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Nucleic Acids Res. 2017 Nov 16;45(20):11800-11820. doi: 10.1093/nar/gkx860.

Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803.

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Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.
Laboratory of Intracellular Bacterial Pathogens, Department of Microbial Biotechnology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain.
ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.
School of Biomedical & Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth PL6 8BU, UK.


In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.

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