with the HPS model previously. Further taking advantage of the fact that the HPS model maintains sequence specificity we explore the role of charge patterning on controlling RNA incorporation into condensates. With increased charge patterning we observe formation of structured or patterned condensates which suggests the possible roles of RNA in not only shifting the phase boundaries but also introducing microscopic organization in MLOs.

scholarly journals Structural Diversity of Sense and Antisense RNA Hexanucleotide Repeats Associated with ALS and FTLD

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 525 ◽  
Author(s):  
Tim Božič ◽  
Matja Zalar ◽  
Boris Rogelj ◽  
Janez Plavec ◽  
Primož Šket
Keyword(s):  
Antisense Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Structural Diversity ◽  
Complex Nature ◽  
Rna Transcripts ◽  
Rich Sense ◽  
C9orf72 Gene ◽  
First Time ◽  
Frontotemporal Lobar Dementia

The hexanucleotide expansion GGGGCC located in C9orf72 gene represents the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). Since the discovery one of the non-exclusive mechanisms of expanded hexanucleotide G4C2 repeats involved in ALS and FTLD is RNA toxicity, which involves accumulation of pathological sense and antisense RNA transcripts. Formed RNA foci sequester RNA-binding proteins, causing their mislocalization and, thus, diminishing their biological function. Therefore, structures adopted by pathological RNA transcripts could have a key role in pathogenesis of ALS and FTLD. Utilizing NMR spectroscopy and complementary methods, we examined structures adopted by both guanine-rich sense and cytosine-rich antisense RNA oligonucleotides with four hexanucleotide repeats. While both oligonucleotides tend to form dimers and hairpins, the equilibrium of these structures differs with antisense oligonucleotide being more sensitive to changes in pH and sense oligonucleotide to temperature. In the presence of K+ ions, guanine-rich sense RNA oligonucleotide also adopts secondary structures called G-quadruplexes. Here, we also observed, for the first time, that antisense RNA oligonucleotide forms i-motifs under specific conditions. Moreover, simultaneous presence of sense and antisense RNA oligonucleotides promotes formation of heterodimer. Studied structural diversity of sense and antisense RNA transcripts not only further depicts the complex nature of neurodegenerative diseases but also reveals potential targets for drug design in treatment of ALS and FTLD.

scholarly journals Structural investigations of the RNA-binding properties of STAR proteins

2014 ◽  
Vol 42 (4) ◽  
pp. 1141-1146 ◽  
Author(s):  
Mikael Feracci ◽  
Jaelle Foot ◽  
Cyril Dominguez
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Arginine Methylation ◽  
Structural Basis ◽  
Rna Recognition ◽  
Structural Investigations ◽  
Post Translational Modifications ◽  
Rna Targets ◽  
Rna Export ◽  
Transcriptional Gene Regulation

STAR (signal transduction and activation of RNA) proteins are a family of RNA-binding proteins that regulate post-transcriptional gene regulation events at various levels, such as pre-mRNA alternative splicing, RNA export, translation and stability. Most of these proteins are regulated by signalling pathways through post-translational modifications, such as phosphorylation and arginine methylation. These proteins share a highly conserved RNA-binding domain, denoted STAR domain. Structural investigations of this STAR domain in complex with RNA have highlighted how a subset of STAR proteins specifically recognizes its RNA targets. The present review focuses on the structural basis of RNA recognition by this family of proteins.

scholarly journals Post-Translational Modifications Modulate Proteinopathies of TDP-43, FUS and hnRNP-A/B in Amyotrophic Lateral Sclerosis

2021 ◽  
Vol 8 ◽  
Author(s):  
Stefania Farina ◽  
Francesca Esposito ◽  
Martina Battistoni ◽  
Giuseppe Biamonti ◽  
Sofia Francia
Keyword(s):  
Phase Transition ◽  
Amyotrophic Lateral Sclerosis ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cajal Bodies ◽  
Post Translational Modifications ◽  
P Granules ◽  
Sequence Complexity ◽  
Lateral Sclerosis ◽  
Liquid Liquid Phase Separation

It has been shown that protein low-sequence complexity domains (LCDs) induce liquid-liquid phase separation (LLPS), which is responsible for the formation of membrane-less organelles including P-granules, stress granules and Cajal bodies. Proteins harbouring LCDs are widely represented among RNA binding proteins often mutated in ALS. Indeed, LCDs predispose proteins to a prion-like behaviour due to their tendency to form amyloid-like structures typical of proteinopathies. Protein post-translational modifications (PTMs) can influence phase transition through two main events: i) destabilizing or augmenting multivalent interactions between phase-separating macromolecules; ii) recruiting or excluding other proteins and/or nucleic acids into/from the condensate. In this manuscript we summarize the existing evidence describing how PTM can modulate LLPS thus favouring or counteracting proteinopathies at the base of neurodegeneration in ALS.

scholarly journals Deciphering how naturally occurring sequence features impact the phase behaviors of disordered prion-like domains

2021 ◽  
Author(s):  
Anne Bremer ◽  
Mina Farag ◽  
Wade M. Borcherds ◽  
Ivan Peran ◽  
Erik W. Martin ◽  
...  
Keyword(s):  
Phase Separation ◽  
Rna Binding ◽  
Driving Forces ◽  
Rna Binding Proteins ◽  
Low Complexity ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Intrinsically Disordered ◽  
Lysine Residues ◽  
Arginine Residues

AbstractPhase separation of intrinsically disordered prion-like low-complexity domains (PLCDs) derived from RNA-binding proteins enable the formation of biomolecular condensates in cells. PLCDs have distinct amino acid compositions, and here we decipher the physicochemical impact of conserved compositional biases on the driving forces for phase separation. We find that tyrosine residues make for stronger drivers of phase separation than phenylalanine. Depending on their sequence contexts, arginine residues enhance or weaken phase separation, whereas lysine residues weaken cohesive interactions within PLCDs. Increased net charge per residue (NCPR) weakens the driving forces for phase separation of PLCDs and this effect can be modeled quantitatively. The effects of NCPR also weaken known correlations between the dimensions of single chains in dilute solution and the driving forces for phase separation. We build on experimental data to develop a coarse-grained model for accurate simulations of phase separation that yield novel insights regarding PLCD phase behavior.

scholarly journals An Emerging Role for Post-translational Modifications in Regulating RNP Condensates in the Germ Line

2021 ◽  
Vol 8 ◽  
Author(s):  
Jennifer A. Schisa ◽  
Mohamed T. Elaswad
Keyword(s):  
Phase Separation ◽  
Binding Proteins ◽  
Rna Binding ◽  
Germ Line ◽  
Rna Binding Proteins ◽  
Model Systems ◽  
Subsequent Formation ◽  
Post Translational Modifications ◽  
Rnp Granules

RNA-binding proteins undergo regulated phase transitions in an array of cell types. The phase separation of RNA-binding proteins, and subsequent formation of RNP condensates or granules, occurs during physiological conditions and can also be induced by stress. Some RNP granules have roles in post-transcriptionally regulating mRNAs, and mutations that prevent the condensation of RNA-binding proteins can reduce an organism’s fitness. The reversible and multivalent interactions among RNP granule components can result in RNP complexes that transition among diffuse and condensed states, the latter of which can be pathological; for example, in neurons solid RNP aggregates contribute to disease states such as amyotrophic lateral sclerosis (ALS), and the dysregulation of RNP granules in human germ cells may be involved in Fragile X-associated primary ovarian insufficiency. Thus, regulating the assembly of mRNAs and RNA-binding proteins into discrete granules appears to provide important functions at both cellular and physiological levels. Here we review our current understanding of the role of post-translational modifications (PTMs) in regulating the condensation of RNA-binding proteins in the germ line. We compare and contrast the in vitro evidence that methylation inhibits phase separation of RNA binding proteins, with the extent to which these results apply to the in vivo germ line environment of several model systems. We also focus on the role of phosphorylation in modulating the dynamics of RNP granules in the germ line. Finally, we consider the gaps that exist in our understanding of the role of PTMs in regulating germ line RNP granules.

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