Appendix 1—table 1. All growth conditions used in the Reg-Seq study.

Heat shocked cells were exposed to 42°C for 5 min upon reaching OD 0.3 as this is known to induce transcription by ${\sigma }^{32}$ (Arsène et al., 2000). Low oxygen growth cells were grown in a flask sealed with parafilm with minimal oxygen, although some was present as no anaerobic chamber was used. This level of oxygen stress was still sufficient to activate FNR binding, thus activating anaerobic metabolism. For cells grown with iron, upon reaching OD of 0.3 iron was added and cells were incubated for 10 min before harvesting RNA. Growth without cAMP was accomplished by the use of the JK10 strain (Kinney et al., 2010) which does not maintain its cAMP levels.

Growth conditions
M9 with glucose (0.5%)
M9 with acetate (0.5%)
M9 with arabinose (0.5%)
M9 with xylose (0.5%) and arabinose (0.5%)
M9 with succinate (0.5%)
M9 with trehalose (0.5%)
M9 with glucose (0.5%) and 5 mM sodium salycilate
LB
heat shock in M9 with glucose (0.5%)
LB in low oxygen
zinc, 5 mM ZnCl in M9 with glucose (0.5%)
iron, 5 mM FeCL in M9 with glucose (0.5%)
no cAMP in M9 with glucose (0.5%)