We identified 49 genes that contain a putative Fur binding site (Table

3 – columns 1 & 2 and Additional file 2: Table S2). Figure 2 Logo graph of the information matrix from the alignment of Fur-regulated genes in S. Typhimurium. The height of each column of characters represents information, measured in bits, for that specific position and the height of each individual character represents the frequency of each nucleotide. Table 3 Newly Identified Genes Regulated by Fur That Contain a Predicted Fur Binding Site Gene Function Fold Daporinad Changea Predicted Fur Binding Sequenceb rlgA Putative resolvase 2.8 AAAATTAAAATCGTTGGC map c Methionine aminopeptidase 2.6 AAATTGAGAATCATTCTG rpsB 30S ribosomal subunit protein S2 4.0 AAATTGAGAATCATTCTG yajC Tranlocase protein, IISP family 3.2 GTAATGCAAAGCATAAAA nrdR c Putative transcriptional regulator 2.5 GAAACGGTAAAAATTACC sucC Succinyl-CoA synthetase, beta subunit 4.1 CTAAAGATAACGATTACC cmk Cytidine monophosphate kinase 2.7 AAAAAGTAAATCATTGTC STM1013 Gifsy-2 prophage, regulatory

protein 2.8 AAAATCAAAATCAGTAAC STM1133 c Putative dehydrogenase -4.2 ATAATGAGTAGAATTGTT nth c Endonuclease III 2.9 GAAAAGCGTACCATTCCC ldhA c Fermentative D-lactate dehydrogenase -4.0 AATATGCTTAAAATTATC ynaF c Putative universal stress protein -37.3 GAAATAGATATAATTTAT hns Histone like ALK inhibitor protein 3.1 ACAATGCTTATCATCACC STM1795 c Homolog of glutamic dehydrogenase 5.8 AAAAAGATAAAAATAACC STM2186 Putative glutamate synthase -8.8 AAATTGAGAATAGTTATT eutC c Ethanolamine ammonia lyase -4.1 ATAATGCCCATCGTTTCC eutB c Ethanolamine ammonia lyase -3.2 AAACTGATAAACATTGCC yffB c Putative glutaredoxin 2.6 GAAATTCGAATAAATAAT iroN c TonB-dependent siderophore

receptor 9.1 CTAATGATAATAATTATC yggU c Cytoplasmic protein 3.5 ATAACGCTAAGAATAAAC STM3600 c Putative sugar kinase SPTLC1 -6.8 CTGATGCTCATCATTATT STM3690 Putative lipoprotein -4.2 ATAAACATTATAATTATA rpoZ c RNA polymerase, omega subunit 3.9 AATAAGATAATCATATTC udp c Uridine phosphorylase -5.4 CAATAAATAATCAATATC yjcD c Putative xanthine/uracil permease 2.8 AAAAAGCAAACGATTATC dcuA Anaerobic dicarboxylate transport protein -5.8 CAAATAACAACAATTTAA a Ratio of mRNA, Δfur/14028s b Predicted Fur binding site located within -400 to +50 bp relative to ATG c Indicates the predicted Fur binding site is located on the reverse strand a. Fur as a repressor Genes associated with metal AR-13324 mw homeostasis were up-regulated in Δfur. These included the well characterized genes/operons involved in iron homeostasis (i.e., entABEC, iroBCDE, iroN, fes, tonB, fepA, bfr, bfd), Mn2+ transport genes (i.e., sitABC), and copper resistance (i.e., cutC) [58–65] (Additional file 2: Table S2). Expressions of genes involved in xylose metabolism (xylBR) were increased 3.7 and 2.9-fold, respectively, in Δfur relative to the WT (Additional file 2: Table S2). In addition, the glycolytic genes pfkA and gpmA were 3.3-and 5.