Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides

Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Cultures with low aeration, which underwent strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures, which showed little variation in levels of dissolved oxygen. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. While the majority of genes (80-85%) are not differentially expressed across growth phases, other genes exhibited growth phase-dependent expression patterns. Gene expression in outgrowth phase was strongly influenced by the length of the preceding stationary phase. After 57 h in stationary phase a much larger number of genes was induced after dilution, 35% of which are known to be controlled by the alternative sigma factors RpoHI and/or RpoHII. Growth experiments with mutant strains assign an important function in stationary phase and especially in outgrowth to these sigma factors and genes for both sigma factors showed growth phase-dependent expression. Besides the known consensus sequences for the RpoH sigma factors, some new consensus sequences were identified in subsets of growth phase-dependent genes suggesting regulation by common transcription factors. Overall design: 4 phases