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Non-coding RNA mediates the defense-associated reverse transcriptase (DRT) anti-phage oligomerization transition.

Jie Han1,2,3, Bin Liu1,2, Jingjing Tang4,5

  • 1Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), State Key Laboratory of Experimental Hematology, Tianjin Medical University Cancer Institute and Hospital, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.

The EMBO Journal
|August 20, 2025
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Summary

Defense-associated reverse transcriptase (DRT) systems provide prokaryotic antiviral defense. This study reveals the DRT9 system

Keywords:
Bacterial Antiviral DefenseDRT9Non-coding RNAProtein-Primed cDNA SynthesisReverse Transcriptase

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Area of Science:

  • Molecular Biology
  • Microbiology
  • Structural Biology

Background:

  • Defense-associated reverse transcriptase (DRT) systems are crucial for prokaryotic defense against viral infections.
  • The precise molecular mechanisms of DRT systems, particularly their structural dynamics and activation processes, remain largely uncharacterized.
  • Understanding these systems is vital for deciphering microbial immunity and developing novel antiviral strategies.

Purpose of the Study:

  • To elucidate the molecular mechanisms and structural basis of the two-component DRT9 system's antiviral activity.
  • To characterize the role of non-coding RNA (ncRNA) in DRT9 system assembly and activation.
  • To investigate the structural transitions and enzymatic activation of DRT9 reverse transcriptase (RT) upon substrate binding.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) to determine high-resolution structures of DRT9 in various functional states.
  • Biochemical assays to analyze protein-primed DNA synthesis activity and substrate binding.
  • Phylogenetic analysis and functional assays to identify key protein domains and their roles.

Main Results:

  • The DRT9 system comprises a reverse transcriptase (RT) and a non-coding RNA (ncRNA), exhibiting protein-primed DNA synthesis upon phage infection.
  • Cryo-EM structures revealed DRT9 RT forms a dimer of dimers with ncRNA, transitioning to a trimer of dimers upon substrate binding.
  • ncRNA facilitates cooperative self-assembly, and substrate binding induces conformational changes via a "lock-switch" mechanism for enzymatic activation.
  • A unique N-terminal helix extension was identified as essential for ncRNA stabilization and enzymatic activity, distinguishing DRT9 from other RT systems.

Conclusions:

  • The DRT9 system employs a unique ncRNA-mediated oligomerization and conformational switching mechanism for antiviral defense.
  • The identified N-terminal helix extension is critical for DRT9 function, highlighting novel aspects of reverse transcriptase activity.
  • This study expands the known functional and mechanistic diversity of DRT systems, offering insights into microbial antiviral strategies.