Phase-to-Phase With Nucleoli - Stress Responses, Protein Aggregation and Novel Roles of RNA

Abstract

Protein- and RNA-containing foci and aggregates are a hallmark of many age- and mutation-related neurodegenerative diseases. This article focuses on the role the nucleolus has as a hub in macromolecule regulation in the mammalian nucleus. The nucleolus has a well-established role in ribosome biogenesis and functions in several types of cellular stress responses. In addition to known reactions to DNA damaging and transcription inhibiting stresses, there is an emerging role of the nucleolus especially in responses to proteotoxic stress such as heat shock and inhibition of proteasome function. The nucleolus serves as an active regulatory site for detention of extranucleolar proteins. This takes place in nucleolar cavities and manifests in protein and RNA collections referred to as intranucleolar bodies (INBs), nucleolar aggresomes or amyloid bodies (A-bodies), depending on stress type, severity of accumulation, and material propensities of the macromolecular collections. These indicate a relevance of nucleolar function and regulation in neurodegeneration-related cellular events, but also provide surprising connections with cancer-related pathways. Yet, the molecular mechanisms governing these processes remain largely undefined. In this article, the nucleolus as the site of protein and RNA accumulation and as a possible protective organelle for nuclear proteins during stress is viewed. In addition, recent evidence of liquid-liquid phase separation (LLPS) and liquid-solid phase transition in the formation of nucleoli and its stress responses, respectively, are discussed, along with the increasingly indicated role and open questions for noncoding RNA species in these events.

Keywords: amyloidosis; non-coding RNA; nucleoli; proteasome inhibition; protein aggregation; stress responses.

FIGURE 1

Nucleolar formation and stress responses involve phase separation and transition events. After cell division in late mitosis, nucleoli start to reform by reactivated rRNA transcription and liquid-liquid phase separation events. By early interphase, each individual NOR containing the rDNA repeats are surrounded by a functional nucleolus. Later during the interphase, the small nucleoli fuse to typically form 1–2 mature nucleoli in diploid, non-transformed cells. Nucleolar cavities can be detected in S-phase cells or upon cellular stress, such as DNA damage. When cells are exposed to severe proteotoxic or e.g., heat stress, nucleolar aggressomes and amyloid bodies are formed within one or more nucleoli of a nucleus, involving liquid-solid transition of aggregate contents.

FIGURE 2

Nucleolar reorganization upon stress. The nucleolus reacts to different types of stress by structural deformations. (A) A normal interphase nucleolus under homeostasis shows tripartite structure composed around rDNA. (B) Upon DRB treatment, when RNApolI transcription remains active but rRNA processing is impaired, so called nucleolar necklaces are formed. (C) Nucleolar segregation, or nucleolar caps, are formed when RNApolI transcription is inactivated, e.g., with Actinomycin D. (D) Nucleolar aggresomes are formed within the nucleolus, in the nucleolar detention centers, upon proteotoxic insults such as proteasome inhibition and heat schock. This may or may not involve inhibited RNApolI activity.