The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control

In the present study, we showed that a fur deletion mutant of S. oneidensis could utilize TCA compounds. Consistently, expression of the TCA cycle genes acnA and sdhA was not down-regulated in the mutant. To explore this observation further, we identified a ryhB gene in Shewanella species and experimentally demonstrated the gene expression. Further experiments suggested that RyhB was up-regulated in fur mutant, but that AcnA and SdhA were not controlled by RyhB.These cumulative results delineate an important difference of the Fur-RyhB regulatory cycle between S. oneidensis and other γ-proteobacteria. This work represents a step forward for understanding the unique regulation in S. oneidensis.Fur (Ferric uptake regulator) is a global transcription factor that regulates a diversity of biological processes such as iron homeostasis, TCA cycle metabolism, acid resistance, oxidative stress response, chemotaxis and pathogenesis (reviewed in [1]). The active, DNA-binding form of this regulator is as a Fur homodimer complexed with ferrous iron. The DNA target recognized by Fe2+-Fur is a 19-bp inverted repeat sequence called a "Fur box" (GATAATGATAATCATTATC) [2]. The binding of Fe2+-Fur to a "Fur box" in the promoter regions of target genes effectively prevents the recruitment of the RNA polymerase holoenzyme, and thus represses transcription [3,4].Although Fur typically acts as a transcriptional repressor, it also appears to positively regulate certain genes in E. coli [5,6]. This paradox was understood only recently, with the discovery of a 90-nt small RNA named RyhB [7]. RyhB negatively regulates a number of target genes by base pairing with their mRNAs and recruiting RNaseE, thus causing degradation of the mRNAs [7,8]. The ryhB gene itself is repressed by Fur via a "Fur box" in its promoter; thus, Fur repression of the negative regulator RyhB manifests as indirect positive regulation by Fur. The targets of RyhB include genes encoding iron-storage protein (Bfr) and enzymes