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Bioinformatics Analysis Reveals PPR Genes Modulation by Ahyp-miR0005 Under Abiotic Stress Across Diverse Plant

Vladimir Flores Benavides1, Ricardo A Chávez Montes2, Flor de Fátima Rosas Cárdenas1

  • 1Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla km 1.5, Tlaxcala 90700, Mexico.

Plants (Basel, Switzerland)
|September 13, 2025
PubMed

Insights

This study identifies Ahyp-miR0005 targets in amaranth, revealing its role in regulating pentatricopeptide repeat (PPR) proteins. Modulating these targets may enhance plant abiotic stress tolerance through retrograde signaling.

Area of Science:

  • Plant molecular biology
  • Gene regulation
  • Abiotic stress response

Background:

  • MicroRNAs (miRNAs) are key regulators of gene expression in plants.
  • Pentatricopeptide repeat (PPR) proteins are crucial for organelle function and retrograde signaling between plastids and the nucleus.
  • Ahyp-miR0005 is an amaranth-specific miRNA predicted to target PPR proteins.

Purpose of the Study:

  • To identify the specific target genes of Ahyp-miR0005 in amaranth.
  • To investigate the association of Ahyp-miR0005 with the PPR protein family across multiple plant species.
  • To explore the role of Ahyp-miR0005 in plant responses to abiotic stress.

Main Methods:

  • Bioinformatic analysis to predict miRNA targets and analyze miRNA binding site distribution.
  • Cleavage inhibition assays to validate miRNA-target interactions.
  • Interaction network analysis and gene expression profiling using the Arabidopsis eFP Browser.

Main Results:

  • Identified GUN-1, ABO5, and MORF1 as key target genes of Ahyp-miR0005.
  • Demonstrated co-expression of target genes under stress conditions.
  • Observed significant transcriptional changes in predicted targets under six abiotic stress conditions.
  • Showed that abiotic stresses modulate the expression of Ahyp-miR0005 target genes in amaranth.

Conclusions:

  • Ahyp-miR0005 regulates PPR proteins involved in retrograde signaling between plastids and the nucleus.
  • Modulating Ahyp-miR0005 expression could potentially enhance plant abiotic stress tolerance.
  • This miRNA-target interaction offers a novel strategy for improving crop resilience to environmental challenges.
Keywords:
PPR proteinsabiotic stressamaranthmiRNA spongemiRNAs

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