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Biological Chemistry

Understanding Of Bacterial Protein’s Defense Strategy Could Lead To Antibiotics

Mechanistic Studies: Two research teams unveil how the transcription factor CueR helps regulate copper levels in bacteria

by Stu Borman
October 20, 2015 | A version of this story appeared in Volume 93, Issue 42

Apo-CueR Mechanism.
Credit: Adapted from PNAS
Apo-CueR (blue), which has no bound copper, promotes formation of a “dead-end” complex, which stops RNA polymerase from transcribing the bacterial gene copA. Holo-CueR (red), which has copper bound, aids transcription by first forming a nonworking “closed” intermediate with the copA promoter and RNA polymerase, followed quickly by formation of an “open” complex.

Bacteria have evolved molecular strategies for regulating the export of toxic metals from their innards. Two independent studies now pinpoint the details of one of these strategies, which protects bacteria from toxic copper concentrations. The work could aid the discovery of antibiotics that target this process to compromise bacterial defenses.

The studies provide complementary structural and mechanistic views that reveal how a transcription factor called CueR activates or represses the gene copA, which encodes the CopA protein, a bacterial efflux pump that rids bacterial cells of copper. In August, Alfonso Mondragón, Thomas V. O’Halloran, and coworkers at Northwestern University reported crystal structures that provide atomic-level pictures of the activation and repression processes (Science 2015, DOI: 10.1126/science.aaa9809). And more recently, Peng Chen and coworkers at Cornell University revealed the dynamic molecular mechanisms of the two processes (Proc. Natl. Acad. Sci. USA 2015, DOI: 10.1073/pnas.1515231112).

Both studies provide “an explosion of structural and mechanistic insights that show how CueR actually works,” says David Giedroc of Indiana University, an expert on transcriptional metalloregulatory proteins. The findings, Giedroc adds, are likely general and applicable to the entire family of transcription regulators to which CueR belongs. These regulators, called MerRs, help bacteria defend against oxidative stress and evade antibiotics in addition to removing copper and other metals.

Scientists have known that the promoter region of copA, which is the starting point for gene transcription, has a “suboptimal” sequence that’s two base pairs too long. So when RNA polymerase lands on the promoter to begin transcription, it can’t align its recognition site perfectly with the sequence. The Northwestern team’s crystal structures show how holo-CueR—CueR bound to Cu(I)—activates transcription by kinking and unwinding the promoter, aligning it better with the RNA polymerase recognition site. The researchers’ findings also reveal how apo-CueR—CueR without Cu(I)—represses transcription by bending the promoter in a way that further impairs its ability to engage RNA polymerase productively.

The Cornell researchers revealed details about CueR’s regulatory mechanism by using single-molecule fluorescence resonance energy transfer. The team discovered that holo-CueR drives RNA polymerase to bind to the promoter, forming a nonworking “closed” intermediate that changes quickly to an “open” complex that promotes CopA production. Apo-CueR, in contrast, drives formation of a “dead-end” complex in which the enzyme binds to the promoter in a nonproductive way. The open and dead-end complexes cannot interconvert directly.

Sarah L. J. Michel of the University of Maryland School of Pharmacy, a specialist in metalloregulatory proteins, notes that MerR proteins “sense metals and drugs and turn on efflux pumps to get them out of bacteria. It would be terrific if these new findings could be used to inhibit this interaction.” For example, she asks, “would there be a way to lock in the dead-end conformation, and would that then represent a new route to antibiotic drug design?”


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