1. OEB 192 – 10.11.01 Genetic & physiological basis of adaptation (Goddard et al., 2005. Nature) (Cooper, 2007. PLoS Biol.)

3. (Chou et al., 2009. PLoS Genetics) Was metal availability a stress? Yes – and insertion was beneficial What effect did IS have? Generated hybrid promoter Increased icuAB mRNA by over 20-fold TonB-dependent outer membrane transporter Periplasmic binding protein IS insertion upstream of metal transporter

4. (Chou et al., 2009. PLoS Genetics) How could we be so bad at making media? Noted trace metal mix changed color with light… Light exposure increased rate and eliminated advantage Increased dosage of trace metals also increased growth Which metal? 4 of 7 metals stimulated growth… Basis of metal limitation EDTA nearly 100% chelating EDTA is light-sensitive Each metal affects chelation of all Answer: Cobalt Only one which limits growth in EDTA- free media Gives advantage for mutant

5. (Chou et al., 2009. PLoS Genetics) Incredible genetic parallelism Examined isolates from all experiments in the lab… 0/8 S-evolved populations had icuAB mutation 30/3230/32 evolved with M had new icuAB allele All were ISMex4, into only 2 sites Large advantage, 3 possible reasons for high rate: ISMex4 ~10 kb icuA icuB Target sequence 2 o structure Local hopping

6. (Chou et al., 2009. PLoS Genetics) Physiological basis of fitness advantage Evolved icuAB allele only an advantage on C 1 or C 2 compounds In common: glyoxylate regeneration pathway Two vitamin B 12 -requiring reactions (has Co) Glyoxylate or cobalamin stimulated wild-type in MP media Later Co-limitation independently discovered via metabolomics (Keifer et al., 2009. PLoS One)

11. Wednesday (11/3): Fitness & optimality