Acclimation to nitrogen starvation is indispensable for the survival of cyanobacteria under natural environmental conditions. SigE and Rre37 are transcriptional regulators whose transcript and protein levels increase during nitrogen starvation. Previous work has shown that overexpression of either sigE or rre37 in the unicellular cyanobacterium Synechocystis sp. PCC 6803 activates the expression of genes related to sugar catabolism and polyhydroxybutyrate (PHB) biosynthesis, although their transcript levels were measured using the cells grown under nitrogen-replete conditions or after 4 h of nitrogen depletion. In this study, the transcript levels were quantified at one day after nitrogen depletion in the wild-type, sigE-overexpressing, and rre37-overexpressing cells. The results showed decreased expression of sugar catabolic enzymes after one day of nitrogen depletion in the wild-type strain. The levels of transcripts related to glycogen catabolism, glycolysis, and PHB biosynthesis were not increased by either sigE or rre37 overexpression after one day of nitrogen depletion. The expression of genes related to nitrogen assimilation and nitrate/nitrite transport was also reduced by either sigE or rre37 overexpression after nitrogen starvation, suggesting the genetic engineering had a phase-dependent effect on gene expression during nitrogen starvation. (C) 2014, The Society for Biotechnology, Japan. All rights reserved.