Biology subjects

Codispoti, S.

Publications and source records attributed to Codispoti, S..

3 recordsLinked to original sources

bioRxiv2026

The glycine-arginine-rich motif of 53BP1 modulates RNA interactions necessary for its liquid-liquid phase separation during DNA Damage Response

The DNA damage response relies on the rapid assembly of repair factors into foci with properties of liquid-liquid phase separation, driven by de novo transcription of damage-induced RNAs. 53BP1 is a key component of these condensates, yet the molecular determinants driving this process remain unknown. Here, through computational, structural and in vitro approaches, we identify the oligomerization domain of 53BP1 and its glycine-arginine-rich (GAR) motif as crucial for RNA interactions and phase separation. Biophysical characterization reveals that 53BP1-RNA condensates can progressively mature into a more stable state, and that GAR mutants display aberrant material properties. Using a cellular model of telomere fusion events, we demonstrate that the GAR motif is essential for 53BP1-mediated DNA repair, which depends on the combined contributions of RNA binding and appropriate condensate biophysical properties. Therefore, RNA-driven 53BP1 condensation is functionally required to maintain genome integrity.

biophysics↗

bioRxiv2025

The Dark Side of Biomolecular Condensates: Quantifying the Role of Nucleic Acids

Liquid-Liquid Phase Separation (LLPS) is being increasingly recognized as a major organizational principle for proteins and nucleic acids (NAs) in cells, as well as a promising strategy for synthetic biology and biomedical applications. Extensive work has explored the role of protein sequence and properties in the regulation of LLPS. On the contrary, the role of nucleic acids has often been overlooked. Here, to fill this gap we focus on model systems made of oligonucleotides with tuned lengths and degree of hybridization, mixed with a moderately charged, disordered peptide. Combining multiple length scales through experiments and molecular dynamics simulations, we unravel the distinct effect of the properties of NAs on the phase behavior and we propose a metric for the stability of biocondensates. We also characterize the conditions for the onset of liquid crystalline order in the droplets and we show that it is associated with a dramatic slowing down of the dynamics of oligonucleotides, while peptides retain high mobility. Our results can be generalized to natural and non-natural NAs of arbitrary structure, providing a guide for the design of synthetic NA-containing coacervates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/683552v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@179be04org.highwire.dtl.DTLVardef@1aa0192org.highwire.dtl.DTLVardef@4d411aorg.highwire.dtl.DTLVardef@1ed238d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability

The ribosome, owing to its exceptional conservation and biological importance, harbours a remarkable molecular fossil known as the protoribosome. It surrounds the peptidyl transferase center (PTC), responsible for peptide bond formation. While previous studies have demonstrated the PTC activity in RNA alone, our investigation reveals the intricate roles of the ribosomal protein fragments (rPeptides) within the ribosomal core. This research highlights the significance of rPeptides in stability and coacervation of two distinct protoribosomal evolutionary stages. The 617nt "big" protoribosome model which associates with rPeptides specifically, exhibits a structurally defined and rigid nature, further stabilised by the peptides. In contrast, the 136nt "small" model, previously linked to peptidyltransferase activity, displays greater structural flexibility. While this construct interacts with rPeptides with lower specificity, they induce coacervation of the "small" protoribosome across a wide concentration range, which is concomitantly dependent on the RNA sequence and structure. Moreover, these conditions protect RNA from degradation. This phenomenon suggests a significant evolutionary advantage in the RNA-protein interaction at the early stages of ribosome evolution. The distinct properties of the two protoribosomal stages suggest that rPeptides initially provided compartmentalization and prevented RNA degradation, preceding the emergence of specific RNA-protein interactions crucial for the ribosomal structural integrity. 3 keypoints- The most ancient fragments of ribosomal peptides trigger coacervation of protoribosome - The protoribosome coacervation provides protection against RNA degradation - Coacervation is more profound with a smaller and more flexible model of the protoribosome

biophysics↗