Two genes, STM1586 (coding for a putative periplasmic protein) and sitA were up-regulated 76.1 and 53.8-fold, respectively, in Δfur (Additional file 2: Table S2). These two genes exhibited the highest differential expression in Δfur. Intriguingly, the microarray data showed that the gene for adenloysuccinate synthetase (purA), which is required for adenosine 5′ monophosphate synthesis, was up-regulated 3.5-fold in Δfur. Incidentally, purA mutants are known to be highly attenuated and have been

used in developing in vivo expression technology (IVET) to detect promoters activated during S. Typhimurium infection [66, 67]. Transcription of the cytochrome-o ubiquinol oxidase operon (cyoABCDE) and the high affinity cytochrome-d Crenolanib terminal oxidase genes (cydAB) was buy LY3023414 repressed by Fur (Additional file 2: Table S2). Interestingly, BMN 673 clinical trial aerobic expression of cydAB is repressed by H-NS, which is relieved by the response regulator ArcA [68]. In addition, we detected increased expression of hns in Δfur (Additional file 2: Table S2), and earlier work

detected in vivo binding of Fur to the upstream region of hns [29]; this strongly indicates that Fur directly represses hns under anaerobic conditions. How or if H-NS may interact in the anaerobic regulation of cydAB under our conditions is unknown, since the repression of cydAB by H-NS does not appear to occur under anaerobic conditions [68]. Genes associated with DNA repair and purine metabolism (nrdAB, nth, recA, and nei) were repressed by Fur under anaerobic conditions (Additional file 2: Table S2), thus

implicating Fur as a regulator of DNA repair and de novo synthesis. Fur was found to repress ydiE (STM1346) and a putative Fur binding site was found upstream of the start codon, where the expression of the gene was 7.4-fold higher in the mutant than in the wild-type (Additional file 2: Table S2). In Yersinia enterocolitica, YdiE has a conserved HemP (COG4256) Interleukin-2 receptor domain, and is encoded within the hemin uptake operon [69]. Although S. Typhimurium is not known to utilize host’s heme, previous work has established a Fur binding site upstream of ydiE and hemP in S. Typhimurium and Y. enterocolitica, respectively [16, 69]. This indicates that our bioinformatic analyses indeed agree with experimentally identified Fur binding sites. b. Fur as an activator Anaerobic transcription of the fumarate reductase (frdABD) operon and the aspartase gene (aspA) was significantly lower in Δfur (i.e., Fur is serving as an activator); however, the genes coding for the alpha and beta subunits of succinyl-CoA synthetase (sucCD) were up-regulated 4.1 and 2.7-fold, respectively (Additional file 2: Table S2). These genes (i.e., frdABD, aspA, sucCD) and fumAB (fumarate hydratase) are members of the reductive branch of the TCA cycle. We assayed for fumarate reductase (FRD) in cell-free extracts from anaerobic cultures and found that Fur is required for the anaerobic transcription and activity of FRD in S.