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RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation.

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The bacterial transcription factor RapA dislodges RNA polymerase (RNAP) from DNA post-termination, preventing harmful R-loop formation and maintaining genome stability. This ATPase activity is crucial for controlling transcriptional noise.

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Area of Science:

  • Bacterial transcription
  • Genome stability
  • Molecular mechanisms of DNA-protein interactions

Background:

  • Escherichia coli RNA polymerase (RNAP) can remain bound to DNA after transcription termination, forming a post-termination complex (PTC).
  • The SWI2/SNF2 ATPase RapA is responsible for removing RNAPs from DNA in PTCs.

Purpose of the Study:

  • To determine the structural basis of PTCs and RapA's interaction with them.
  • To elucidate the mechanism by which RapA dislodges RNAP from DNA.
  • To investigate RapA's role in preventing R-loop formation in vivo.

Main Methods:

  • Determination of post-termination complex structures on negatively supercoiled DNA with and without RapA.
  • Biochemical assays to observe RapA-mediated disruption of PTCs.
  • In vivo studies to assess RapA's role in controlling R-loop formation.

Main Results:

  • Core RNAP in PTCs can unwind DNA and initiate RNA synthesis, leading to R-loop formation.
  • Nucleotide binding to RapA induces a conformational change that opens the RNAP clamp, facilitating DNA reannealing and dissociation.
  • RapA was shown to control cytotoxic R-loop formation in vivo, likely by disrupting PTCs.

Conclusions:

  • RapA dislodges RNAP from post-termination complexes by inducing conformational changes that promote DNA reannealing.
  • RapA plays a critical role in preventing R-loop formation, thereby maintaining bacterial genome stability.
  • Analogous ATPases may commonly act on PTCs to suppress transcriptional noise and R-loop formation across bacteria.