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Caenorhabditis elegans FBF-1 and FBF-2 C-terminal intrinsically disordered regions differentially regulate

Hope R Hawthorne1, Chen Qiu1, Traci M Tanaka Hall2

  • 1Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.

RNA (New York, N.Y.)
|August 6, 2025
PubMed

Insights

PUF proteins FBF-1 and FBF-2 maintain germline stem cells by binding RNA. Differences in their C-terminal regions fine-tune RNA-binding activity and autoinhibition, revealing paralog divergence in RNA-binding proteins.

Area of Science:

  • Molecular Biology
  • Genetics
  • Developmental Biology

Background:

  • PUF proteins are RNA-binding proteins crucial for gene regulation.
  • In *C. elegans*, FBF-1 and FBF-2 maintain germline stem cells by repressing differentiation-promoting mRNAs.
  • The C-terminal intrinsically-disordered regions (CTs) of PUF proteins, specifically FBF-2, are known to be important for function, but FBF-1 CT function was unclear.

Purpose of the Study:

  • To investigate how differences in the C-terminal tails (CTs) of FBF-1 and FBF-2 impact their molecular function, particularly RNA binding and autoinhibition.
  • To determine if the PUF-interacting motif (PIM) in the CTs of FBF-1 and FBF-2 contributes to differential regulation.

Main Methods:

  • Crystal structure analysis of FBF-1.
  • Biochemical assays to assess RNA binding affinity.
  • Creation and analysis of FBF-1/FBF-2 chimeric proteins to study domain interactions.

Main Results:

  • The FBF-1 CT did not impact its RNA binding, unlike the FBF-2 CT.
  • A PIM in the FBF-1 CT was found to bind its RNA-binding domain (RBD), similar to FBF-2.
  • Chimeric proteins revealed that the FBF-2 CT can autoinhibit FBF-1 RNA binding, and altering the PIM in FBF-2 reduced its autoinhibition.

Conclusions:

  • Paralogous PUF proteins, FBF-1 and FBF-2, exhibit distinct regulatory mechanisms despite high sequence conservation.
  • The FBF-2 CT plays a crucial role in autoinhibition, which can be modulated by its PIM.
  • These findings highlight how variations in intrinsically disordered regions and specific motifs allow RNA-binding protein paralogs to fine-tune their functions.
Keywords:
PUF proteinRNA-binding proteinfem-3 binding factorintrinsically disordered region

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