Phosphorylation regulates arginine-rich RNA-binding protein solubility and oligomerization

Kundinger, Sean R.; Dammer, Eric B.; Yin, Luming; Hurst, Cheyenne; Shapley, Sarah; Ping, Lingyan; Khoshnevis, Sohail; Ghalei, Homa; Duong, Duc M.; Seyfried, Nicholas T.

doi:10.1016/j.jbc.2021.101306

Cited by 12 publications

(7 citation statements)

References 92 publications

(119 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RS domains among our new SR-related proteins are heavily phosphorylated regardless of whether they are classified as RBPs, consistent with PTM-dependent regulation of their activity in both canonical and noncanonical functions (Giannakouros et al 2011). Recently, increased phosphorylation of RS domains was shown to enhance LLPS and recruitment to nuclear speckles (Greig et al 2020)a membraneless compartment with liquid-like properties -whereas dephosphorylation was associated with mislocalization, oligomerization, and aggregation SR/SR-related proteins (Kundinger et al 2021). Therefore, widespread phosphorylation of RS domains may represent a remarkably generic yet potent mechanism to regulate the localization, solubility, and activity of SR/SR-related proteins, though likely in conjunction with unique, site-specific effects.…”

Section: Discussionsupporting

confidence: 72%

Expansion and functional analysis of the SR-related protein family across the domains of life

Cascarina

Ross

2022

RNA

View full text Add to dashboard Cite

Serine/Arginine-rich (SR) proteins comprise a family of proteins that is predominantly found in eukaryotes and plays a prominent role in RNA splicing. A characteristic feature of SR proteins is the presence of an S/R-rich low-complexity domain (RS domain), often in conjunction with spatially distinct RNA recognition motifs (RRMs). To date, 52 human proteins have been classified as SR or SR-related proteins. Here, using an unbiased series of composition criteria together with enrichment for known RNA binding activity, we identified >100 putative SR-related proteins in the human proteome. This method recovers known SR and SR-related proteins with high sensitivity (~94%), yet identifies a number of additional proteins with many of the hallmark features of true SR-related proteins. Newly identified SR-related proteins display slightly different amino acid compositions yet similar levels of post-translational modification, suggesting that these new SR-related candidates are regulated in vivo and functionally important. Furthermore, candidate SR-related proteins with known RNA-binding activity (but not currently recognized as SR-related proteins) are nevertheless strongly associated with a variety of functions related to mRNA splicing and nuclear speckles. Finally, we applied our SR search method to all available reference proteomes, and provide maps of RS domains and Pfam annotations for all putative SR-related proteins as a resource. Together, these results expand the set of SR-related proteins in humans, and identify the most common functions associated with SR-related proteins across all domains of life.

show abstract

Section: Discussionsupporting

confidence: 72%

Expansion and functional analysis of the SR-related protein family across the domains of life

Cascarina

Ross

2022

RNA

View full text Add to dashboard Cite

show abstract

“…The importance of phosphorylation in the regulation of biomolecular condensates has been demonstrated through the central role of casein kinase 2 (CK2) and dual-specificity tyrosine kinase 3 (DYRK3) in the disassembly of stress granules 39 and nuclear speckles during mitosis 40 . Recent studies have shown a global impact of phosphorylation on condensation of RNA-binding proteins 41 . However, the site-specific information necessary to understand mechanisms of phosphoregulation of protein condensation is unknown.…”

Section: Discussionmentioning

confidence: 99%

Systematic discovery of biomolecular condensate-specific protein phosphorylation

et al. 2022

View full text Add to dashboard Cite

Reversible protein phosphorylation is an important mechanism for regulating (dis)assembly of biomolecular condensates. However, condensate-specific phosphosites remain largely unknown, thereby limiting our understanding of the underlying mechanisms. Here, we combine solubility proteome profiling with phosphoproteomics to quantitatively map several hundred phosphosites enriched in either soluble or condensate-bound protein subpopulations, including a subset of phosphosites modulating protein–RNA interactions. We show that multi-phosphorylation of the C-terminal disordered segment of heteronuclear ribonucleoprotein A1 (HNRNPA1), a key RNA-splicing factor, reduces its ability to locate to nuclear clusters. For nucleophosmin 1 (NPM1), an essential nucleolar protein, we show that phosphorylation of S254 and S260 is crucial for lowering its partitioning to the nucleolus and additional phosphorylation of distal sites enhances its retention in the nucleoplasm. These phosphorylation events decrease RNA and protein interactions of NPM1 to regulate its condensation. Our dataset is a rich resource for systematically uncovering the phosphoregulation of biomolecular condensates.

show abstract

“…5 D). A recent study reported that dephosphorylated SRSF2, a RBP involved in mRNA splicing, formed higher molecular weight detergent-insoluble oligomers [ 40 ]. Consistent with this report, we identified several phosphorylation sites on Larp1 that were significantly decreased after 14 days of PFF treatment (Table 1 ) and may explain the decreased Larp1 observed in the insoluble fraction.…”

Section: Resultsmentioning

confidence: 99%

Broad proteomics analysis of seeding-induced aggregation of α-synuclein in M83 neurons reveals remodeling of proteostasis mechanisms that might contribute to Parkinson’s disease pathogenesis

Lumpkin,

Patel,

Potts

et al. 2024

Mol Brain

View full text Add to dashboard Cite

Aggregation of misfolded α-synuclein (α-syn) is a key characteristic feature of Parkinson’s disease (PD) and related synucleinopathies. The nature of these aggregates and their contribution to cellular dysfunction is still not clearly elucidated. We employed mass spectrometry-based total and phospho-proteomics to characterize the underlying molecular and biological changes due to α-syn aggregation using the M83 mouse primary neuronal model of PD. We identified gross changes in the proteome that coincided with the formation of large Lewy body-like α-syn aggregates in these neurons. We used protein-protein interaction (PPI)-based network analysis to identify key protein clusters modulating specific biological pathways that may be dysregulated and identified several mechanisms that regulate protein homeostasis (proteostasis). The observed changes in the proteome may include both homeostatic compensation and dysregulation due to α-syn aggregation and a greater understanding of both processes and their role in α-syn-related proteostasis may lead to improved therapeutic options for patients with PD and related disorders.

show abstract

Phosphorylation regulates arginine-rich RNA-binding protein solubility and oligomerization

Cited by 12 publications

References 92 publications

Expansion and functional analysis of the SR-related protein family across the domains of life

Expansion and functional analysis of the SR-related protein family across the domains of life

Systematic discovery of biomolecular condensate-specific protein phosphorylation

Broad proteomics analysis of seeding-induced aggregation of α-synuclein in M83 neurons reveals remodeling of proteostasis mechanisms that might contribute to Parkinson’s disease pathogenesis

Contact Info

Product

Resources

About