Cell-Free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers Within Hydrogels

By Masato Kato, T. Han, S. Xie, Kevin Shi, Xinlin Du, Leeju C. Wu, Hamid Mirzaei, E. Goldsmith, J. Longgood, Jimin Pei and 9 more. Cell, 2012

1,908 citations recorded by the source corpus.

Summary: Eukaryotic cells contain assemblies of RNAs and proteins termed RNA granules. Many proteins within these bodies contain KH or RRM RNA binding domains as well as low complexity (LC) sequences of unknown function. Exposure of cell or tissue lysates to a biotinylated isoxazole (b-isox) chemical precipitated hundreds of RNA binding proteins with significant overlap to the constituents of RNA granules. The LC sequences within these proteins are both necessary and sufficient for b-isox-mediated aggregation, and these domains can undergo a concentration-dependent phase transition to a hydrogel-like state in the absence of the chemical. X-ray diffraction and EM studies revealed the hydrogels to be composed of uniformly polymerized amyloid-like fibers. Unlike pathogenic fibers, the LC sequence-based polymers described here are dynamic and accommodate heterotypic polymerization. These observations offer a framework for understanding the function of LC sequences as well as an organizing principle for cellular structures that are not membrane invested.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0d549fb7b136d99bf2bdd868b74782b191da4344

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Citations in the corpus

Stress granules as crucibles of ALS pathogenesis (2013, background): “Importantly, these labile fibrillar assemblies enable a phase transition to hydrogel structures that are capable of retaining RNAs and RNA-binding proteins that are specific to the protein forming the gel (Han et al., 2012; Kato et al., 2012).”
The Central Dogma Decentralized: New Perspectives on RNA Function and Local Translation in Neurons (2013, background): “Adding to the complexity is the recent observation that lowcomplexity regions of RNA-binding proteins are sufficient to create reversible RNA granule-like structures (Kato et al., 2012).”
Phosphorylation of the FUS low‐complexity domain disrupts phase separation, aggregation, and toxicity (2017, positive): “Recent work strongly points to the ability of these domains to form functional interactions with specific sets of proteins bearing similar low-complexity (or prion-like) domains (Kato et al , 2012; Molliex et al , 2015).”
ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function (2015, methodology): “Neurotoxicity Is Driven by the FUS Low-Complexity Domain The N-terminal low-complexity (LC) domain of FUS (residues 2–214) has been reported to induce the assembly of wild-type FUS into hydrogel-like assemblies (Han et al., 2012; Kato et al., 2012).”
Spatiotemporal control of intracellular phase transitions using light-activated optoDroplets (2016, neutral): “…light-activatable phase separation, but it is unclear whether the resulting clusters are liquid-like droplets, or more gel-like assemblies ((Kato et al., 2012), (Patel et al., 2015), (Murakami et al., 2015), (Weber and Brangwynne, 2012), (Zhang et al., 2015), (Lin et al., 2015), (Molliex…”
m6A-dependent regulation of messenger RNA stability (2013, neutral): “6k) 27,28 .”
Protein Phase Separation: A New Phase in Cell Biology (2018, background): “McKnight and coworkers found that concentrated solutions of different IDRs could, over time, spontaneously form hydrogels [39], similar to existing observations made regarding FG-repeat-containing nuclear pore proteins [46].”
Structured states of disordered proteins from genomic sequences (2016, positive): “Most recently, low complexity sequences have also been associated with physiological prion-like polymers that form hydrogels and membrane-less compartments, such as Fus and hnRNPA2 (Hyman et al., 2014; Kato et al., 2012; Kwon et al., 2013; Patel et al., 2015).”
Tau protein liquid–liquid phase separation can initiate tau aggregation (2018, positive): “…to a gel-like state, which is characterized by an increase in viscoelasticity and, hence, a decrease in molecular diffusion rates in the gel state (Kato et al , 2012), we performed FRAP microscopy of freshly prepared p-tau441 droplets that contained 10% of fluorescently labeled protein of the…”
Competing protein-RNA interaction networks control multiphase intracellular organization (2020, positive): “Notwithstanding tremendous attention focused on self-associating IDRs in LLPS (Elbaum-Garfinkle et al., 2015; Kato et al., 2012; Lin et al., 2015; Molliex et al., 2015; Nott et al., 2015; Patel et al., 2015; Wang et al., 2018), studies have shown that both ODs and RBDs have essential roles in conden”
Stress-triggered phase separation is an adaptive, evolutionarily tuned response (2017, background): “Pab1 hydrogels, however, are distinct from previ- 1036 Cell 168, 1028–1040, March 9, 2017 ously reported RNA-binding-protein hydrogels (Kato et al., 2012; Molliex et al., 2015) in that they form at physiological concentrations and do not require a low-complexity region.”