A Repetitive DNA Element Regulates Expression of the Helicobacter pylori Sialic Acid Binding Adhesin by a Rheostat-like Mechanism
Figure 6
The T-tract length affects the local DNA structure of the sabA promoter.
A) In silico DNA structure predictions of the PsabA (−166 to +74) harboring different repeat tract lengths and nucleotide compositions, using the AA Wedge model (http://www.lfd.uci.edu/~gohlke/dnacurve/). The analyzed DNA fragments contain T9-, T13-, T18- or A13-tracts. The structures shown represent the 3D DNA helix backbone, displayed in three dimensions. B) Gel migration of DNA fragments containing the PsabA with different repeat tract lengths and compositions. The DNA samples, same set as in Fig. 6A, were run at 4°C in a Tris-Glycine 4.5% polyacrylamide gel that was stained with GelRed. The DNA size marker (bp) is shown to the left. C) Alignment of PsabA DNA fragments analyzed as pdb structures in the Protean 3D software (Lasergene, DNASTAR). The T-tract was extended by 1 thymine (T) at a time (from 13 to 18), and predictions were made as in Fig. 6A. The image shows one view from a selected angle, with the T-tract marked in black and by an arrow. The different T-variants are labeled in shades of gray, see Fig. 6D. D) A 1D plot of the shape of the PsabA DNA helix, visualized in the y orientation (left diagram) and in the z orientation (right diagram). The coordinates were generated from the predictions in Fig. 6C. The black arrows mark the position of the T-tract in the DNA helix.