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Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain

Figure 1

MarA logo and structure.

The height of each letter in the sequence logo is proportional to the frequency of that base at that position. The height of the stack at each position is the information content [39]. The sine wave on the logo has the same helical twist as B-form DNA (10.6 bp) [32] and its position was assigned based on the MarA-DNA cocrystal structure [28]. The structure of E. coli MarA is positioned above the logo to show which bases each helix specifically binds [28]. Three residues in helix 3 (red helix on the structure) specifically contact DNA bases. Arrows show which bases these residues specify. We randomized these three residues and selected for variants that had altered affinity. Binding domain selections (BD select), MITOMI experiments, and in vivo binding site selections (BS select) were performed with variants of the mar MarA binding site. A red ‘N’ specifies bases that were varied for each experiment. For binding site and binding domain selections, these variants were cloned into the selection plasmid in the MarA binding site (Figure 2B). The information content for this logo is 12.60.9 bits.

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1002614.g001