Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7

Bacteriophage T7 infects Escherichia coli and evades the host restriction/modification system. The Ocr protein of T7 was shown to exist as a dimer mimicking DNA and to bind to host restriction enzymes, thus preventing the degradation of the viral genome by the host. Here we report that Ocr can also inhibit host transcription by directly binding to bacterial RNA polymerase (RNAP) and competing with the recruitment of RNAP by sigma factors. Using cryo electron microscopy, we determined the structures of Ocr bound to RNAP. The structures show that an Ocr dimer binds to RNAP in the cleft, where key regions of sigma bind and where DNA resides during transcription synthesis, thus providing a structural basis for the transcription inhibition. Our results reveal the versatility of Ocr in interfering with host systems and suggest possible strategies that could be exploited in adopting DNA mimicry as a basis for forming novel antibiotics.Bacteria and viruses have long been fighting amongst themselves. Bacteriophages are a type of virus that invade bacteria; their name literally means ‘bacteria eater’. The bacteriophage T7, for example, infects the common bacteria known as Escherichia coli. Once inside, the virus hijacks the bacterium’s cellular machinery, using it to replicate its own genetic material and make more copies of the virus so it can spread. At the same time, the bacteria have found ways to try and defend themselves, which in turn has led some bacteriophages to develop countermeasures to overcome those defences. Many bacteria, for example, have restriction enzymes which recognise certain sections of the bacteriophage DNA and cut it into fragments. However, the T7 bacteriophage has one well-known protein called Ocr which inhibits restriction enzymes. Ocr does this by mimicking DNA, which led Ye et al. to wonder if it could also interrupt other vital processes in a bacterial cell that involve DNA. Transcription is the first step in a coordinated process that turns the genetic information stored in a cell’s DNA into useful proteins. An enzyme called RNA polymerase decodes the DNA sequence into a go-between molecule called messenger RNA, and it was here that Ye et al. thought Ocr might jump in to interfere. To begin, Ye et al. examined the structure of Ocr when it binds to RNA polymerase using an imaging technique called cryo-electron microscopy. Ocr has been well-studied before, its structure previously described, but not when attached to RNA polymerase. The analysis showed that Ocr gets in the way of specific molecules, called sigma factors, that show RNA polymerase where to start transcription. Ocr binds to RNA polymerase in exactly the same pocket as part of sigma factors do, which is also the place where DNA must be to be decoded to make messenger RNA. Ye et al. then performed experiments to show Ocr interfering with binding to RNA polymerase did indeed disrupt transcription. This means Ocr is quite versatile as it interferes with the RNA polymerase of the bacterial host and its restriction enzymes. Ocr’s strategy of mimicking DNA to interrupt transcription could be adopted as an approach to develop new antibiotics to stop bacterial infections. DNA transcription is an essential cellular process – without it, no cell can replicate and survive – and RNA polymerase is already a validated target for drugs. Following Ocr’s lead could provide a new way to stop infections, if the right drug can be designed to fit.