Nuclear bodies formed by polyQ-ataxin-1 protein are liquid RNA/protein droplets with tunable dynamics

Abstract

A mutant form of the ataxin-1 protein with an expanded polyglutamine (polyQ) tract is the underlying cause of the inherited neurodegenerative disease spinocerebellar ataxia 1 (SCA1). In probing the biophysical features of the nuclear bodies (NBs) formed by polyQ-ataxin-1, we defined ataxin-1 NBs as spherical liquid protein/RNA droplets capable of rapid fusion. We observed dynamic exchange of the ataxin-1 protein into these NBs; notably, cell exposure to a pro-oxidant stress could trigger a transition to slower ataxin-1 exchange, typical of a hydrogel state, which no longer showed the same dependence on RNA or sensitivity to 1,6-hexanediol. Furthermore, we could alter ataxin-1 exchange dynamics either through modulating intracellular ATP levels, RNA helicase inhibition, or siRNA-mediated depletion of select RNA helicases. Collectively, these findings reveal the tunable dynamics of the liquid RNA/protein droplets formed by polyQ-ataxin-1.Within eukaryotic cells, complex biochemical reactions are facilitated by the concentration and restriction of key enzymes, substrates and regulators within well-defined membrane-bound organelles. In addition, numerous membrane-less intracellular compartments are important for a range of essential activities in both the cytoplasm (e.g. stress granules storing RNA molecules from stalled translation in response to environmental stresses 1 ) and the nucleus (e.g. nucleoli functioning in the biogenesis of ribosome subunits 2 , Cajal bodies in the processing and modification of short non-coding RNAs 3 , or promyelocytic leukemia (PML) bodies acting as sumoylation factories in response to interferon and oxidative stress 4 ). The formation of many of these membrane-less organelles is now understood to proceed via a phase separation process of specific constituent proteins, RNA and/or DNA molecules 5 . Thus, after a certain critical concentration threshold is exceeded, molecular assemblies of these constituents are formed with liquid-like behaviors that include fusing ability, viscous fluid dynamics, and high exchange rates with their surroundings in the nucleoplasm or cytoplasm 6-10 . This process of protein phase separation is now viewed as an essential mechanism for efficient compartmentalization that can be rapidly responsive to environmental challenges or intracellular changes 11,12 .Proteins that can undergo phase separation usually contain sequences conforming to either a low complexity region (LCR) or prion-like domain (PrLD) 8,11,13 ; these are protein domains typically with low amino acid diversity and little conformational heterogeneity 5,11 . These disordered structural characteristics can also contribute to an additional change known as protein phase transition, in which liquid-like condensates continue to become less dynamic and so form a more viscoelastic hydrogel or solid-like fibrous aggregates 12,14 . Many factors can promote the phase transition process such as time, pH, and altered amino acid sequences arising from gene mutations 8,9,15,16 . Thus, sequences typically co...

The ataxin-1 interactome reveals direct connection with multiple disrupted nuclear transport pathways

“…Notably, our assessment of ataxin-1 aggregate formation by analytical ultracentrifugation analyses of lysates prepared from these cells, showed increased aggregates for both GFP-ataxin-1 [85Q] and the non-pathogenic GFP-ataxin-1[85Q] S766A (Supplementary Fig. 1d), emphasising that aggregation state and visible body size do not always change in parallel as has been reported for the huntingtin protein with an expanded polyQ tract 24,25 and as we have recently observed for polyQ-ataxin-1 26 . These ataxin-1 nuclear bodies were distinct from nucleoli, as defined by co-staining for nucleolin that remained largely unchanged in size or morphology in the presence of ataxin-1 expression or arsenite exposure ( Supplementary Fig.…”

dSCOPE: a software to detect sequences critical for liquid-liquid phase separation

“…The top 5 TFs were SPEN, SRCAP, PRR12, HOXB3, and CIC. In these enriched TFs, CIC usually cooperates with ATXN1 to play a role in the development of the central nervous system, and ATXN1 is a proven phase separation protein (55). In addition, SPEN also regulates the notch signaling pathway (56).…”

SATB1-mediated chromatin landscape in T cells

“…However, SATB1 could function similarly to the signaling molecules like STAT3, SMAD3 and β-catenin which use their IDRs ( Figure 4 ) to target phase separated transcriptional and/or other condensates [ 116 ]. One IDR region of SATB1 is directly extended by a poly-Q region, which is also known to drive phase separation [ 104 , 105 , 117 , 118 ].

Figure 4.

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