The computational analyses identified a single 14-bp consensus motif in the input dataset (Figure 3). This recognition weight matrix consisted of two conserved pentamers (5′-CAAAA-3′) in tandem (with the first one being much less conserved), separated by the 4-bp linker sequence 5′-NCAG-3′. The linker sequence composition is not random in that positions 7 and 8 in the motif contain a well-conserved C and A residue, respectively (Figure 3). Other two-component GW786034 purchase Selleck SHP099 response regulators that also recognize a tandem repeat sequence include phosphorylated CpxR (CpxR-P) and OmpR-P.

The closest known homolog of S. oneidensis SO2426 is CpxR [21]. Intriguingly, the predicted SO2426 recognition sequence Ro-3306 manufacturer resembles the proposed CpxR binding box [5'-GTAAA-(N)5-GTAAA-3'] [33, 34]. The MR-1 cpxR gene was down-regulated three-fold in Δso2426 mutant cells challenged with chromate [21] compared to a three-fold induction that was observed for wild-type MR-1 cells under similar conditions [15]. The CpxAR two-component system functions in responding to cell envelope stress and external environmental stimuli,

leading to the activation of genes involved in repairing misfolded proteins [1, 35, 36]. The Cpx system has been implicated in a number of cellular responses including the activation of outer membrane porins [37], stationary phase-induced survival mechanisms [38], and pH stress [39]. Given the activation of CpxR orthologs such as SO2426 during periods of chromate stress in S. oneidensis MR-1 [15, 21] and Flavopiridol (Alvocidib) copper stress in E. coli [40], it is suspected that Cpx and analogous systems operate to overcome oxidative membrane and protein damage induced by exposure to toxic metal ions. Figure 3 Identification of a predicted

consensus SO2426-binding motif in S . oneidensis MR-1 using computational methods. A sequence logo representation [51] of a 14-bp motif model was derived using promoter regions directly upstream of 46 clustered genes exhibiting down-regulated expression in a Δso2426 mutant strain of MR-1 [21]. The error bars indicate standard deviations. For the present study, we used an input dataset for SO2426 recognition site prediction consisting of 46 genes showing similar down-regulated temporal expression patterns in the Δso2426 mutant [21]. As computational analysis showed, a number of these co-regulated genes were preceded by a conserved tandem repeat (5′-CAAAANCAGCAAAA-3′) and included genes so2280 (a putative bcr), so1188, so1190, so3025, so3062, ftn, so1580, so 2045, so3030, so3032, viuA, and so4743 (see Table 1).