“…Indeed, many of the genes encoding components of the ferrous iron or heme uptake systems, components of the three siderophore biosynthetic pathways, various outer membrane siderophore receptors, and the TonB-ExbD system are upregulated when UPEC strains are grown in urine or in mouse models of urinary tract infections (18, 21, 57-59) (see Table S6 in the supplemental material). While in some cases the individual role of Fur or RyhB in controlling gene expression had been demonstrated or inferred (27,43,60), our global approaches of ChIP-seq, RNA-seq, and proteomics, allowed us to confirm predictions, distinguish between positive or negative impacts of Fur and RyhB, and identify new roles for these iron-responsive regulators on a genome-wide scale. Additional direct targets for Fur regulation within known pathogenicity islands were identified, such as a member of the major facilitator transport superfamily (ShiF), microcin H47 maturation enzymes (MchBCDEF), two predicted TonB dependent ironsiderophore receptors (Iha and IreA), a second system for ferric siderophore uptake referred to as the Fit pathway (c3771-3775) (41), an alternate isozyme (c1220) for synthesis of shikimate, an intermediate of aromatic amino acids, enterobactin and salmochelin synthesis.…”