2D). In cluster D the dctA gene coding for the DctA dicarboxylate import system was found. The DctA dicarboxylate import system [37] is well characterised and a broad substrate range has been identified [38]. This dicarboxylate import system is known to be essential for symbiosis since it is supposed to Target Selective Inhibitor Library provide the cells in the bacteroid state with tricarbonic acid (TCA) cycle intermediates from the host plant, e.g. succinate, malate, and

fumarate. A group of genes in this cluster points to an induced fatty acid degradation. The gene smc00976 is coding for a putative enoyl CoA hydratase and smc00977 and smc02229 are coding for putative acyl CoA dehydrogenase proteins. With glpD, a gene coding for a glycerol-3-phosphate dehydrogenase find more involved in the glycerol degradation could also be found in cluster D. The transient induction of genes involved in fatty acid degradation might be related to a lack of energy or the modification of the membrane lipid composition. Cluster E contains genes involved in nitrogen metabolism, ion transport and methionine metabolism Cluster E consists of 22 genes whose expression was lowered in response to the pH shift. The expression was lowered up to 10 minutes after pH shift and then stayed constant until the end of the time course experiment (Fig. 2E). Cluster E contains genes involved in nitrogen metabolism.

The gene glnK codes for a PII Carnitine palmitoyltransferase II nitrogen regulatory protein activated under nitrogen limiting conditions and forms together with amtB, which encodes a high affinity ammonium transport system, an operon. The GlnK protein could also be identified as lower expressed after a short exposure of S. medicae cells to low pH [27].

It was argued by Reeve et al. that this observation might be related to some crosstalk between nitrogen and pH sensing systems during the early pH adaptation [27]. With metF, metK, bmt, and ahcY four genes involved in the methionine metabolism were also grouped in this cluster, while two other met genes were grouped into cluster F (metA) and cluster G (metH), respectively. The distribution of these genes to two other clusters of down-regulated genes might be due to the fact the met genes are not organised in an operon, but dispersed over the chromosome. S-adenosylmethionine is formed from methionine by MetK and is the major methylation compound of the cell that is needed e.g. for polyamine- or phosphatidylcholine biosynthesis. The connection between the down-regulation of the methionine metabolism and the pH response is not clear. It was shown that various abiotic stresses result in a rapid change of cellular polyamine levels [39–41]. Several genes belonging to ion uptake systems were located in cluster E, like the complete sitABCD operon and phoC and phoD of the phoCDET operon. The sitABCD operon codes for a manganese/iron transport system [42, 43].