Interaction modulation through arrays of clustered methyl-arginine protein modifications

Abstract

Systematic analysis of human arginine methylation events bifurcates its signaling mechanism, functioning either in isolation akin to canonical PTM regulation or clustered within disordered protein sequence. Hundreds of proteins contain methyl-arginine clusters and are more prone to mutation and more tightly expression-regulated than dispersed methylation targets. Arginine clusters in the highly methylated RNA binding protein SYNCRIP were experimentally shown to function in concert providing a tunable protein interaction interface. Quantitative immuno-precipitation assays defined two distinct cumulative regulatory mechanisms operating across 18 proximal arginine-glycine motifs in SYNCRIP. Functional binding to the methyl-transferase PRMT1 was promoted by continual arginine stretches while interaction with the methyl-binding protein SMN1 was arginine content dependent irrespective of linear position within the unstructured region. This study highlights how highly repetitive di-amino acid motifs in otherwise low structural complexity regions can provide regulatory potential, and with SYNCRIP as an extreme example how PTMs leverage these disordered sequences to drive cellular functions.

Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication

“…Interestingly, many SARS-CoV-2 N-interacting proteins (27 of 119, Figure 2 B) contained multiple RGG/RG motifs including DEAD/DExH family of RNA helicases DDX21, DDX54, DHX30, DHX57, and heterogeneous nuclear ribonucleoproteins hnRNPA1, A3, D, DL, G (RBMX), R, U, UL1 and UL2 ( Table 1 ). Many of these N-interacting proteins, such as G3BP1 [ 50 ], FAM98A [ 51 ], FXR1 [ 52 ], hnRNPA1 [ 53 ], hnRNPUL1 [ 54 ], SYNCRIP [ 55 ], ILF3 [ 56 ], and SERBP1[ 57 ] are known PRMT1 substrates.…”

Global analysis of protein arginine methylation

“…We show that ArgMet-NMR enables detection of methylation patterns in purified proteins incubated with PRMT1. Methylation by PRMTs in the human proteome occurs preferentially (but not exclusively) within glycine-arginine- and proline-glycine-methionine-rich regions (Cheng et al, 2007; Thandapani et al, 2013; Woodsmith et al, 2018), but specific consensus sequences targeted by most of the human PRMTs remain to be identified. Our approach provides a toolbox for fast and label-free screening for PRMT selectivity in purified proteins/peptides.…”

“…Methylarginines are predominantly found in intrinsically disordered protein regions, e.g. RG/RGG regions, which are intimately connected to LLPS (Chong et al, 2018; Guccione and Richard, 2019; Woodsmith et al, 2018). A large proportion of the proteins implicated in LLPS are known targets for ArgMet, and therefore LLPS could be regulated by their ArgMet (Chong et al, 2018; Guccione and Richard, 2019; Lorton and Shechter, 2019).…”

“…Methylarginines are predominantly found in intrinsically disordered protein regions, e.g. RG/RGG regions, which are intimately connected to LLPS (Chong et al, 2018;Guccione and Richard, 2019;Woodsmith et al, 2018).…”

Arginine Methylation Regulates SARS-CoV-2 Nucleocapsid Protein Function and Viral Replication

“…Interestingly, many SARS-CoV-2 N-interacting proteins (27 of 119, Figure 2B) contained multiple RGG/RG motifs including DEAD/DExH family of RNA helicases DDX21, DDX54, DHX30, DHX57, and heterogeneous nuclear ribonucleoproteins hnRNPA1, A3, D, DL, G (RBMX), R, U, UL1 and UL2 (Table 1). Many of these N-interacting proteins, such as G3BP1 50 , FAM98A 51 , FXR1 52 , hnRNPA1 53 , hnRNPUL1 54 , SYNCRIP 55 , ILF3 56 , and SERBP1 57 are known PRMT1 substrates. N protein-interactome changed significantly by two proteins with MS023 treatment.…”