UvrA first recognizes the lesion-induced conformational change in the DNA and hands off the damage to UvrB for verification. It has been proposed that one monomer of UvrA can interact with Mfd, whereas the other monomer engages UvrB. Single-molecule studies have shown that the UvrAB complex searches for DNA damage using both 3D and 1D sliding on DNA ( 8). This process exposes Mfd’s UvrB homology domain, which is believed to attract UvrA to the damaged site. Mfd undergoes a large conformational change during its handling of stalled RNAP. Mfd is a multidomain protein that shares a protein fold with UvrB and this motif is responsible for the interaction face with UvrA. Once the stalled RNAP has been removed from the damage site, Mfd or UvrD are thought to recruit the UvrAB complex (made up of a UvrA dimer and one or two UvrB molecules) to the site of the damage. ( 7) in PNAS, Nigel Savery’s group at the University of Bristol have found that the Mfd protein that normally accompanies the translocating RNAP can be sent ahead of a blocked RNAP to scout for damage in the transcribed strand and facilitate the recruitment of the bacterial NER machinery.ĭuring the past 15 y structural biologists and biochemists have described in wonderful detail how bacterial NER proteins process and remove DNA damage (reviewed in ref. However, nature has gone even further in devising ways to find and remove potentially RNAP-blocking DNA damage. As described below, Mfd targets the nucleotide excision repair system to sites of damage through its direct interaction with a stalled RNAP. This second approach more closely resembles what is thought to occur in mammalian cells during TCR ( 6). 4), whereas in a newly discovered alternative pathway UvrD (helicase II) tows the RNAP backward (upstream) with the help of the transcription elongation factor, NusA ( 5). The Mfd (mutation frequency decline) protein, also called transcription-repair coupling factor, uses its helicase fold and ATP hydrolysis to literally push RNAP forward (downstream) past the damaged site ( Fig. In bacteria, two different TCR pathways have emerged involving two different DNA helicases, which help to displace RNAP. Thus, the repair “coupling factors,” which recognize the stalled RNAP, must work to both displace the polymerase and simultaneously enlist the repair proteins to remove the damage. However, before DNA repair enzymes obtain access, the stalled RNAP must be pushed away from the lesion by the action of DNA translocases. This latter pathway, called transcription-coupled repair (TCR), first reported in mammalian cells and then in bacteria, is initiated when RNA polymerase (RNAP) is arrested at a DNA lesion embedded in the transcribed strand ( 2, 3). NER is initiated in two general ways: by damage recognition proteins that survey the entire genome for damage or lesion-induced transcriptional stalling. These and other helix-distorting lesions are removed by a highly conserved process called nucleotide excision repair (NER) that is found in every kingdom of life ( 1). Common forms of DNA damage found in nature include cyclobutane pyrimidine dimers and 6-4 photoproducts induced by UV-irradiation. A cell’s genome is under constant threat of damage, which if not repaired can lead to mutations or cell death.
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