Genome-wide transcriptome analysis of hydrogen production in synechocystis : towards the identification of new players

We report the development of new and robust tools for facile integration and meaningful representation of the high throughput data acquired during the study of the genome-wide responses to environmental challenges or genetic modifications of the best-studied cyanobacterium Synechocystis sp. PCC6803, which has the potential for the photoproduction of sustainable bio-fuels such as hydrogen. These new tools comprise (i) the new design of pan-genomic oligonucleotide DNA microarray to monitor the transcriptome responses of not only the circular chromosome (3.57 Mb; 3,317 genes) but also the 7 plasmids (0.38 Mb; 408 genes altogether), and (ii) the SVGMapping a computational method to map omic experimental data onto custom-made templates, depicting metabolic pathways, cellular structures and/or biological processes. We validated our tools, through the identification and representation of the global transcriptome changes triggered by the deletion of abrB2, the gene we recently found to encode the repressor of the hydrogenase hox operon directing the production of hydrogen. We show here, for the first time, that AbrB2 is a master regulator that regulates (mostly negatively) a large number of chromosomal genes involved in regulation, metal transport and protection against oxidative stress, as well as numerous plasmid genes of as yet unknown function. That AbrB2 regulates 12 regulator genes in addition to the hox operon suggesting that the regulation of hydrogen production might be more complex than anticipated a hypothesis currently tested in our laboratory. Furthermore, our data suggest that plasmids carry several genes of unknown function, which have been overlooked so far, are involved in hydrogen metabolism, among other important cellular processes mentioned above. Consequently, we believe that the present report will stimulate both basic and applied researches on plasmid functions and their likely relation with hydrogen production.