Sinorhizobium meliloti.
As revealed in microarrays, the expression of most S. meliloti genes that have candidate RirA-boxes in their regulatory regions is significantly induced under iron-limiting conditions and in the rirA mutant [37]. These include the rhizobactin biosynthesis and uptake genes, the heme acquisition hmu gene locus and the hemin receptor shmR, various ferrisiderophore ABC transporters and outer membrane receptors, the exbBD components of TonB-dependent iron transporters, and the ferric cation ABC transporter fbp (highlighted in blue in Table S1). S. meliloti genes involved in the Fe-S cluster synthesis (suf) are predicted members of both RirA and Irr regulons, and these genes were differentially expressed in the rirA mutant but not under iron-limiting conditions [37]. However, this large-scale transcriptomic study did not reveal some of the iron uptake genes that we found to be associated with candidate RirA-boxes in S. meliloti genome (hmuR, fhuA, fecIR, and rhtX2-viuA). And, vice versa, many genes that are differentially expressed in the rirA mutant are not preceded by significant RirA-box sequences. These apparent discrepancies may indicate that the deregulated iron uptake in the rirA mutant might cause secondary transcriptome changes; for example, by altering the intracellular Fe concentrations. Also, RirA may affect gene expression via regulatory cascades that include other transcription factors (e.g., RhrA, FecIR, AraX).