The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803

<jats:title>Abstract</jats:title><jats:p>Cyanobacteria exhibit a great capacity to adapt to different environmental conditions through changes in gene expression. Although this plasticity has been extensively studied in the model cyanobacterium <jats:italic>Synechocystis</jats:italic> sp. PCC 6803, a detailed analysis of the coordinated transcriptional adaption across varying conditions is lacking. Here, we report a meta-analysis of 756 individual microarray measurements conducted in 37 independent studies-the most comprehensive study of the <jats:italic>Synechocystis</jats:italic> transcriptome to date. Using stringent statistical evaluation, we characterized the coordinated adaptation of <jats:italic>Synechocystis</jats:italic>’ gene expression on systems level. Evaluation of the data revealed that the photosynthetic apparatus is subjected to greater changes in expression than other cellular components. Nevertheless, network analyses indicated a significant degree of transcriptional coordination of photosynthesis and various metabolic processes, and revealed the tight co-regulation of components of photosystems I, II and phycobilisomes. Detailed inspection of the integrated data led to the discovery a variety of regulatory patterns and novel putative photosynthetic genes. Intriguingly, global clustering analyses suggested contrasting transcriptional response of metabolic and regulatory genes stress to conditions. The integrated <jats:italic>Synechocystis</jats:italic> transcriptome can be accessed and interactively analyzed via the CyanoEXpress website (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://cyanoexpress.sysbiolab.eu">http://cyanoexpress.sysbiolab.eu</jats:ext-link>).</jats:p>