Phase separation via protein-protein and protein-RNA networks coordinates ribosome assembly in the nucleolus

• Published in: Biochimica et biophysica acta. General subjects Vol. 1869; no. 10; p. 130835
• Main Authors: Dogra, Priyanka, Kriwacki, Richard W.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.09.2025
• Subjects: Animals; Cancer; Cell Nucleolus - genetics; Cell Nucleolus - metabolism; Chromosomal Proteins, Non-Histone - metabolism; Humans; Neurodegenerative diseases; Nuclear Proteins - metabolism; Nucleolar organization; Nucleolin; Nucleophosmin; Phase Separation; Protein-RNA interactions; Ribosome biogenesis; Ribosomes - genetics; Ribosomes - metabolism; RNA, Ribosomal - genetics; RNA, Ribosomal - metabolism; RNA-Binding Proteins - metabolism; DFC; circRNAs; PR; Ribosome biogenesis; PS; PNC; ETS; ALS; ITS; ABTdensity; RRM; LETN; FBL; PTBP1; NBD; PDFC; IDR; RNAPI; RNAPII; RRP15; pRNA; Neurodegenerative diseases; SSF1; NOR; LoNA; ARF; DKC1; Phase separation; NCL; TDP-43; FTD; snoRNPs; FC; RP; lncRNAs; NR; DPR; PNCTR; DDX21; PARP; RNAPIII; C9ORF72; TCOF1; OD; UBF; SURF6; GC; LYAR; Protein-RNA interactions; NOP56/NOP58; HMG domains; NPM1; FUS; snoRNAs; GR; CDK2; PAPAS; MDM2; Nucleolar organization; SLERT; ABTscore; Cancer
• ISSN: 0304-4165; 1872-8006; 1872-8006
• DOI: 10.1016/j.bbagen.2025.130835

The nucleolus, the largest membraneless organelle in the nucleus, functions as the site for ribosome biogenesis. While long known for its complex and dynamic structure, our mechanistic understanding of nucleolar organization has advanced dramatically in the past 15 years. The process of phase separation (PS) facilitates the compartmentalization of ribosomal components with assembly factors in the nucleolus, underlying complex ribosome biogenesis processes. Multicomponent PS creates multiple nucleolar sub-compartments that function from inside out as a ribosome assembly line. In this review, we discuss the molecular basis of nucleolar organization, including how different types of protein-protein and protein-RNA interactions create the multilayered architecture that enables ribosome biogenesis. Key proteins including nucleolin, fibrillarin, and nucleophosmin mediate nucleolar compartmentalization through their unique structural features and multivalent interactions. The processes of ribosomal RNA (rRNA) transcription, modification and splicing, and folding are spatially and temporally segregated within different regions of the nucleolus. rRNA matures and changes form along this processing continuum, continually altering its interactions with proteins, creating multiple separate liquid phases that establish sub-compartments. We highlight how both folded domains and intrinsically disordered regions (IDRs) in nucleolar proteins contribute to multivalent interactions underlying PS and nucleolar compartmentalization. We also discuss how perturbation of nucleolar PS alters nucleolar structure, dynamics, and function and contributes to a range of pathological conditions. [Display omitted] •Phase separation drives nucleolar organization and ribosome biogenesis.•Protein-protein and protein-RNA interactions establish the multilayered nucleolar architecture.•Both folded domains and disordered regions of nucleolar proteins mediate multivalent interactions and phase separation.•Multiple nucleolar sub-compartments create an inside-out ribosome assembly line.•Disrupted nucleolar phase separation leads to pathological conditions.