Background: Environmental pH stress constitutes a limiting factor for S. meliloti survival and development. The

response to acidic pH stress in S. meliloti is versatile and characterized by the differential expression of genes

associated with various cellular functions. The purpose of this study was to gain detailed insight into the participation of sigma factors in the complex stress response system of S. meliloti 1021 using pH stress as an

effector.

Results: In vitro assessment of S meliloti wild type and sigma factor mutants provided first evidence that the sigma

factor RpoH1 plays a major role in the pH stress response. Differential expression of genes related to rhizobactin

biosynthesis was observed in microarray analyses performed with the rpoH1 mutant at pH 7.0. The involvement of

the sigma factor RpoH1 in the regulation of S. meliloti genes upon pH stress was analyzed by comparing timecourse

experiments of the wild type and the rpoH1 mutant. Three classes of S. meliloti genes could be identified,

which were transcriptionally regulated in an RpoH1-independent, an RpoH1-dependent or in a complex manner.

The first class of S. meliloti genes, regulated in an RpoH1-independent manner, comprises the group of the

exopolysaccharide I biosynthesis genes and also the group of genes involved in motility and flagellar biosynthesis.

The second class of S. meliloti genes, regulated in an RpoH1-dependent manner, is composed of genes known

from heat shock studies, like ibpA, grpE and groEL5, as well as genes involved in translation like tufA and rplC.

Finally, the third class of S. meliloti genes was regulated in a complex manner, which indicates that besides sigma

factor RpoH1, further regulation takes place. This was found to be the case for the genes dctA, ndvA and smc01505.

Conclusions: Clustering of time-course microarray data of S. meliloti wild type and sigma factor rpoH1 mutant

allowed for the identification of gene clusters, each with a unique time-dependent expression pattern, as well as

for the classification of genes according to their dependence on RpoH1 expression and regulation. This study

provided clear evidence that the sigma factor RpoH1 plays a major role in pH stress response.