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 (YlqF) is a known 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 (REFERENCE). YlqF has previously been associated with the assembly of the 50S ribosomal subunit. B. subtillus in which YlqF was inhibited showed slow growth 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/YawG family (Leipe, D. et. al. 2002). Computational biological methods incorporating phylogenetic, structural an functional analyses, will be applied to test the hypothesis that YlqF of Bacillus subtilis is a GTPase. In addition the prospect of YlqF’s involvement in 50S ribosomal assembly will be discussed.

structure...

Our aim for this experiment we aim to determine the overall function of 1pujA. To do this we will directly investigate the function using stragies 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 with help us better understand the function of 1pujA. 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 searches we hope to create a viable hypothesis for the overall function of 1pujA.