TABLE 1.

Iron-responsive Fur regulon in Y. pestisa

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  • a For DP, the RNA from WT cells treated with 100 μM DP was compared to that with the addition of 40 μM FeCl3. For fur, the mRNA expression in the fur mutant was compared to that in the WT strain grown under iron-rich conditions. The numerical data for DP and fur are presented as the mean change of mRNA level for each gene under the paired growth conditions. A positive number represents the fold increase, while a minus sign indicates a fold decrease. Data for nondifferentially regulated genes and those with missing data (MD) are indicated in boldface type. The microarray results have been published previously (35).

  • b The term “Verified” indicates that there was the discrepancy between the data determined by RT-PCR and microarray (a total of ten operons); for eight of them the subsequent primer extension assay verified the rationality of the RT-PCR results. ND, not determined. *, RT-PCR and/or microarray indicated that the transcription of the corresponding genes was independent of both Fur and iron; this was further confirmed by the primer extension assay.

  • c The gene identification numbers were derived from the genome annotation of Y. pestis CO92. Putative operons (35 in all) are boxed, and vertical arrows indicate the transcriptional organization. The genes YPO1011-1012 and YPO0778-0770 are harbored in a continuous genomic region in KIM and 91001, encoding a putative siderophore-based iron acquisition system. This genomic region splits into two separate genomic loci (YPO1011-1012 and YPO0778-0770) in CO92, probably due to the IS sequence-base homologous recombination. Thus, YPO1011-1012 and YPO0778-0770 was considered to be a single putative operon in Y. pestis. As expected, the EMSA showed that His-Fur bonds to the upstream DNA region of YPO1011, the first gene of the above siderophore-based system, rather than that of YPO0778 (see also Fig. 2) that was actually an internal member of this system.

  • d The strand/distance of the Fur site upstream of transcriptional start site/matching score are indicated.

  • e Matching the predicted Y. pestis Fur box within the 500-bp promoter regions was performed by using the program patser-matrix (see the text). The most strongly matched Fur site was indicated with a weight score for each promoter DNA.