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Co-crystalization reveals the interaction between AtYchF1 and ppGpp.

Ming-Yan Cheung1, Xiaorong Li2, Yee-Shan Ku1

  • 1Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.

Frontiers in Molecular Biosciences
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Summary

Arabidopsis thaliana G-protein AtYchF1 binds and hydrolyzes ppGpp, a molecule that normally stunts plant growth. This interaction impacts stress responses and nucleotide signaling in plants.

Keywords:
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Area of Science:

  • Plant molecular biology
  • Biochemistry
  • Structural biology

Background:

  • AtYchF1 is a cytosolic G-protein in Arabidopsis thaliana with known relaxed nucleotide-binding specificity.
  • It interacts with GTP, ATP, and 26S rRNA and acts as a negative regulator of biotic and abiotic stresses.
  • Cytoplasmic accumulation of guanosine tetraphosphate (ppGpp) typically inhibits plant growth and development.

Purpose of the Study:

  • To investigate the interaction between AtYchF1 and ppGpp.
  • To elucidate the functional and structural consequences of ppGpp binding to AtYchF1.
  • To understand the role of AtYchF1 in nucleotide signaling and stress response.

Main Methods:

  • Co-crystallization of AtYchF1 with ppGpp.
  • In vitro pull-down assays to confirm binding.
  • Hydrolytic biochemical assays to assess enzyme activity.
  • Structural analysis of the AtYchF1-ppGpp complex.

Main Results:

  • AtYchF1 binds and hydrolyzes ppGpp.
  • ppGpp binding inhibits AtYchF1's interaction with ATP, GTP, and 26S rRNA.
  • AtGAP1 does not activate AtYchF1's ppGpp hydrolyzing activity.
  • Structural analysis reveals ppGpp binding alters AtYchF1 conformation, potentially hindering hydrolysis at His136 and affecting interactions with other molecules like 26S rRNA.

Conclusions:

  • AtYchF1 directly interacts with and hydrolyzes ppGpp, suggesting a novel regulatory role.
  • The binding of ppGpp modulates AtYchF1's activity and interactions, impacting nucleotide signaling pathways.
  • Findings suggest conserved YchF proteins may play a role in regulating ppGpp levels across different species.