Unexpected pH-dependent DNA Binding of CooA, a CO-Sensing Transcription Factor from Rhodospirillum rubrum

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CooA, a CO-sensing heme protein, acts as a transcriptional activator of CO metabolizing proteins in Rhodospirillum rubrum and other bacteria through sequence-specific DNA binding. Prior research has indicated that a reduced iron center and CO gas were necessary for CooA to achieve its active conformation and bind DNA. To determine if other reaction conditions facilitate CooA activation, the role of pH on CooA DNA binding was tested. Using a fluorescence anisotropy assay, Fe(III) CooA was observed to bind DNA without the presence of gas under acidic conditions (pH < 7). Specifically, DNA binding was quantified from pH 4 – 10, and optimal binding was observed at approximately pH 4. These results are discussed in light of the normal CO-dependent activation mechanism of CooA proteins.