Rescue and repair of stalled ribosome damaged by ribosome-specific ribotoxins

Project Summary/Abstract In biology, there are two fundamental conflicts: the conflicts between organisms and the conflicts between organisms and viruses. During the conflicts, a variety of offensive and defensive weaponry are employed by organisms and viruses. While the molecular mechanisms of the conflicts between organisms and viruses have been extensively studied, significantly less have been carried out with the conflicts between organisms. During the conflicts between organisms, protein toxins are frequently employed as the offensive weapons. Among them, ribotoxins constitutes one of the biggest groups. In fact, colicin E3 was the first ribotoxin to be characterized 50 years ago. It makes a single but precise cut of 16S rRNA in the decoding center of bacterial ribosome, resulting in stalled ribosome and eventual cell death. Over the last half of a century, it is unclear whether there exists a biological system that is able to reverse the ribosomal damage by colicin E3 to allow cell to survive. Employing approaches of bioinformatics, biochemistry, structural biology, and microbiology, we have uncovered a bacterial two-component system, RtcB and PrfH, as the antidote of colicin E3. Specifically, bacterial PrfH recognizes the damaged and stalled ribosome and performs ribosomal rescue. This is followed by RtcB repairing the damaged 30S ribosomal subunit. The sequential events described above are supported by abundant preliminary data from both our in vitro and in vivo studies. In this application, we plan to significantly expand our preliminary studies to systematically characterize the rescue and repair of bacterial ribosome with specific damage in the decoding center with the following three main aims: 1) We will provide insight into bacterial PrfH recognizing and rescuing the damaged and stalled 70S ribosome in vitro; 2) We will biochemically and structurally characterize bacterial RtcB in vitro, with the emphasis of PrfH-coupled RtcB repairing the damaged 30S ribosomal subunit; and 3) We will elucidate in vivo biological functions of RtcB-PrfH using an in vivo attenuated RNA damage system we have developed.