Modular structure enables TRCF protein to both halt transcription and repair DNA

veryone needs a little push now and then. Even proteins. In new research from Seth Darst’s lab at Rockefeller University, the structure of one of the pushiest proteins in bacteria is finally brought to light.

Among the most stable complexes in a cell is the attachment between DNA and RNA polymerase, an enzyme responsible for reading the genetic information encoded in that DNA. In bacteria, only three known mechanisms can interrupt this complex. One of them involves the Transcription-Repair Coupling Factor (TRCF), a protein that the cell uses to cut short the DNA transcription process when it gets stuck at sites of DNA damage. TRCF binds to both the DNA and the polymerase, and then pushes the polymerase off of the DNA. After clearing the way, TRCF then recruits repair proteins to fix the damaged DNA. These functions of TRCF explain why damaged DNA being actively transcribed by RNA polymerase is repaired much more rapidly than other areas of DNA, a process called transcription-repair coupling.

Using x-ray crystallography, Alexandra Deaconescu, a graduate fellow, has now solved the structure of TRCF — showing that the protein employs a modular structure to allow for conformational changes so that TRCF’s recruitment of the repair machinery doesn’t interfere with its interruption of transcription.

“TRCF does double duty,” says Darst, head of the Laboratory of Molecular Biophysics. “We know that the protein has different domains for the different jobs, one binds to the polymerase and another binds to the repair machinery. But you don’t want both domains to be active at the same time. A conformational change in the protein is definitely needed between these two steps.”

Mammalian cells also have this link between transcription and DNA repair, though the system is more complicated. By studying bacteria, however, scientists hope to learn more about how transcription works in humans. TRCF is part of a superfamily of motor proteins that also includes the vertebrate proteins Swi/Snf, which are important for remodeling packed DNA, opening it up so that proteins can have access. How TRCF does its job should help scientists understand how Swi/Snf proteins work too.

“Having a structure for TRCF provides a framework for the design and interpretation of future experiments,” says Darst. “And it will provide mechanistic insights into how TRCF is able to perform its dual functions.”

Cell 124: 507-520 (February 10, 2006)

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