Overall the observed induction of exo genes is in agreement with the mucoid phenotype observed for S. meliloti after growing on low pH plates (data not shown). In low pH soils this response could be a strategy of the cell to establish a more favourable microenvironment by secreting succinoglycan. It was shown that an EPS I overproduction results in a reduced nodulation efficiency [54], therefore Belnacasan supplier the induction of EPS I biosynthesis genes could also be one of the reasons for the observed limited nodulation efficiency of rhizobia in low pH soils [2]. Figure 4 Map of genes in the EPS I biosynthesis region on pSymB and their expression in response

to acidic pH. The EPS I biosynthesis gene region on pSymB is schematically displayed with its genes given by open arrows coloured according to the K-means cluster distribution. Gene names are given below. Black arrows indicate known operon structures in this region. The graph above shows on the Y-axis the time after pH-shift and on the Z-axis for each time point the expression of the corresponding genes by the M value. Whereas the exo gene expression was increased, several selleck kinase inhibitor genes of chemotaxis and flagellar biosynthesis (flgB, flgG, flgL, flgF, flgC, flgE, fliE, flbT, motA, mcpU) were decreased in their expression levels. After 63 minutes of low pH treatment

the genes have reached the highest level of repression. VisR is the main activator of the flagellar genes and forms together with VisN the top layer of a hierarchy of three expression classes. Since the visN gene expression was decreased early in the time course experiment (therefore visN was grouped into cluster E) the other flagellar genes follow the repression of their activator [55]. The gene coding for the subordinated regulator Rem [56] was also decreasingly expressed with time, but did not reach the threshold for clustering. A detailed

consideration of the expression levels of the flagellar biosynthesis genes on the chromosome (Fig. 5) reveals a repression of the complete region, with some parts responding stronger than others. The decreased expression level of motA, flgF and flgE is likely to be a result of their first position in an operon. It is noticeable that among the 10 down-regulated and strongly responding isothipendyl flagellar genes in cluster F five are coding for parts of the rod (flgF, flgB, flgC, fliE and flgG) and two for parts of the hook (flgE and flgL) of the flagellum. The genes motA, fliM, fliN and fliG are proposed to form an operon [55]. While the expression of motA, which is coding for a transmembrane proton channel protein, was decreased in the time course experiment, the other three genes which encode flagellar switch proteins did not respond to the shift to acidic pH. If this behaviour is caused by a specific regulation or is due to mRNA degradation processes cannot be answered.