In previous work, Sello and Davis identified a cluster of genes in Streptomyces bacteria that encode enzymes for breaking down a lignin-derived compound called protocatechuate. Under normal circumstances, those genes were inactive essentially switched off. Only when bacteria were grown in a medium containing protocatechuate did the genes switch on and produce the appropriate enzymes. In an effort to understand this phenomenon, Sello and Davis discovered that a transcription factor a kind of protein that attaches itself to DNA called PcaV was involved in switching the genes on and off. The next step, and the focus of this new research, was figuring out how PcaV controls gene expression.
Sello and Davis proposed a model for how it might work. They proposed that PcaV probably binds to DNA in a way that physically prevents the transcription of the lignin-degrading genes, turning them off. In order to explain how the genes are switched on in the presence of protocatechuate, they proposed that the compound might compromise the ability of PcaV to bind to DNA, which would expose the genes and allow them to be expressed.
A series of experiments provided support for their model. In a test tube, the researchers established that PcaV tightly binds to specific DNA sequences in close proximity to the gene cluster in question, validating the first half of the model. To confirm the second half, Sello and his colleagues exposed the PcaV-DNA complex to protocatechuate. They found that PcaV loses its affinity for DNA in the presence of the compound.
"So we can say that protocatechuate attenuates the DNA binding activity of the PcaV protein, which permits expression of the genes," Sello said. "We now have evidence that validates our model."
Sello and his colleagues then dug down into the process a little further. Using a technique called pro
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