2. A brief history of antibiotics (co-evolution of antibiotics and their resistance) ? 1940195019601970198019902000 The Dark Ages (Semmelweis) PrimordialGolden Pharmacologic Biochemical Genomic HTS Target Disenchantment (Semmelweis) (again!) Penicillinase discovery Antibiotic resistance plasmids Increasing Antibiotic Resistance Transmissible fluoroquinolone resistance FDA Office of New Drugs THE LEAN YEARS *** MRSA: UK*, US** Production: 50kg……………………………………………………………………………>10 6 tons

3. Side Effects of Streptomycin Headache Nausea Hearing difficulties, deafness Ringing sensation in the ears Loss of balance Fatigue Difficulty in passing urine Itchy rashes on the skin but it cured TB! Albert Schatz and Selman Waksman Who deserved the Prize?

4. Fifty years of “Industrial Research” on Antibiotics Environmental Doubling time: months Aeration: low Nutrients: variable Carbohydrate: limited Water: variable Temperature: 0-40 pH: 2-10 Yield: µgrams Environmental Doubling time: months Aeration: low Nutrients: variable Carbohydrate: limited Water: variable Temperature: 0-40 pH: 2-10 Yield: µgrams Production Doubling time: hours Aeration: high *Nutrients: high and constant Carbohydrate: high Water: unlimited Temperature: 25-30 pH: 6-7 Yield: grams Production Doubling time: hours Aeration: high *Nutrients: high and constant Carbohydrate: high Water: unlimited Temperature: 25-30 pH: 6-7 Yield: grams *Typical substrates for fermentation Molasses (blackstrap) Fish Meal (herring, anchovy) Citrus pulp Asparagus juice Cottonseed oil Malt extract Beef extract Bovine blood Pork liver Distillers solubles Hydrolysed rabbit fur

5. SOME NUMBERS Number of bacteriophages on Earth1x10 31 Number of bioactive molecules in the Parvome>5x10 30 Number of microbes on Earth5x10 30 Number of stars in the Universe7x10 21 Number of humans on Earth6x10 9 Number of microbes in all humans6x10 23 Number of human cells in one human1x10 13 Number of microbial cells in one human gut1x10 14 Number of human genes in one human2.5x10 4 Number of microbial genes in one human gut3x10 6 Combined length of all bacteriophages on Earth10 8 Ly Diameter of the Milky Way10 5 Ly * The US national debt>1x10 14 * Number of bubbles in one bottle of Champagne1x10 5 (Revised from Kyrpides, 2009 )

7. (Rumbaugh, 2007) The Parvome Inter-Kingdom Signalling

8. Origins and Evolution of Bioactive Small Molecules Distribution: universal, ancient Bioactivities: wide range, concentration-dependence Receptors: mostly macromolecules (cross-species) Structures: small number of major classes (with decoration) Biosynthesis: frequently “assembly line” Properties and applications: multitudinous

9. The Ages of Planet Earth

10. (bio)Chemical Evolution Hadean Period LUCA (Last Universal Common Ancestor) (Modern) Tree of Life (RNA World) Ribozymes Meteorites and primordial reactions “Specialised” Microbial & Plant Metabolism Primary Secondary

11. The Tree of Life -2.0 -4.0 -0.1 -3.0 Origin of Earth (4.5 Billion years) Last common ancestor 2.3 1.5 1.0 Proteobacteria Cyanobacteria Plants Drosophila Crenarchaeota Euryarchaeota Gram positives Mouse 0.1 ? 3.8 Anoxic (H 2, NH 3, CO 2,) Chemical evolution/ Prebiotic synthesis of biomolecules Origin of oxygenic photosynthesis Increasing [O 2 ] in atmosphere Origin of Metazoans 20% [O 2 ] Cambrian Precambrian Age of Dinosaurs Origin of Eukaryotes Origin of Prokaryotes 2.1 Amitochondriate Bacteria Eukaryotes Archaea

12. Aminoglycoside biosynthesis in a streptomycete

13. MODULAR ASSEMBLY LINES FOR BIOACTIVE COMPOUNDS Polyketide synthase Nonribosomal peptide synthase Tetracycline, rapamycin, erythromycin Daptomycin, polymixin, vancomycin

14. Carbonaceous meteorites as sources of chemical intermediates Pizzarello & Shock (2010)

15. Primordial amino acid components of non-ribosomal peptides β-alanine, α-aminobutyric acid, β-aminobutyric acid, γ-amino-butyric acid, α-amino-isobutyric acid, α,γ-diaminobutyric acid, α,β- diaminopropionic acid, α-hydroxy-γ-aminobutyric acid, isoserine, N- methylalanine, 3-methylglutamic acid, isovaline, norvaline, sarcosine etc…

16. Diketopiperazines: potential catalysts and signals There are at least three mechanisms for the synthesis of DKPs!

17. Targets (binding sites) of bioactive small molecules and macromolecular evolution Transcription (rifampicin, streptolydigin) Replication (novobiocin) *Translation (tetracycline, streptomycin, chloramphenicol) Cell wall synthesis (penicillin, vancomycin) Metabolic pathways (azaserine) Did bioactive small molecule interactions play roles in the evolution of cellular macromolecules such as ribosomes and polymerases?

18. Antibiotic Binding Sites (Receptors) on Prokaryote Ribosomes 30S50S This 2.5 mD macromolecule is the sensor/receptor for many signals.

19. A model for the chronological evolution of the ribosome based on accretion from existing structures. (Note: no interactions with small molecules!) Harish and Caetano-Anolles (2012) PLoS ONE 7(3): e32776. doi:10.1371/journal.pone.0032776

20. The Davies Lab, October 2011

21. Tantalus Mountains,BC KEEP CLEAN Wash your hands!

22. PNAS 2012,in press. THE FUTURE!

23. Analysis of interactive bacterial cell networks Watrous et al 2012.

24. Microbes maketh man (people are not only people)