Haloferax volcanii is a halophilic archaeon that is frequently used as a model organism for biochemical and genetic studies in Archaea. We report here the use of a custom tiled DNA microarray and describe the changes in RNA populations under several basic physiological conditions: during balanced growth and during stationary phase, in both defined and complex media, during growth in low or high NaCl concentrations, and during carbon starvation. Expected results include higher expression levels of genes associated with transcription and translation being higher during balanced growth than during stationary phase, and the induction of genes associated with amino acid biosynthesis during balanced growth in defined medium. Altering NaCl concentrations of the media did not appear to have strong overall effects; the most notable differences were seen in the expression of Na+ associated transporters. Under carbon starvation, an overall decrease in expression levels was observed. Particular themes of interest include the differential expression of two groups of genes: 1) those encoding bacterial-like regulatory proteins, whose functions in archaeal systems have yet to be fully understood, and 2), those encoding proteins of “unknown” function. The latter is of particular interest because approximately a third of all genes in the genome fall within this category, and there appear to be genes that are strongly regulated under specific conditions. The microarray data presented in this work will serve as a foundation
for future work on the mechanism of global gene regulation.
Microarray data and past biochemical studies suggest that the general transcription factors TFB2 and TFB1 play roles in the nitrogen starvation response and the heat shock response. Deletion mutants of either gene did not show a growth phenotype, indicating that they are nonessential and are not required during normal growth. [35S]-methionine radiolabeling and Western analysis revealed that the heat shock response occurred in the absence of TFB2, showing that although TFB2 itself is a heat shock protein, it is not a central regulator for the response. Consistent with TFB2’s role as a downstream member of the heat shock proteins, overexpression of TFB2 did not result in the induction of heat shock responsive genes. RT-PCR and mass spectroscopy confirmed the induction of tfb1 under nitrogen starvation and also showed that the absence of TFB1 did not affect the transcription of other nitrogen associated genes, such as prkA, a serine threonine kinase, indicating that it is not a central regulator in the nitrogen starvation response.