Investigation of the DNA sequences recognized by CmpR, a low-CO₂ responsive transcriptional regulator of Synechococcus elongatus PCC 7942

Abstract

CO₂ assimilation by cyanobacteria is very efficient because of the operation of the CO₂-concentrating mechanism (CCM), which is activated in response to CO₂ deficiency. In Synechococcus elongatus PCC 7942, a LysR-type transcriptional regulator CmpR regulates transcription of the CCM-related genes, including the cmpABCD operon, the sbtA gene, and the ndhF3D3chpY operon. CmpR is similar to bacterial CbbR proteins, which is known to recognize and bind to the CbbR motif (TNA-N_7/8-TNA). The regulatory region of cmpABCD is 950 bp long and has been shown by gel shift assay to have several binding sites for CmpR. Moreover, this region contains seven CbbR-binding motifs (cmp1-cmp7), mutations in three of which (cmp3, 5, 6) inhibit the low-CO₂ response of the promoter, suggesting CmpR binding to these sites. In this study, we investigated the binding of CmpR to the DNA fragments carrying cmp3, 5 and 6, respectively. Surprisingly, modification of cmp3 and 6 did not affect the CmpR binding, indicating that CmpR can bind to DNA sequences other than those containing the CbbR motif.