Proteins barge in to turn off unneeded genes

September 6, 2012 by Bill Steele, Cornell University
A few Angstroms make all the difference. The CueR protein binds to DNA at the start of a gene that protects against copper poisoning. When copper atoms bind to CueR, the protein changes shape just enough to twist the DNA - such a small distance that it can't be drawn in two dimensions - to turn on transcription of the gene. When the gene is no longer needed, the original form of CueR unceremoniously kicks the copper-bound form away, turning off transcription quickly to save energy.

(—The sorcerer's apprentice started a water-carrying system, but couldn't stop it, and soon he was up to his neck in water, and trouble. Living cells have a better design: When they activate a gene, they have a system in reserve to turn it off. The cell does not want to waste energy making proteins it no longer needs. Cornell researchers have identified two mechanisms cells use and found they are designed to be quick.

Peng Chen, associate professor of chemistry and , and colleagues report the discovery in the online edition of the Proceedings of the National Academy of Sciences Sept. 4. "The generic is for the activator to fall off, then the repressor binds," Chen said. "What we have found is two pathways that are much more efficient."

The work was done in bacteria and could lead to new ways to kill , Chen said. It also represents a step forward in understanding regulation that could apply further up the evolutionary ladder.

The involved take place on the scale of single molecules, far too small to observe through a microscope. To monitor these processes, the researchers tagged proteins and sites with molecules that fluoresce and change their fluorescence intensity when they meet, so that a flash of light appears or changes when a takes place. The fluorescence change is triggered by a rearrangement of as the tagging molecules come together, beginning when they are near (a matter of nanometers) and becoming brighter as they close in. By tagging one end of a , the researchers can tell by the brightness of the signal which orientation the protein takes in binding to DNA.

The researchers worked with bacteria for which copper is toxic. These bacteria possess genes that code for a protein that grabs and shoves them out through the cell wall. Ordinarily a protein called CueR binds to the chromosome in front of the sites of these genes and distorts the DNA, preventing the gene from being transcribed. When copper atoms bind to CueR it changes its configuration, allowing enzymes to transcribe the genes to make the protective proteins.

When the copper threat is gone another form of CueR, circulating in solution in the cell, replaces the copper-modified form, turning off the gene. By watching and timing the reactions, the Cornell researchers determined that the turnoff protein either shoves the bound protein out of the way or "assists" it in detaching and then moves into the vacant space. These mechanisms are up to 70 times faster than waiting for the activator to go away on its own, the research showed. It is likely that bacteria use similar methods for turning off protection against other toxic metals, they said.

The study also showed that the CueR protein can bind to the DNA in two different orientations and can spontaneously flip between them without completely detaching. In one orientation it binds only at the specific gene it is supposed to control. In the other it attaches nonspecifically to DNA. The researchers suggest that this may make it easier for the protein to get to where it's needed quickly, by attaching to the DNA strand and sliding along until it finds the specific site, then flipping into working mode.

The research was supported primarily by the National Institutes of Health and partly by the National Science Foundation.

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