Integrated transcriptomic and metabolomic characterization of the low-carbon response using an ndhR mutant of Synechocystis sp. PCC 6803

The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms, and, hence it is tightly controlled. We studied the Ci-dependent transcriptional and metabolic regulation in the Synechocystis sp. PCC 6803 wild type compared to a DndhR mutant that is defective in the main transcriptional repressor for Ci acquisition genes, NdhR (CcmR). The analysis revealed that many protein-coding genes, which are normally repressed in presence of high CO2 concentrations (HC), were already strongly expressed in ∆ndhR, whereas other genes were strongly down-regulated in mutant cells pointing towards a possible activating role of NdhR. A conserved NdhR-binding motif was identified in the promoters of de-repressed genes. Interestingly, the expression of some NdhR-regulated genes remained further inducible under low CO2 conditions (LC) indicating the involvement of additional, NdhR-independent Ci-regulatory mechanisms. Intriguingly, we also found the expression of 52 asRNAs and 34 potential ncRNAs affected by Ci supply, but most of them appear not to be regulated by NdhR and thus could contribute to NdhR-independent carbon-regulation. In contrast to the transcriptome, the metabolome in ∆ndhR cells appeared similar to that of wild-type cells under HC conditions. This observation and the delay of the metabolic responses to the LC-shift in ∆ndhR, specifically the lack of transient increases in intermediates of photorespiratory pathways comprising 2-phosphoglycolate, glycolate and glycine, supports the hypothesis that the deregulation of gene expression in the DndhR mutant successfully pre-acclimates cyanobacterial cells under HC conditions to a low Ci supply. We analyzed gene expression in Synechocystis sp. PCC 6803 WT as well as a ndhR mutant at HC (5% CO2) as well as 3h and 24h after shift to LC (air). For each strain (WT/∆ndhR) and each sampling point, 2 biological replicates were analyzed, however, the ∆ndhR mutant at 24h after LC shift was analyzed in triplicates.