Year of Award

2009

Document Type

Thesis

Degree Type

Master of Science (MS)

Other Degree Name/Area of Focus

Biomolecular Structure & Dynamics

Department or School/College

Division of Biological Sciences

Committee Chair

Walter E. Hill

Commitee Members

David Poulsen, J. Stephen Lodmell

Keywords

16S rRNA, 30S assembly, dynamics, ribosome, S17

Abstract

Living cells are dependent upon protein synthesis for virtually all cellular functions. The cellular machine responsible for protein synthesis, called the ribosome, is formed through the association of two unequally sized subunits, each composed of RNA and proteins. Proper assembly of each subunit is essential to ribosome function and therefore essential to the cellular life cycle. Previous studies focused on dissecting the assembly of the small ribosomal subunit (30S subunit) from E. coli have shown that 21 proteins sequentially assemble on the 16S rRNA at multiple nucleation sites. For the first time, we are able to monitor changes in the secondary and tertiary structure of the 16S rRNA upon the addition of single proteins during assembly by using time-dependent chemical probing. Results from these studies suggest that protein S17 induces multiple structural changes in 16S rRNA by first binding to helix 11 and then helix 7. S20 also induces changes in the rRNA by interacting with helix 9, 11, 44 and 13 in that order. These structural formations and rearrangements then prepare the binding sites for additional proteins (S12 and S16, respectively). This study demonstrates that time-dependent chemical probing is able to monitor the assembly of the 30S subunit at a level of detail never before seen. These studies also suggest that many motifs in the 16S rRNA structure are formed as a result of the proteins binding, lending evidence to the hypothesis that the function of ribosomal proteins is to shape and/or hold the RNA structure in place.

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© Copyright 2009 Christopher James Woolstenhulme