E. Growth-phase dependent gene expression—light limitation and stationary phase.
One specific objective was to determine the nature of gene expression as the cells alter their physiological growth state in response to changes in light intensity and their nutritional and physical environment. Under typical laboratory batch growth conditions, cyanobacteria grow exponentially then transition to a light limited stage of linear growth before finally reaching a non-growth stationary phase. Our results indicated that there is widespread differential gene regulation during the change from exponential to linear growth in the cyanobacterium and that much of this is due to changes in light intensity based on self-shading Foster et al. (2007). Specifically: 1) many photosynthesis and regulatory genes have lower transcript levels; 2) individual genes such as sigH, phrA, isiA which encode a group 4 sigma factor, a DNA photolyase and a chl-binding protein, respectively, were strongly induced; 3) the loss of SigB significantly impacted the differential expression of genes; this included the up-regulation of the photosynthesis and specific regulatory genes as well as a general down-regulation of the hypothetical and unknown genes. This helped to develop the model in Fig. 2, and also gave important information on the sigma cascade, which led to the production of sigH to be used in transcription during the stationary phase and the importance of the photolyase phrA under these conditions. In addition, we also determined that a cluster of genes sll1722 to sll1725 were strongly upregulated during the light limited phase. These are genes that demonstrated homology to E. coli genes involved with exopolysaccharide production. The results indicate that EPS production is enhanced in stationary phase and correlates with data from the DmrgA mutant that growth-phased dependent EPD production protected against peroxide stress.
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