Translation of proteins by the ribosome is key aspect of life. Structural studies have provided a three- dimensional view of the 2.5 megaDalton 70S ribosomal particle, and revealed the active sites for decoding of genetic information and peptide bond formation. Mechanistic views have revealed the basic steps of translation: initiation, elongation and termination. However, limited dynamic information about how the translational machinery changes conformation and composition are available. Our research focuses on providing a dynamic view of translation using single-molecule approaches. The current proposal builds on the progress in observing ribosomal dynamics in real time using single- molecule fluorescence approaches. We will monitor the underlying dynamics of translation in four specific aims. First, we will explore the mechanism of initiation, in which the 70S ribosomal particle assembles at the correct start codon;we will use single molecule fluorescence to understand intersubunit joining and dynamics, the role of factors in initiation, and movements of tRNAs, factors and ligands during the process. These experiments will be complemented by single-molecule force measurements to map the energetics of mRNA-ribosome interaction.
In aim 2, we will explore the nature of intersubunit conformational changes that underlie both initiation and elongation. We will determine the nature of the barrier to rotation using both fluorescence and force and explore how factor and tRNA dynamics are correlated to ribosomal motions. We will determine the effects of ribosomal mutations and composition, as well as antibiotics, on conformational dynamics.
In aim 3, we will apply new single-molecule instrumentation to perform single-molecule experiments under high concentrations (50nM-5M) of labeled tRNAs, ribosomes or factors. These experiments harness zero mode waveguides, and will allow us to observe rapid changes in ribosome composition, and correlate conformational changes with each other. Finally, in aim 4, the dynamics of ribosomal translation will be explored during translation to understand codon and mRNA context effects. We will use intersubunit FRET, tRNA colocalization and ribosome mRNA -FRET to determine dynamics effects on model mRNAs, and then use these systems to explore the dynamics of rare recoding events. The results of this project should reveal a dynamic view of translation and continue to provide insights into the mechanism of action of antibiotics.

Public Health Relevance

The ribosome synthesizes proteins in the cell. This proposal aims to provide a molecular movie of how the ribosome performs this task, and how synthesis of proteins might be controlled in the cell. We will use methods of single-molecule biophysics to explore ribosome dynamics.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function C Study Section (MSFC)
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Lewis, Catherine D
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Stanford University
Schools of Medicine
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Noriega, Thomas R; Chen, Jin; Walter, Peter et al. (2014) Real-time observation of signal recognition particle binding to actively translating ribosomes. Elife 3:
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Simonetti, Angelita; Marzi, Stefano; Billas, Isabelle M L et al. (2013) Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor. Proc Natl Acad Sci U S A 110:15656-61
Tsai, Albert; Uemura, Sotaro; Johansson, Magnus et al. (2013) The impact of aminoglycosides on the dynamics of translation elongation. Cell Rep 3:497-508
Chen, Jin; Tsai, Albert; Petrov, Alexey et al. (2012) Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics. J Am Chem Soc 134:5734-7
Masuda, Tomoaki; Petrov, Alexey N; Iizuka, Ryo et al. (2012) Initiation factor 2, tRNA, and 50S subunits cooperatively stabilize mRNAs on the ribosome during initiation. Proc Natl Acad Sci U S A 109:4881-5

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