Structural and mechanistic basis of anti-termination of Rho-dependent transcription termination by bacteriophage P4 capsid protein Psu

Nucleic Acids Res. 2013 Aug;41(14):6839-56. doi: 10.1093/nar/gkt336. Epub 2013 May 22.

Abstract

The conserved bacterial transcription terminator, Rho, is a potent target for bactericidal agents. Psu, a bacteriophage P4 capsid protein, is capable of inducing anti-termination to the Rho-dependent transcription termination. Knowledge of structural and mechanistic basis of this anti-termination is required to design peptide-inhibitor(s) of Rho from Psu. Using suppressor genetics, cross-linking, protein foot-printing and FRET analyses, we describe a conserved disordered structure, encompassing 139-153 amino acids of Rho, as the primary docking site for Psu. Also a neighbouring helical structure, comprising 347-354 amino acids, lining its central channel, plays a supportive role in the Rho-Psu complex formation. Based on the crystal structure of Psu, its conformation in the capsid of the P4 phage, and its interacting regions on Rho, we build an energy-minimized structural model of the Rho:Psu complex. In this model, a V-shaped dimer of Psu interacts with the two diagonally opposite subunits of a hexameric Rho, enabling Psu to form a 'lid' on the central channel of the latter. We show that this configuration of Psu makes the central channel of Rho inaccessible, and it causes a mechanical impediment to its translocase activity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / antagonists & inhibitors
  • Capsid Proteins / antagonists & inhibitors
  • Capsid Proteins / chemistry*
  • Capsid Proteins / genetics
  • Cross-Linking Reagents
  • Cysteine / chemistry
  • Edetic Acid / analogs & derivatives
  • Edetic Acid / chemistry
  • Fluorescence Resonance Energy Transfer
  • Models, Molecular
  • Mutation
  • Protein Footprinting
  • Rho Factor / chemistry*
  • Rho Factor / genetics
  • Rho Factor / metabolism
  • Transcription Termination, Genetic*

Substances

  • Capsid Proteins
  • Cross-Linking Reagents
  • Rho Factor
  • polarity suppression factor, bacteriophage P4
  • 1-(4-bromoacetamidobenzyl)EDTA
  • Edetic Acid
  • Adenosine Triphosphatases
  • Cysteine