F/YGG-motif is an intrinsically disordered nucleic-acid binding motif

Abstract

Heterogeneous nuclear ribonucleoproteins (hnRNP) function in RNA processing, have RNA-recognition motifs (RRMs) and intrinsically disordered, low-complexity domains (LCDs). While RRMs are drivers of RNA binding, there is only limited knowledge about the RNA interaction by the LCD of some hnRNPs. Here, we show that the LCD of hnRNPA2 interacts with RNA via an embedded Tyr/Gly-rich region which is a disordered RNA-binding motif. RNA binding is maintained upon mutating tyrosine residues to phenylalanines, but abrogated by mutating to alanines, thus we term the RNA-binding region ‘F/YGG motif’. The F/YGG motif can bind a broad range of structured (e.g. tRNA) and disordered (e.g. polyA) RNAs, but not rRNA. As the F/YGG otif can also interact with DNA, we consider it a general nucleic acid-binding motif. hnRNPA2 LCD can form dense droplets, by liquid–liquid phase separation (LLPS). Their formation is inhibited by RNA binding, which is mitigated by salt and 1,6-hexanediol, suggesting that both electrostatic and hydrophobic interactions feature in the F/YGG motif. The D290V mutant also binds RNA, which interferes with both LLPS and aggregation thereof. We found homologous regions in a broad range of RNA- and DNA-binding proteins in the human proteome, suggesting that the F/YGG motif is a general nucleic acid-interaction motif.

In-Silico Analysis of pH-Dependent Liquid-Liquid Phase Separation in Intrinsically Disordered Proteins

“…It is well established that tyrosines are important residues in LLPS since their involvement in π-π [ 36 ] or cation-π [ 11 , 37 ] interactions are key for the weak multivalent contact that sustain liquid droplets. In this way, an increasing number of Tyr-to-Ser substitutions in the LCD of FUS has been linked with a reduction in the formation of droplets at pH 7.5 [ 9 ].…”

Interaction of hnRNPB1 with Helix-12 of hHOTAIR Reveals the Distinctive Mode of RNA Recognition That Enables the Structural Rearrangement by LCD

“…Apparently, the LCD segment shows a biased behavior toward the RNA structure without sequential preference, but which motif within the LCD domain is responsible for this structurally biased recognition is unknown. Recent work has shown that the ’YGG motif’ within the LCD region of the hnRNPA2 protein (amino acid 239–306, designated nucleic acid interaction domain 1 (NAID1)) is responsible for the broad spectrum of RNA and DNA recognition . Based on our observation that the mutation of purine to cytosine did not affect the interaction of the LCD region with helix-12, we tend to speculate that the ’YGG motif’ is responsible for this structural bias.…”

“…Recent work has shown that the 'YGG motif' within the LCD region of the hnRNPA2 protein (amino acid 239−306, designated nucleic acid interaction domain 1 (NAID1)) is responsible for the broad spectrum of RNA and DNA recognition. 13 Based on our observation that the mutation of purine to cytosine did not affect the interaction of the LCD region with helix-12, we tend to speculate that the 'YGG motif' is responsible for this structural bias. Moreover, the 'YGG motif' may be the driving force for the high binding affinity between LCD and Helix-12 and thus may be involved in the unwinding activity.…”

“…The involvement of the LCD of related protein hnRNPA1 in the interstrand annealing of RNA has been demonstrated. , Additionally, recent studies have shown the role of the RGG box of hnRNPA1 (LCD region), enhancing UP1 (tandem RRMs) to structurally unfold the RNA G-quadruplex through structure-specific interactions . Notably, recent studies on the LCD of hnRNPA2/B1 have shown its interaction with a wide range of structured and disordered RNA; hence, it will be interesting to explore its interaction with hHOTAIR . Deeper insights into the molecular recognition of LCD and its interplay with RRMs that defines its affinity or specificity to hHOTAIR will be important to elucidate its role in establishing lncRNA–RNA interaction.…”

Specificity and mechanism of 1,6 hexanediol-induced disruption of nuclear transport

“…Unrelated to nuclear transport, 1,6HD has also been widely used to dissolve liquid-liquid phase separated compartments in cells and to dissolve condensates in in vitro studies. With aggregationprone peptides, the alcohol dissolves hydrogels (Molliex et al 2015;Kroschwald, Maharana, and Simon 2017;Shi et al 2017) but not fibers (Lin et al 2016;Van Lindt et al 2022). In cells, the interpretation of effects of 1,6HD are more difficult (Kroschwald, Maharana, and Simon 2017) and depending on the cell type, growth condition and the concentration and length of treatment different results may be obtained.…”