Nitrate and starvation dependent transcription in Aspergillus nidulans

Nitrogen metabolism in Aspergillus nidulans is subject to regulation by the GATA transcription factor AreA which is required for the utilization of a wide range of nitrogen sources other than glutamine or ammonium. The level of AreA activity is regulated by intracellular glutamine levels that vary in response to nitrogen supplementation. For nitrate assimilation, which involves two transporters (CrnA, CrnB), nitrate reductase (NiaD) and nitrite reductase (NiiA), the respective genes are subject to regulation at the level of transcription, including nitrogen metabolite repression mediated by AreA and induction mediated by nitrite or nitrate, mediated by a second transcription factor, NirA. Both transcription factors act synergistically to regulate the expression of all four structural genes when nitrogen is limiting or either nitrate or nitrite is available. In this study we dissect the nitrogen limitation effect mediated by AreA form the nitrate/nitrite specific effect mediated by NirA on the transcriptome level. Keywords: Nitrate/nitrogen limitation response Wild type pabaA1 (WT) strain and nirA637 pabaA1 (nirA loss of function (nirA637)) strains were used in this study. First, WT repressed (ammonium) was compared to WT induced (nitrate) obtaining all genes that are differently transcribed by either nitrogen limitation and/or nitrate induction. Seven biological repetitions were analyzed on seven microarray slides, including 3 dye swaps. Second, WT repressed was compared to WT starved (no nitrogen source available) to obtain genes that are regulated by AreA mediated nitrogen limitation. Four biological repetitions were analyzed on four slides including two dye swaps. Third, nirA637 repressed was compared to nirA637 induced also to obtain AreA dependent genes and genes that are nitrate but not AreA dependent. Four biological repetitions were analyzed on four slides including two dye swaps.