Washington University in St. Louis
Campus Box 1137
One Brookings Drive
St. Louis, MO 63130-4899
DBBS graduate programs Biochemistry Program
Plant and Microbial Biosciences Program
Molecular Cell Biology Program
Computational and Molecular Biophysics Program
Organismal growth and viability is dependent on the faithful decoding of genomic information into functional protein sequences. The overall fidelity of protein synthesis appears to be limited by the action of the ribosome, which is the biological machine responsible for the decoding of the messenger RNA into protein in all domains of life. In addition to careful substrate selection, the ribosome retrospectively monitors the quality of the just completed step by examining the tRNA-mRNA interaction in the P site to prematurely terminate protein synthesis if mistakes are detected. This latter retrospective editing mechanism depends on the class II release factor 3 (RF3). The long-term goal of my laboratory is to expand our understanding of the mechanisms that govern translational fidelity, and their impact on cellular fitness and codon evolution.
Our immediate goal is to find out how the signal is communicated from a perturbed mRNA-tRNA interaction in the P site to the A site. We are also interested in how the activity of release factors is modulated on sense codons in the presence of a perturbed mRNA-tRNA interaction, and the structural cues that are responsible for this activity. These related goals are built around pre-steady state kinetics approaches in the context of mutated translation components, and low-resolution structural probing techniques. On a different front, we are interested in exploring the effects of translational fidelity on the overall gene expression and regulation at the elongation step through the use of proteomic, genomic and bioinformatic tools.
By discovering specific protein products that are potentially regulated by premature termination, key information about gene regulation and its relation to codon bias rules is likely to be delineated. Finally, we plan to characterize the editing mechanism in eukaryotes. Our preliminary data indicate that the mechanism involves novel factors that are yet to be identified. We plan to take unbiased approaches to identify these factors and characterize them in vivo as well as in an in vitro reconstituted system.
Collectively, these planned studies are key in understanding the fundamental process of decoding by the ribosome and its effect on gene regulation. Furthermore, recently there has been much interest and discussion about the selection pressure imposed by the ribosome on gene evolution; our research program is likely to contribute to understanding of this relationship and experimentally substantiate some of the theoretical discussions
Zaher, H. S. and Unrau, P. J. (2007). “Selection of an improved RNA polymerase ribozyme with superior extension and fidelity”. RNA, 13(7):1017-26.
Zaher, H. S. and Green, R. (2009). “Quality control on the ribosome following peptide bond formation”. Nature, 457(7226): 161-166.
Zaher, H. S. and Green, R. (2009). “Fidelity at the molecular level: lessons from protein synthesis”. Cell, 136(4): 746-762. (review)
Zaher H. S., Green R. (2010). “Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection”. Mol. Cell, 39(1):110-120.
Zaher, H. S., Shaw, J. J., Strobel, S. A. and Green, R. (2011). “The 2'-OH group of the peptidyl-tRNA stabilizes an active conformation of the ribosomal PTC”. EMBO J, 30(12):2445-53.
Zaher, H. S. and Green, R. (2011). “A primary role for release factor 3 in quality control during translation elongation in Escherichia coli”. Cell, 147(2):396-408.