The differential expression of some genes was obviously only of temporary need for the cell until about 20 minutes after pH shift (as indicated by clusters D and G). Possibly an Bcl-2 inhibitor increasing demand for energy causes the activation of the dicarboxylate transport system gene dctA and of several genes of the fatty acid degradation (cluster D) while at the same time genes for nitrogen uptake and utilization (cluster G) and amino acid biosynthesis were lower expressed. The latter was clearly indicated by the lowered expression of several methionine metabolism genes.
Several genes contributing to the EPS I biosynthesis were up-regulated in response to the acidic pH shift. The secretion of EPS I might be an attempt
of the cell to ameliorate the environment. In parallel a decreasing expression of motility genes can be regarded as an attempt AMN-107 of the cell to save energy. The transcriptional response of S. meliloti 1021 towards low pH showed several parallels to the response in A. tumefaciens , with the induction of the exo genes and the repression of motility genes. Mechanisms to actively compete against a lowered pH like e.g. in E. coli by decarboxylation of amino acids (for review see ) could not be identified. Emricasan clinical trial Possibly in oligotrophic soils a metabolisation of amino acids is inappropriate. Overall this work showed that the short term response to acidic pH stress does not result in a simple induction or repression of genes, but in a sequence of responses varying in their intensity over time. This indicates that a comprehensive analysis of the transcriptional response
of a cell confronted with a new environmental situation requires a monitoring over a longer period of time and not only FER the analysis of a snap shot. Obviously, the response to acidic pH is not based on a few specific genes, but involves several genes associated with various cellular functions. On the other hand, a considerable part of the responding genes belongs to the group of hypothetical genes. These genes represent promising objectives for future investigations. Methods Media and growth conditions S. meliloti strain 1021 was cultivated in Erlenmeyer flasks at 30°C in Vincent minimal medium (VMM)  and shaken at 140 rpm. With exception of 37 μM iron(III) choride no additional metals have been added to the VMM. The pH of the VMM was adjusted by using either HCl or NaOH. Precultures were grown in tryptone yeast complex medium  with appropriate antibiotics (600 μg/ml streptomycin). For pH shift experiments cells of three independent cultures were grown in 100 ml buffered VMM (20 mM BisTris) to an o.D.580 of 0.8. All of the following steps were carried out under gentle conditions using pre-warmed equipment.