Worthy of mention is that a program called TargetRNA  identified possible base pairing between ryhB and Fur genes (Figure 5), implying the possibility of a regulatory feedback loop. Such a regulatory circuit has recently been verified in E. coli . In addition, several genes involved in anaerobic respiration, such as those encoding alcohol dehydrogenase II (AdhB), anaerobic DMSO reductase (DmsA-1), NADH:ubiquinone oxidoreductase subunit (NqrC-2) and two c-type cytochromes (ScyA & SO1659), possess extensive complementary regions with ryhB (Figure 5). Although interesting, these predictions require experimental
validation involving a ryhB null mutant. Nevertheless, we have not been able to generate the mutant despite of www.selleckchem.com/products/gdc-0068.html multiple attempts, which might be attributed to technical difficulties or the possibility that ryhB is an essential gene in S. oneidensis. Figure 5 Complementarity between RyhB and its potential targets. The alignment shows the predicted AZD0530 clinical trial interaction between RyhB and the anti-sense strand of target genes. The numbers represent the start and end positions of the nucleotides. All of the base pairing is considered significant, as judged by p value less than 0.01 . The differences we observed in the RyhB regulon, relative to that of E. coli, are perhaps not surprising in light of the low level of sequence conservation among ryhB genes in phylogenetically
related bacteria, implying that ryhB evolves at a rapid pace. Thus
far, the only persistent structural features among the known ryhB homologs are the presence of an upstream Fur binding site and a region complementary to the SodB mRNA. The former has been employed to identify ryhB in P. aeruginosa . Accumulating evidence suggests that regulatory pathways Fenbendazole in S. oneidensis are distinct from other γ-proteobacteria. For example, the E. coli cAMP receptor protein (CRP) controls the transcription of a number of catabolic genes, but its S. oneidensis homolog is involved in regulation of anaerobic respiration . Also, a major regulator of anaerobic respiration in E. coil (FNR) shows little involvement in anaerobic respiration in S. oneidensis [32–34]. Furthermore, the regulons of the global regulators ArcA and Fur are clearly distinct from that in other bacteria despite significant overlap [10, 35]. Conclusions In accordance with current findings of distinct gene regulatory pathways in S. oneidensis, our study provides evidence to delineate the unique RhyB gene regulation in S. oneidensis. Methods Growth conditions and strain construction M1 defined medium  was used. Cell growth was measured by a type FP-1100-C Bioscreen C machine (Thermo Labsystems) at 600 nm after growing cells to mid-logarithmic phase and diluting 1:100 into 300 μl fresh medium. Triplicate cultures were used to determine average and standard deviation.