All experiments were performed with E. coli MG1655 (fnr+ rph-1) (Coli Genetic Stock Center #6300) and its isogenic derivatives. MG1655-ΔmoaA753::FRT-FRT was constructed by P1 transduction of the ΔmoaA753::FRT-kan-FRT allele from the Keio collection (44) into MG1655, followed by elimination of the kan marker using plasmid pCP20, which expresses flippase (FLP) recombinase (45). MG1655 derivatives carrying the ΔmoaA753::FRT-FRT, ΔdeoD780::FRT-FRT, Δapt754::FRT-FRT Δhpt743::FRT-FRT, and Δgpt756::FRT-kan-FRT alleles were likewise constructed by the addition of kan-containing gene deletions from the Keio collection followed by elimination of the kan marker using pCP20 on each iteration.

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