Fig. 7: Model for transcriptional silencing in cluster A mycobacteriophages.

a The Mycobacterium smegmatis RNA polymerase (PDB 5VI5) is colored as follows: α subunits: pink, β subunit: gray, β′ subunit: cyan, ω subunit: dark purple, σ^A subunit: red, and RNA polymerase-binding protein RBPA: black. The TipsytheTRex repressor is shown in surface view and colored as in Fig. 1a, and it has been rotated forward by ∼90° relative to the orientation observed in Fig. 1. All nucleic acid in the figure is colored green, and the direction of transcription is indicated with an arrow. The repressor may inhibit transcription elongation by either serving as a steric block or by halting the polymerase via protein:protein interactions. b Zoomed in view showing the position of the RNA polymerase β′ insert (colored cyan) relative to the C-terminal region of the Stoperator domain of the repressor (colored orange). The remaining regions of the RNA polymerase are colored in gray for clarity. c Same view as in panel b but with electrostatic potentials shown (red: negative potential, blue: positive potential, white: neutral) for the RNA polymerase β′ insert and C-terminal region of the Stoperator domain of the repressor. Circles are drawn around areas of positive and negative charge for the β′ insert and C-terminal region of the repressor, respectively.