Introduction 5

Introduction

Previous studies have located GTPases in a diverse array of bacteria and in all eukaryotes. GTPases are characterised by their use of GTP instead of ATP as a substrate. They are known to regulate many fundamental cellular processes such as translation, cell-signalling, intracellular trafficking and cytoskeletal re-organisation. The NKxD and Walker B motifs of GTPases specify the utilisation of GTP. 1pujA is a known Ylqf GTPase of Bacillus subtilis (Matsuo, Y et. al. 2006). B. Subtilis is a gram positive, catalase positive bacterium commonly found in soil. B. Subtilis has also been reffered to as Bacillus globigii, Hay bacillus or Grass bacillus (Wiki 2007). YlqF has previously been associated with the assembly of the 50S ribosomal subunit. B. subtillus cells in which YlqF activity was inhibited showed slow growth rates and a build up of mis-folded 50S ribosomal subunits (Matsuo, Y et. al. 2006). A hypothesised circular permutation of the NKxD motif N-terminal of the Walker A motif (primary structure) is characteristic of GTPases of the Ylqf family (Leipe, D. et. al. 2002). Our aim for this study is to determine the overall function of 1pujA and related YlqF proteins. To do this we will investigate the function using stratagies such as literature searches, function prediction programs and programs that utilize additional high-throughput functional data. The structure and evolution of the protein will also be investigate with hopes that this additional information will help us better understand the function of YlqF proteins. Structure will be investigated using web tools specific for structure comparison and structure analysis. Finally Evolution will be determined using sequence searches, multiple sequence alignment and the building of a phylogenetic tree. Using data gathered from all these sources we hope to create a viable hypothesis for the overall function of YlqF proteins. In addition the prospect of YlqF’s involvement in 50S ribosomal assembly will be discussed.

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