Macromolecular Condensation Organizes Nucleolar Sub-Phases to Set Up a pH Gradient

King, Matthew R.; Ruff, Kiersten M.; Lin, Andrew Z.; Pant, Aniruddha; Farag, Mina; Lalmansingh, Jared M.; Wu, Tingting; Ouyang, Wei; Fossat, Martin J.; Lew, Matthew D.; Lundberg, Emma; Vahey, Michael D.; Pappu, Rohit V.

doi:10.2139/ssrn.4520791

Cited by 6 publications

(24 citation statements)

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“…Loss of either component results in mis-condensation of nucleolar factors away from rDNA in vivo [ 81 , 82 ]. Further, in vitro reconstitutions of FC-like condensates require only rDNA, UBF, and at least one FC-localized protein containing IDRs that feature blocks of lysine residues (K-blocks) that are interspersed by regions rich in glutamic acid residues [ 46 ]. Therefore, rDNA, UBF, and proteins containing IDRs featuring K-blocks and E-rich-regions appear necessary and sufficient to drive FC formation.…”

Section: Nucleolar Sub-phases Are Defined By Distinct Macromolecular ...mentioning

confidence: 99%

“…Increasing the copy numbers of UBF in Xenopus oocytes via mRNA injection leads to enlarged oocytes, which corroborates its established role as an FC scaffold. Increasing the copy numbers of TCOF1 can result in a similar phenotype, but only if mRNA loads are at least 5-times higher than that of UBF [ 46 ]. These findings suggest that TCOF1 expression, which is spatiotemporally regulated to facilitate ribosome biogenesis in fast growing cells such as the developing neural crest, could be used to tune FC size and possibly rRNA output.…”

Section: Nucleolar Sub-phases Are Defined By Distinct Macromolecular ...mentioning

confidence: 99%

“…These findings suggest that TCOF1 expression, which is spatiotemporally regulated to facilitate ribosome biogenesis in fast growing cells such as the developing neural crest, could be used to tune FC size and possibly rRNA output. Among the FC proteins that feature K-blocks and E-rich-regions are RNA polymerase I and Topoisomerase I, as well as the FC and DFC enriched proteins nuclear casein kinase and cyclin-dependent kinase substrate (NUCKS) and ly-1 antibody reactive (LYAR) [ 46 , 84 ] ( Figure 1f ).…”

Section: Nucleolar Sub-phases Are Defined By Distinct Macromolecular ...mentioning

confidence: 99%

“…Further, at least three categories of non-rRNA factors have been shown to play a role in DFC condensation. These factors are Arg (R) and Gly (G) rich (RG-rich) IDRs present in C/D box and H/ACA snoRNPs [ 27 , 92 ], the rRNA chaperones nucleolin (NCL) and DDX21 [ 46 , 73 ], and the lncRNAs SLERT and LoNA [ 57 , 93 , 94 ] ( Figure 1g ). All these factors are involved in key functions of the DFC, which include the proper folding, splicing, and chemical modification of rRNA.…”

Section: Nucleolar Sub-phases Are Defined By Distinct Macromolecular ...mentioning

confidence: 99%

“…The underlying compositional organization of nucleolar sub-phases is coming into focus, thanks largely to high-throughput microscopy [ 44 , 45 ]. A recent study leveraged these datasets to show that the distinct compositional biases of intrinsically disordered regions (IDRs) of proteins that localize to the FC, DFC or GC creates a proton gradient radiating inward from the nucleoplasm into the nucleolus, with the FC/DFC being more acidic than the outer rim of the GC [ 46 ]. The presence of a proton gradient could set up a proton motive force [ 47 ] to help facilitate the creation of opposing fluxes in active nucleoli.…”

Section: Introductionmentioning

confidence: 99%

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Emergent microenvironments of nucleoli

King,

Ruff,

Pappu

2024

Nucleus

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In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions

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Section: Nucleolar Sub-phases Are Defined By Distinct Macromolecular ...mentioning

confidence: 99%

Section: Nucleolar Sub-phases Are Defined By Distinct Macromolecular ...mentioning

confidence: 99%

Section: Nucleolar Sub-phases Are Defined By Distinct Macromolecular ...mentioning

confidence: 99%

Section: Nucleolar Sub-phases Are Defined By Distinct Macromolecular ...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Emergent microenvironments of nucleoli

King,

Ruff,

Pappu

2024

Nucleus

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Biomolecular condensates are characterized by interphase electric potentials

Posey,

Bremer,

Erkamp

et al. 2024

Preprint

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Biomolecular condensates form via processes that combine phase separation and reversible associations of multivalent macromolecules. Condensates can be two- or multi-phase systems defined by coexisting dense and dilute phases. Here, we show that solution ions can partition asymmetrically across coexisting phases defined by condensates formed by intrinsically disordered proteins or homopolymeric RNA molecules. Our findings were enabled by direct measurements of the activities of cations and anions within coexisting phases of protein and RNA condensates. Asymmetries in ion partitioning between coexisting phases vary with protein sequence, condensate type, salt concentration, and ion type. The Donnan equilibrium set up by asymmetrical partitioning of solution ions generates interphase electric potentials known as Donnan and Nernst potentials. Our measurements show that the interphase potentials of condensates are of the same order of magnitude as membrane potentials of membrane-bound organelles. Interphase potentials quantify the degree to which microenvironments of coexisting phases are different from one another. Importantly, and based on condensate-specific interphase electric potentials, which are membrane-like potentials of membraneless bodies, we reason that condensates are mesoscale capacitors that store charge. Interphase potentials lead to electric double layers at condensate interfaces. This helps explain recent observations of condensate interfaces being electrochemically active.

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Driving forces for condensation of synapsin are governed by sequence-encoded molecular grammars

Hoffmann,

Ruff,

Edu

et al. 2024

Preprint

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Brain functioning relies on orchestrated synaptic vesicle dynamics and controlled neurotransmitter release. Multiple biomolecular condensates coexist at the pre- and post-synapse and they are driven by condensation that combines binding, phase separation, and percolation. In pre-synapses, intrinsically disordered regions (IDRs) of synaptic proteins are drivers of condensation that enable clustering of synaptic vesicles (SVs). Although sequences of IDRs are poorly conserved across evolution, our computational analysis reveals the existence of non-random compositional biases and sequence patterns (molecular grammars) in IDRs of pre-synaptic proteins. For example, synapsin-1, which is essential for condensation of SVs, contains a conserved valence of arginine residues and blocks of polar and proline residues that are segregated from one another along the linear sequence. We show that these conserved features are crucial for driving synapsin-1 condensationin vitroand in cells. Our results highlight how conserved molecular grammars drive the condensation of key proteins at the pre-synapse.

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Macromolecular Condensation Organizes Nucleolar Sub-Phases to Set Up a pH Gradient

Cited by 6 publications

References 0 publications

Emergent microenvironments of nucleoli

Emergent microenvironments of nucleoli

Biomolecular condensates are characterized by interphase electric potentials

Driving forces for condensation of synapsin are governed by sequence-encoded molecular grammars

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