Genome-wide responses of Synechocystis PCC6803 to nitrogen deprivation

Genome-wide responses of Synechocystis PCC6803 to nitrogen deprivation

Vladimir Krasikov1, Eneas Aguirre-von-Wobeser1, Jef Huisman1, Bas Ibelings2, Hans C.P. Matthijs1
1Universiteit van Amsterdam, Amsterdam, the Netherlands;
2Netherlands Institute of Ecology, Limnological Institute, Nieuwersluis, the Netherlands.
Survival under nitrogen limitation requires major changes in cyanobacterial physiology. Those changes are made possible by alterations in gene expression. A microarray study was conducted with a new microarray platform for Synechocystis PCC6803 that was recently designed in our laboratory (Aguirre von Wobeser, manuscript in preparation, see _052, this meeting). In our project we have compared control cells and cells that were starved for nitrogen during 12 hours. Synechocystis has no capacity for fixation of molecular nitrogen. Cells grown in standard BG-11 medium, were harvested by centrifugation, one half of the cells was resuspended at the original density in standard BG11 medium, the other half of the cells was re-suspended in nitrogen free BG-11 medium. After 12 hours of continued growth, cells were collected for RNA extraction, RNA quality control preceded dye label incorporation into the cDNA with reverse transcriptase. The cDNA was hybridized with the microarray slides. These first results with our array design rendered sufficient quality data. We routinely use a minimum of three biological replicates. The data were extracted and processed with locally designed statistical methods. The results indicated that over 300 genes were upregulated while over 400 genes were downregulated. The changes in gene expression were consistent with existing knowledge on adapatation to nitrogen deprivation [1]. Genes encoding components of the photosynthetic apparatus, including phycobilisome synthesis were clearly down regulated. Consistently, phycobilisome degradation proteins were up regulated. On the other hand, many genes that play key roles in nitrogen metabolism and transport of nitrogenous compounds were up regulated. Several sensory-response regulators were found differentially expressed, suggesting their involvement in nitrogen starvation acclimation.
[1] Sauer J, Schreiber U, Schmid R, Volker U, Forchhammer K (2001) Nitrogen starvation-induced chlorosis in Synechococcus PCC 7942. Low-level photosynthesis as a mechanism of long-term survival. Plant Physiol. 126: 233-243