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Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators.

Jin Young Kang1, Rachel Anne Mooney2, Yuri Nedialkov3

  • 1The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.

Cell
|June 12, 2018
PubMed
Summary

The universally conserved NusG and RfaH proteins regulate bacterial transcription by stabilizing RNA polymerase elongation complexes. Structural studies reveal how they prevent backtracking and how RfaH specifically targets operon polarity suppressor sites.

Keywords:
Spt5nontemplate DNAtranscription elongationtranscription pausing

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Genetics

Background:

  • NusG, RfaH, and Spt5 are essential transcription elongation factors conserved across all domains of life.
  • Bacterial NusG enhances RNA polymerase (RNAP) elongation by preventing backtracking and coordinating termination/translation.
  • RfaH, a NusG paralog, specifically acts at operon polarity suppressor (ops) sites to prevent pausing.

Purpose of the Study:

  • To elucidate the structural mechanisms by which NusG and RfaH regulate RNAP elongation complexes (ECs).
  • To understand how RfaH confers specificity to ops sites and suppresses pausing.
  • To provide insights into the conserved function of NusG/RfaH/Spt5 family proteins.

Main Methods:

  • Single-particle cryoelectron microscopy (cryo-EM) was employed to determine high-resolution structures.
  • Structures of ECs interacting with NusG or RfaH at ops sites were solved.
  • Comparative structural analysis was performed to understand differential factor binding and function.

Main Results:

  • Both NusG and RfaH stabilize ECs by promoting base-pairing of upstream DNA, suppressing backtracking.
  • The RfaH-opsEC structure reveals specific recognition of ops hairpins and tighter EC binding compared to NusG.
  • RfaH binding sterically hinders the RNAP conformation required for hairpin-induced pausing.

Conclusions:

  • NusG and RfaH share a common mechanism of suppressing backtracking via DNA chaperoning.
  • RfaH possesses unique features for ops site recognition and enhanced EC stabilization, excluding NusG.
  • The uncovered mechanisms highlight the conserved and specialized roles of these fundamental transcription regulators.