This proposal outlines a plan to investigate the mechanism of assembly of E. coli ribosomes both in vitro and in vivo. The ribosome is the macromolecular machine responsible fbr all protein synthesis in cells, and it is efficiently assembled from over 50 components. Using a combination of biophysical methods, we will Investigate the order of events in assembly and the kinetics of assembly in vitro. We will examine the role of assembly cofactors in E. coli, and examine the effects of antibiotics on the assembly process. We have developed a novel isotope pulse-chase assay that enables measurement of binding kinetics for ribosomal proteins using mass spectrometry. We are developing a two-photon fluorescence correlation microscope to monitor the assembly of fluorescently labeled ribosomal proteins in real time. Finally, we are extending our mass spectrometry analysis to isotope pulse experiments in living bacteria, which allows us to directly monitor the biogenesis of ribosomes. Taken together, these studies will provide new mechanistic insights into the critical process of ribosome assembly.

Public Health Relevance

The assembly of ribosomes is essential for protein synthesis In all cells. The proposed studies will help elucidate the understanding of ribosome biogenesis in bacteria. Resulting insights may lead to novel anti-infective strategies.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
5R37GM053757-19
Application #
8617281
Study Section
Special Emphasis Panel (NSS)
Program Officer
Flicker, Paula F
Project Start
1996-02-01
Project End
2018-01-31
Budget Start
2014-02-01
Budget End
2015-01-31
Support Year
19
Fiscal Year
2014
Total Cost
$419,542
Indirect Cost
$198,148
Name
Scripps Research Institute
Department
Type
DUNS #
781613492
City
La Jolla
State
CA
Country
United States
Zip Code
92037
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Davis, Joseph H; Tan, Yong Zi; Carragher, Bridget et al. (2016) Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell 167:1610-1622.e15
Earnest, Tyler M; Lai, Jonathan; Chen, Ke et al. (2015) Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly. Biophys J 109:1117-35
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Popova, Anna M; Williamson, James R (2014) Quantitative analysis of rRNA modifications using stable isotope labeling and mass spectrometry. J Am Chem Soc 136:2058-69
Stokes, Jonathan M; Davis, Joseph H; Mangat, Chand S et al. (2014) Discovery of a small molecule that inhibits bacterial ribosome biogenesis. Elife 3:e03574
Sashital, Dipali G; Greeman, Candacia A; Lyumkis, Dmitry et al. (2014) A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. Elife 3:
Ban, Nenad; Beckmann, Roland; Cate, Jamie H D et al. (2014) A new system for naming ribosomal proteins. Curr Opin Struct Biol 24:165-9
Gulati, Megha; Jain, Nikhil; Davis, Joseph H et al. (2014) Functional interaction between ribosomal protein L6 and RbgA during ribosome assembly. PLoS Genet 10:e1004694
Jomaa, Ahmad; Jain, Nikhil; Davis, Joseph H et al. (2014) Functional domains of the 50S subunit mature late in the assembly process. Nucleic Acids Res 42:3419-35

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