Transitions: Mechanistic insights into ribosome rescue and quality control in the Archaea

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Cells use a process called translation to synthesize proteins according to the code in an mRNA molecule. Mistakes in translating the code can cause many deleterious effects. Ribosomes are the cellular nanomachines that translate the mRNA code and synthesize proteins. Ribosomes are in constant use and must be reused many times and there are two processes necessary for this reuse. First, after translation of one mRNA concludes, there is an active process called ribosome recycling that separates the ribosome from the mRNA so that it can be reused. Second, sometimes ribosomes stall or even collide during translation and cannot restart on their own; again in this case there is an active process that separates the mRNA from the disrupted ribosomes so that the ribosomes can be reused. This research project will investigate how the least-understood domain of life, known as the archaea, accomplish ribosome rescue and recycling. The project will also provide training for graduate students and include high school students from the Baltimore City public schools in the research.To do the scientific investigations, the research team will use Haloferax volcanii, a halophilic archaeon that is amenable to genetic and biochemical investigation. In aim 1, the researchers will identify protein factors that recognize stalled ribosomes and promote ribosome splitting activity in archaea. They will use genetic and biochemical approaches to discover novel factors that are currently unknown in the archaea. In aim 2, the researchers will determine the landscape of ribosome collisions in archaea. Ribosome collisions result in ribosome dimers called disomes; deep-sequencing of disome-protected fragments will provide a genome-wide characterization of collision motifs and the ability to test the role of novel factors of interest in ribosome rescue, in vivo. In aim 3, the researchers will identify the mechanisms for proteolytic targeting of polypeptides produced by stalled ribosomes. These experiments will provide first knowledge of Ribosome-associated Quality Control (RQC) pathways in archaea.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.