PNAS: A new chemical proteomics approach enables global analysis of arginine dimethylation

Protein arginine methylation plays an important role in regulating protein function in different cellular processes, and its regulation is abnormal, which can lead to a variety of diseases
.

In recent years, there has been increasing evidence that arginine methylation may play an important role
in regulating liquid-liquid phase separation (LLPS) of proteins involved in the dynamic assembly of different membrane-free organelles (MLOs).
However, global recognition and characterization of arginine methylation in regulating the dynamic (decomposition) assembly of proteins LLPS and MLO remains unclear
.

Recently, a research team led by Professor Ye Mingming of the Dalian Institute of Chemical Physics, Chinese Academy of Sciences, in collaboration with Professor Liu Cong of the Shanghai Institute of Organic Chemistry, used a new chemical proteomics method to reveal the pathway
by which arginine dimethylation regulates the proteins LLPS and MLOs.

The study was published Oct.
18 in
the Proceedings of the National Academy of Sciences (PNAS).

Arginine residues were modified by o-dicarbonyl compounds to enrichment arginine-containing polypeptides by borate affinity chromatography
.

In this study, the researchers found that modifications to certain groups on arginine residues can seriously affect this reaction
.
Inspired by this, they developed a spatial effect-based chemical enrichment method (SECEM) to enrich arginine dimethylated peptides from complex peptide mixtures for proteomic analysis
.
They found that the method could improve the recognition performance
of arginine demethylation (DMA) at the proteome level.

By using SECEM, the researchers found that in mammalian cells, DMA sites occurring in RG/RGG motifs are enriched in proteins recognized in different MLOs, specifically stress particles (SGs).

In addition, SECEM further analyzed the dynamic changes of arginine DMA during SG formation and found that the most significant changes in arginine dimethylation occurred at multiple sites in several key SG-containing protein-rich regions of RG/RGG, including G3BP1, FUS, hnRNPA1, and KHDRBS1
.

It is worth noting that mutations at in vitro arginine methylation and dimethylated arginine sites impair the LLPS capacity of these RG/RGG-rich regions, which further validates the important role
of DMA in regulating the protein LLPS.