The cAMP receptor protein, SyCRP1 acts as a transcriptional repressor of CO2-concentrating mechanism genes at high inorganic carbon levels in cyanobacteria

CO2-concentrating mechanism (CCM) is a unique adaptation that evolved in cyanobacteria for inorganic carbon (Ci) sequestration under limiting Ci levels. The CCM is based on several Ci uptake systems and the carboxysome in which RubisCO is confined in a high CO2 environment. Many CCM components are transcriptionally upregulated under low Ci levels through the combined action of the transcriptional factors NdhR, CmpR and the cAMP-binding SyCRP1. Here we show that, SyCRP1 senses the high Ci levels through high cAMP thereby repressing CCM genes. SyCRP1 possess low- and high-affinity cAMP binding sites. Further, the specific interaction of SyCRP1 with membrane lipids was shown. Flag-tagged SyCRP1, when ectopically expressed, was localized to the membrane and released to the cytosol upon cAMP binding under high Ci levels. Finally, ChIP-seq experiments revealed that SyCRP1 binds cis-acting elements at the promoters of multiple transcription units, mainly those involved in CCM. EMSA confirmed SyCRP1's binding to target DNA-elements. Collectively, our results establish SyCRP1 as a transcriptional repressor of the cyanobacterial CCM under high Ci conditions. Overall design: ChIP-seq of 3XFlag tagged SyCRP1 from Synechocystis PCC 6803 grown in BG11 with high CO2 condition. SyCRP1 was expresesed in BG11 that contains 0.17 µM cobalt. Cells grown till 1 OD (730 nm) and for high CO2 condition, 5% (v/v) was supplemented in sterile air for bublling the cultures.