Intrinsically disordered regions: a platform for regulated assembly of biomolecular condensates

Putnam, Andrea; Seydoux, Géraldine

doi:10.1016/b978-0-12-823967-4.00016-6

Cited by 3 publications

(5 citation statements)

References 169 publications

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“…IDRs are commonly invoked as playing the defining role in mediating condensate formation, a theory supported by defining work on several disordered RNA-binding proteins (e.g., FUS 60 and hnRNPA1 3 ) in human diseases that are now well-established model systems. On the other hand, folded domains provide the key scaffolding functions in other condensates, such as in multi-synthetase complexes 40,41,61 , C. elegans germ-granules 15,62 , and pyrenoids from algae 63 . An emerging view holds that condensation can be mediated through electrostatic complementarity or multimerizing domains without any requirement for IDRs 64 .…”

Section: Discussionmentioning

confidence: 99%

“…Intrinsically disordered regions (IDRs) play well-understood roles such as presenting short linear motifs that are recognized by other proteins, 13 sensing and responding to the environment, or folding upon binding to a partner; yet these accepted functions only account for a small fraction of the disorder in the Saccharomyces cerevisiae (hereafter referred as yeast) proteome, for which 64% of proteins are predicted to contain disordered regions of thirty residues or more and the median protein is 19% disordered. Increasingly, IDRs have been assigned an important role in promoting the formation of biomolecular condensates 14 ; however, this relationship is also unclear, as some well-known phase-separating proteins contain little disorder whilst many disordered proteins are known to be highly soluble 15 . Hence, a general function for disordered regions has not been clearly established, though the identification of one could prove important for explaining their pervasive presence in eukaryotic proteomes.…”

Section: Mainmentioning

confidence: 99%

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Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates

To,

Bhagwat,

Tarbox

et al. 2023

Preprint

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Many eukaryotic proteins contain intrinsically disordered regions (IDRs) that intersperse globular folded domains, in contrast with bacterial proteins which are typically highly globular. Recent years have seen great progress in identifying biological functions associated with these elusive protein sequence: in specific cases, they mediate liquid-liquid phase separation, perform molecular recognition, or act as sensors to changes in the environment. Nevertheless, only a small number of IDRs have annotated functions despite their presence in 64% of yeast proteins, stimulating some to question what 'general purpose' they may serve. Here, by interrogating the refoldability of two fungal proteomes (Saccharomyces cerevisiae and Neurosporra crassa), we show that IDRs render their host proteins more refoldable from the denatured state, allowing them to cohere more closely to Anfinsen's thermodynamic hypothesis. The data provide an exceptionally clear picture of which biophysical and topological characteristics enable refoldability. Moreover, we find that almost all yeast proteins that partition into stress granules during heat shock are refoldable, a finding that holds for other condensates such as P-bodies and the nucleolus. Finally, we find that the Hsp104 unfoldase is the principal actor in mediating disassembly of heat stress granules and that the efficiency with which condensed proteins are returned to the soluble phase is also well explained by refoldability. Hence, these studies establish spontaneous refoldability as an adaptive trait that endows proteins with the capacity to reform their native soluble structures following their extraction from condensates. Altogether, our results provide an intuitive model for the function of IDRs in many multidomain proteins and clarifies their relationship to the phenomenon of biomolecular condensation.

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Section: Discussionmentioning

confidence: 99%

Section: Mainmentioning

confidence: 99%

Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates

To,

Bhagwat,

Tarbox

et al. 2023

Preprint

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“…Whether IDR–IDR interactions drive the phase separation of native RNA granules in cells, however, is less clear. IDRs are rarely sufficient to drive phase separation in cells (unless overexpressed) but can augment the condensation of oligomerizing globular domains by linking condensation to environmental inputs such as RNA availability, pH, oxidation state, and temperature ( Riback et al 2017 ; Franzmann et al 2018 ; Kato et al 2019 ; Guillén-Boixet et al 2020 ; Iserman et al 2020 ; Sanders et al 2020 ; Yang et al 2020 ; Putnam and Seydoux 2023 ). For example, the IDR of the P granule protein MEG-3 is not essential for condensation but binds RNA in a sequence-nonspecific manner and is required to recruit low-translation mRNAs to P granules ( Lee et al 2020 ; Schmidt et al 2021 )…”

Section: Properties Of Condensatesmentioning

confidence: 99%

“…Genetic studies have shown that sequencespecific protein-binding domains contribute to RNA granule assembly in cells. For example, oligomerization domains in Edc3, G3BP, and PGL-1 are required to assemble P-bodies, stress granules, and P granules, respectively, likely because these domains mediate the formation of subsoluble RNP complexes (Ling et al 2008;Hanazawa et al 2011;Kedersha et al 2016;Guillén-Boixet et al 2020;Sanders et al 2020;Yang et al 2020) Franzmann et al 2018;Kato et al 2019;Guillén-Boixet et al 2020;Iserman et al 2020;Sanders et al 2020;Yang et al 2020;Putnam and Seydoux 2023). For example, the IDR of the P granule protein MEG-3 is not essential for condensation but binds RNA in a sequencenonspecific manner and is required to recruit low-translation mRNAs to P granules (Lee et al 2020;Schmidt et al 2021) RNA can promote or disrupt protein condensates.…”

Section: Phase Separation Is a Spontaneous Concentrationdependent Pro...mentioning

confidence: 99%

RNA granules: functional compartments or incidental condensates?

2023

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RNA granules are mesoscale assemblies that form in the absence of limiting membranes. RNA granules contain factors for RNA biogenesis and turnover and are often assumed to represent specialized compartments for RNA biochemistry. Recent evidence suggests that RNA granules assemble by phase separation of subsoluble ribonucleoprotein (RNP) complexes that partially demix from the cytoplasm or nucleoplasm. We explore the possibility that some RNA granules are nonessential condensation by-products that arise when RNP complexes exceed their solubility limit as a consequence of cellular activity, stress, or aging. We describe the use of evolutionary and mutational analyses and single-molecule techniques to distinguish functional RNA granules from “incidental condensates.”

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“…Findings from in-vitro and cell culture studies, as well as from C. elegans and Drosophila embryos established principles of RNP condensation by IDR interactions [18][19][20][21][22][28][29][30][31][32][33][34] . The capability and capacity of IDRs to interact can be modified by shifts in temperature and pH [18][19][20][21][22][23]35 , by RNA binding 25,34,36 , and by post-translational modifications [37][38][39] . These suggest potential cellular regulation.…”

Section: Introductionmentioning

confidence: 99%

Multi-Step Cellular Control of Molecular Condensation by Microtubules in Early Oogenesis

Deis

Elkouby

2022

Preprint

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Molecular condensates provide new paradigms in biology, but their cellular regulation is unclear. Condensates undergo phase separation, decreasing their solubility and compartmentalizing their content. In vertebrate oocytes, RNA-protein (RNP) granules form condensates by phase separation, but the underlying mechanisms are unknown. RNP granules localize to the Balbiani body (Bb), a conserved membraneless organelle, that establishes oocyte polarity. Bb loss results in symmetrical eggs and embryonic lethality. Bb granules aggregate around the centrosome in a nuclear cleft, prior to assembling the mature structure. The Bucky ball (Buc) protein nucleates Bb granules and is essential for Bb formation. Howe ver, the dynamics, mechanisms, and regulation of Bb granule nucleation are unclear. While the mature Bb structure was shown to be a rigid, amyloid-like, phase-separated structure in Xenopus, the early phase separation dynamics prior to maturation are completely unknown. Here, by live, genetic, super-resolution microscopy, and FRAP analyses in zebrafish ovaries, we establish that Buc phase-separates Bb granules and that microtubules play multiple stepwise roles in controlling Buc phase separation and Bb formation specifically at the early nuclear cleft stages. We show that Buc first phase-separates into dynamic liquid droplet-like granules that fuse to form the main Bb aggregate. We demonstrate that early aggregated Buc exhibited dynamic turnover and that this turnover requires dynein-mediated trafficking of Buc on a transient lattice of microtubules that we identified. At later stages, microtubules encapsulated the Bb, indicating a structural role. Thus, microtubules organize multiple steps in Bb condensation. Moreover, in the mature Bb, Buc was stable and required for Bb amyloid formation, finalizing Bb condensation. We found for the first time by live imaging, ThT-positive presumptive amyloid b-sheets in the mature zebrafish Bb, that we re absent in buc-/- oocytes. Thus, providing the first genetic evidence for Buc dependent formation of presumptive amyloid fibrils in the Bb. Molecular condensation is often viewe d as a self-assembly process. Here, we propose a novel paradigm for the cellular control over condensation mechanisms by microtubules in development. The regulation of Bb assembly and disassembly in the context of phase separation allows studying these mechanisms in physiological conditions, advancing their understanding in neurodegenerative disease and female reproduction.

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Intrinsically disordered regions: a platform for regulated assembly of biomolecular condensates

Cited by 3 publications

References 169 publications

Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates

Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates

RNA granules: functional compartments or incidental condensates?

Multi-Step Cellular Control of Molecular Condensation by Microtubules in Early Oogenesis

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