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Decoding sequence-structure-function-evolution of basic leucine zippers of aureochromes from heterokont algae.

Madhurima Khamaru1, Debarshi Bose1, Anwesha Deb1

  • 1Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073 WB, India.

Journal of Structural Biology
|December 30, 2025
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Summary

Aureochromes (Aureos), unique blue light photoreceptors, possess distinct bZIP domains crucial for DNA binding. Their unique histidine residue enhances DNA binding and offers insights into transcription factor evolution.

Keywords:
All-atom networkAureochromeBasic leucine zipperEctocarpus siliculosusElectrophoretic mobility shift assay (EMSA)Molecular Dynamics SimulationOptogeneticsPhotosynthetic stramenopilesPhylogeny and (co)evolutionProtein-DNA interaction

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Area of Science:

  • Molecular Biology
  • Structural Bioinformatics
  • Evolutionary Biology

Background:

  • Aureochromes (Aureos) are blue light photoreceptors and transcription factors found exclusively in photosynthetic stramenopiles.
  • Their unique combination of Light-Oxygen-Voltage (LOV) and basic leucine zipper (bZIP) domains makes them ideal for studying light-dependent transcriptional regulation.
  • Aureos' inverse effector-sensor topology presents them as potential optogenetic tools.

Purpose of the Study:

  • To investigate the bZIP domains of Aureos and their interaction with DNA.
  • To compare Aureo bZIPs with plant and opisthokont bZIPs to understand their uniqueness and evolutionary significance.
  • To explore the role of hydrophobic interactions and specific amino acid residues in DNA binding and dimer stability.

Main Methods:

  • Sequence and structural bioinformatics analysis.
  • Network theory and all-atom molecular dynamics simulations.
  • In vitro experiments.

Main Results:

  • Aureos exhibit unique characteristics in DNA binding specificity and dimer stability compared to other bZIPs.
  • Hydrophobic interactions in the zipper region are critical for stabilizing bZIP dimers and facilitating DNA binding.
  • Aureos uniquely possess histidine in their basic region, enhancing DNA binding affinity independently of blue light.

Conclusions:

  • Aureos' bZIP domains possess unique structural and functional properties.
  • Histidine in the Aureo bZIP basic region is a key feature for DNA binding and may represent an evolutionary innovation.
  • These findings advance our understanding of light-dependent gene regulation and provide a basis for optogenetic applications.