1. Transcriptional Signature following Inhibition of Early- Stage Cell Wall Biosynthesis in Staphylococcus aureus A.J O’Neil, J. A. Lindsay, K. Gould, J. Hinds, and I. Chopra ( 2009)Antimicrobial Agents and Chemotherapy 01309-08: 1701-1704 Angela Garibaldi & Ryan Willhite BIOL398-01/S10: Bioinformatics Laboratory April 27, 2010

2. Outline Review of the Experimental Set up Cell Wall Biosynthesis Review of the State I Biosynthesis Pathway Results of GenMAPP, using MAPPfinder tool –Top GO Terms –Relation of significant GO Terms to CWB Conclusions

3. Experimental Design Inhibit the Mur enzymes (A/Z, B, and E) 3 Biological Replicates 2 Technical Replicates 18 hybridizations (6 per condition) Dye swap design – label orientations are reversed

4. Overview of Cell Wall Biosynthesis o Biosynthesis catalyzed by o Mur A-F and MurG enzymes (1-4 steps) o Filled hexagons o Peptidoglycan o GlcNac: N-acetylglucosamine o MurNac: N-acetyl-muramic acid o Orange circles o Carrier lipids- bactoprenol-phosphate o Transglycosylation and pyrophosphorylation (steps 5&6) o Peptide bond between chains o Those in pink boxes are antibiotics and their ways of inhibiting cell-wall synthesis http://images.google.com/imgres?imgurl=http://www.nature.com/nrmicro/journal/v1/n1/i mages/nrmicro727- f2.jpg&imgrefurl=http://www.nature.com/nrmicro/journal/v1/n1/fig_tabnrmicro727_F2.ht ml

5. Stage I Biosynthesis pathway

8. MurB Decrease RNA Modification Transferase activity- peptidal link formation RNA processing- capping, polyadenylation and splicing of mRNA

9. MurB Increase Antioxidant activity –Breaking chain reaction normally leading to biological damage Biotin biosynthesis –Plays role in gluconeogenesis Amide metabolism

10. Stage I Biosynthesis pathway

11. MurE Decrease Translation RNA Binding Non-membrane bound organelle

12. MurE Increase Amine biosynthetic process Results in formation of organic compound with amino group Carboxylic acid biosynthetic process Formation of carboxylic acids Cellular amine biosynthetic process Naturally occuring biologically active amines

13. Stage I Biosynthesis pathway

14. MurA Decrease Amine Biosynthetic Process Organic acid biosynthetic process (Carboxylic acid) Cellular amine (nitrogen) biosynthetic process Oxidoreductase activity, Vitamin B6 Binding

15. MurA Increase Polysacchairide transmebrane transporter activity Polysaccharide localization Arsenate reductase activity

16. Conclusions Not very conclusive results Terms mostly involved with biological processes of a cell Those decreased are essential to cell gene expression and functional protein synthesis, so still unclear on specific relationships