The gene katC is known to be regulated in a heat dependent mechanism by rpoE2 in S. meliloti 1021 [31]. Altogether 15 out of 41 described genes being rpoE2 dependent regulated under heat stress [31] were found exclusively in cluster B. This is not only indicating a possible role of RpoE2 in the pH stress response but also a specific expression profile of the target genes. Besides katC, ndiA, glgA2 and glgX2 the remaining

11 genes are coding for hypothetical proteins. The rpoE2 gene itself was filtered for clustering with maximum log2 fold expression values of 1.36 and 1.07 at time points 18 minutes and 33 minutes, respectively. Cluster C contains among others genes coding for a chaperone 10058-F4 datasheet and a component of a low O2 PARP inhibitor affinity oxidase Cluster C contains 31 genes whose expression continuously increased during the time course experiment (Fig. 2C). With over 50% (16 of 31 genes) this cluster resembles cluster B composed of a large amount of genes coding for hypothetical proteins. In this cluster groEL5 could be found, which was the only differentially

expressed gene coding for a chaperone. This gene has recently been shown to be specialised for the S. meliloti stress response [32]. Besides the DegP1 protease encoding gene, this is the only quality control system found to be up-regulated after the pH shift. In contrast to degP1 the groEL5 gene was not immediately up-regulated after the pH shift, but slowly increasing in its expression level during the time

course. With nex18 a gene with unknown function could be detected, which was already shown IKBKE to be higher expressed during symbiosis and selleck chemical in response to nutrient deprivation stress [33, 34]. The gene cyoB of the cyoABC operon was also included in cluster C. The operon codes for a cytochrome o ubiquinol oxidase, a low O2 affinity oxidase with a high proton pumping activity. It is noteworthy that qxtA, a gene coding for part of the subunit of a high O2 affinity oxidase displayed an expression profile similar to genes of cluster C, but was filtered out for clustering analysis due to missing values for three time points. It is known that an increased ΔpH affects the expression of genes of the oxidative phosphorylation. In S. medicae the transcriptional induction of fixN, a symbiosis related high O2-affinity oxidase with a low proton pumping activity was observed after overnight growth at low pH [19]. For Brucella abortus it was demonstrated that an interruption in the orthologue of the qxtAB operon, named cydAB, caused high acid sensitivity [35]. In E. coli the gene expression of the orthologues of the low O2 affinity oxidase encoded by cyoABC and the qxtAB encoded high O2 affinity oxidase was dependent of the pH [36] with a preferred expression of the high O2 affinity oxidase at low pH. Since both, the cyoABC and the qxtAB systems of S. meliloti have so far not been further investigated, their specific role in the pH response cannot be defined.