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ATP regulates RNA-driven cold inducible RNA binding protein phase separation.

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Protein Science : a Publication of the Protein Society
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Cellular metabolites, particularly nucleotides like ATP, interact with intrinsically disordered proteins such as CIRBP. This interaction affects biomolecular condensate formation, suggesting metabolite inclusion in future in vitro studies.

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ATPCIRBPRG/RGG regionRNA-binding proteindisordered proteinliquid-liquid phase separation

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Background:

  • Intrinsically disordered proteins (IDPs) and regions (IDRs) are crucial for eukaryotic biological functions.
  • IDPs play key roles in biomolecular condensate organization, and their misregulation is linked to neurological disorders.
  • Current in vitro studies often use purified proteins, not reflecting cellular metabolite concentrations.

Purpose of the Study:

  • To investigate the direct interactions between cellular metabolites and a representative condensate-forming protein.
  • To understand how cellular metabolites influence the behavior of intrinsically disordered proteins.

Main Methods:

  • Utilized the cold-inducible RNA-binding protein (CIRBP), an arginine-glycine/arginine-glycine-glycine (RG/RGG)-rich protein, as a model.
  • Studied the binding of various cellular metabolites to CIRBP using in vitro assays.
  • Assessed the impact of metabolite binding on CIRBP's RNA-driven liquid-liquid phase separation.

Main Results:

  • Most abundant cellular metabolites, excluding nucleotides, did not directly bind to CIRBP.
  • Specific nucleotides (ATP, ADP, AMP) and coenzymes (NAD+, NADH, NADP+, NADPH) directly interacted with both the folded RNA-recognition motif and the disordered RG/RGG region of CIRBP.
  • ATP binding to CIRBP inhibited its RNA-driven phase separation.

Conclusions:

  • Cellular metabolites, especially nucleotides and coenzymes, directly interact with intrinsically disordered proteins like CIRBP.
  • These interactions, particularly ATP binding, can modulate the phase separation behavior of condensate-forming proteins.
  • Future in vitro studies of biomolecular condensate formation should incorporate cellular metabolites to better mimic the cellular environment.