Clustering of Aromatic Residues in Prion-like Domains Can Tune the Formation, State, and Organization of Biomolecular Condensates

Biochemistry. 2021 Nov 30;60(47):3566-3581. doi: 10.1021/acs.biochem.1c00465. Epub 2021 Nov 16.

Abstract

In immature oocytes, Balbiani bodies are conserved membraneless condensates implicated in oocyte polarization, the organization of mitochondria, and long-term organelle and RNA storage. In Xenopus laevis, Balbiani body assembly is mediated by the protein Velo1. Velo1 contains an N-terminal prion-like domain (PLD) that is essential for Balbiani body formation. PLDs have emerged as a class of intrinsically disordered regions that can undergo various different types of intracellular phase transitions and are often associated with dynamic, liquid-like condensates. Intriguingly, the Velo1 PLD forms solid-like assemblies. Here we sought to understand why Velo1 phase behavior appears to be biophysically distinct from that of other PLD-containing proteins. Through bioinformatic analysis and coarse-grained simulations, we predict that the clustering of aromatic residues and the amino acid composition of residues between aromatics can influence condensate material properties, organization, and the driving forces for assembly. To test our predictions, we redesigned the Velo1 PLD to test the impact of targeted sequence changes in vivo. We found that the Velo1 design with evenly spaced aromatic residues shows rapid internal dynamics, as probed by fluorescent recovery after photobleaching, even when recruited into Balbiani bodies. Our results suggest that Velo1 might have been selected in evolution for distinctly clustered aromatic residues to maintain the structure of Balbiani bodies in long-lived oocytes. In general, our work identifies several tunable parameters that can be used to augment the condensate material state, offering a road map for the design of synthetic condensates.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids, Aromatic / chemistry
  • Amino Acids, Aromatic / genetics
  • Amino Acids, Aromatic / metabolism
  • Animals
  • Biomolecular Condensates / metabolism*
  • Cell Polarity
  • Cells, Cultured
  • Female
  • Intravital Microscopy
  • Oocytes / cytology
  • Oocytes / metabolism
  • Phase Transition
  • Primary Cell Culture
  • Protein Domains / genetics
  • Protein Engineering
  • T-Box Domain Proteins / chemistry
  • T-Box Domain Proteins / genetics
  • T-Box Domain Proteins / metabolism*
  • Xenopus Proteins / chemistry
  • Xenopus Proteins / genetics
  • Xenopus Proteins / metabolism*
  • Xenopus laevis

Substances

  • Amino Acids, Aromatic
  • T-Box Domain Proteins
  • Xenopus Proteins
  • velo1 protein, Xenopus