Lysine/RNA-interactions drive and regulate biomolecular condensation

Abstract

Cells form and use biomolecular condensates to execute biochemical reactions. The molecular properties of non-membrane-bound condensates are directly connected to the amino acid content of disordered protein regions. Lysine plays an important role in cellular function, but little is known about its role in biomolecular condensation. Here we show that protein disorder is abundant in protein/RNA granules and lysine is enriched in disordered regions of proteins in P-bodies compared to the entire human disordered proteome. Lysine-rich polypeptides phase separate into lysine/RNA-coacervates that are more dynamic and differ at the molecular level from arginine/RNA-coacervates. Consistent with the ability of lysine to drive phase separation, lysine-rich variants of the Alzheimer’s disease-linked protein tau undergo coacervation with RNA in vitro and bind to stress granules in cells. Acetylation of lysine reverses liquid–liquid phase separation and reduces colocalization of tau with stress granules. Our study establishes lysine as an important regulator of cellular condensation.

The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy

“…In contrast, other LLPS systems display small chemical shifts with increasing protein concentrations across the entirety of the protein sequence, suggesting that the interactions that stabilize phase separation are not localized to a particular region (10). In samples near the saturation concentration where a small fraction of the protein undergoes LLPS, other studies have probed the onset of LLPS by measuring the signal intensities in standard one-and twodimensional spectra of the protein remaining in the dispersed phase (17,18). The fraction of protein in the condensed phase contributes very little to the total signal due to enhanced relax-ation rates in the condensed phase, leading to extreme signal broadening and leaving only the signals from the dispersed phase (9,(17)(18)(19)(20)(21)(22).…”

“…In samples near the saturation concentration where a small fraction of the protein undergoes LLPS, other studies have probed the onset of LLPS by measuring the signal intensities in standard one-and twodimensional spectra of the protein remaining in the dispersed phase (17,18). The fraction of protein in the condensed phase contributes very little to the total signal due to enhanced relax-ation rates in the condensed phase, leading to extreme signal broadening and leaving only the signals from the dispersed phase (9,(17)(18)(19)(20)(21)(22). Whereas dispersed phase samples are useful in characterizing certain aspects of protein systems that undergo LLPS, they are limited as conclusions about the condensed phase are indirect.…”

“…Changes in the position or intensity of the resonances corresponding to each residue have been used to map self-interactions and interactions with protein-binding partners and ligands of LLPS systems (9,17,18,20,24,27,37,38). The proteasomal shuttle protein, ubiquilin (UBQLN), phase-separates and localizes to stress granules (37).…”

Mitochondrial cytochromecliberates the nucleophosmin-sequestered ARF tumor suppressor in the nucleolus

“…Recent data has highlighted the key role of linear R-rich elements in the proteins exhibiting heterotypic interactions with NPM (37), yet K-rich stretches can also be involved in the assembly of other membrane-less organelles (e.g. stress granules) (44). According to Kriwacki and co-workers (37), heterotypic interactions require extended NPM conformations, which do occur at physiological ionic strength.…”

DNA binding reorganizes the intrinsically disordered C-terminal region of PSC inDrosophilaPRC1

“…The protein footprinting assay may be especially useful for IDR-nucleic acid interactions. These could include protein-RNA interactions, which can also be mediated by lysine-rich IDRs [42]. In principle, other amino acids involved in nucleic acid interactions could be analyze using similar footprinting approaches [43].…”