Analysis of gene expression in the "clock rescue" and rpaA- "clock rescue" strains of Synechococcus elongatus PCC7942 with RNA sequencing in light/dark conditions

The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate. We investigated the mechanisms underlying this viability defect. We performed RNA-seq experiment using the rpaA- “clock rescue” and “clock rescue” strains and we show that the rpaA- “clock rescue” strain is defective in transcription of genes crucial for utilization of carbohydrate stores at night. Overall design: Enriched mRNA was prepared from synchronized rpaA- “clock rescue” and “clock rescue” S. elongatus cells at twelve indicated time points using the Illumina TruSeq Stranded mRNA Sample Prep Kit and Illumina HiSeq technology. Gene expression in the rpaA- “clock rescue” strain was compared at each time point to the control “clock rescue” strain.