Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder.

Lovisa Stenström,Peter J Thul,Mathias Uhlén,Anthony J Cesnik,Emma Lundberg,Diana Mahdessian,Christian Gnann,Sara Cuylen-Haering,Manuel D Leonetti,Wei Ouyang

doi:10.15252/msb.20209469

Abstract

The nucleolus is essential for ribosome biogenesis and is involved in many other cellular functions. We performed a systematic spatiotemporal dissection of the human nucleolar proteome using confocal microscopy. In total, 1,318 nucleolar proteins were identified; 287 were localized to fibrillar components, and 157 were enriched along the nucleoplasmic border, indicating a potential fourth nucleolar subcompartment: the nucleoli rim. We found 65 nucleolar proteins (36 uncharacterized) to relocate to the chromosomal periphery during mitosis. Interestingly, we observed temporal partitioning into two recruitment phenotypes: early (prometaphase) and late (after metaphase), suggesting phase‐specific functions. We further show that the expression of MKI67 is critical for this temporal partitioning. We provide the first proteome‐wide analysis of intrinsic protein disorder for the human nucleolus and show that nucleolar proteins in general, and mitotic chromosome proteins in particular, have significantly higher intrinsic disorder level compared to cytosolic proteins. In summary, this study provides a comprehensive and essential resource of spatiotemporal expression data for the nucleolar proteome as part of the Human Protein Atlas.

Highlights

One of the most prominent nuclear substructures is the nucleolus, the cellular site for ribosome synthesis and assembly
Out of the 12,393 proteins included in the Human Protein Atlas (HPA) Cell Atlas (v19), we identified 1,318 nucleolar proteins, of which 287 localized to the fibrillar center or dense fibrillar component and 1,031 localized to the whole nucleolus (Dataset EV1)
Functional enrichment analysis of the nucleolar proteome shows that the enriched Gene Ontology (GO) terms for biological process are well in line with the known functions of the nucleoli

Summary

Introduction

One of the most prominent nuclear substructures is the nucleolus, the cellular site for ribosome synthesis and assembly. As opposed to membrane-bound organelles, nucleoli and other nuclear bodies lack enclosing membranes This allows for dynamic cellular responses as these structures can change in size and protein composition when needed. The size and number of nucleoli changes throughout the cell cycle as they fuse together, a process recently suggested to be aided by interactions with the nucleoplasm (Caragine et al, 2019) The formation of these membrane-less, yet spatially distinct structures, is the result of reversible liquid-liquid phase transitions similar to oil in water emulsions (Brangwynne et al, 2009, 2011; Lin et al, 2015). The nucleolus is structurally partitioned into three droplet-like layers with different miscibility (Feric et al, 2016) This separation facilitates a sequential production of ribosomes, from transcription of rDNA at the fibrillar center border (FC) followed by rRNA processing in the dense fibrillar component (DFC) and ribosome assembly in the granular component (GC). Mutations in disordered regions can drastically change the conformation of the protein and since many IDPs function as hub-proteins, altered protein function could initiate a loss-of-function cascade in the cell (Uversky et al, 2008)

Methods

Results

Conclusion