Screening for the target gene of cyanobacterial cAMP receptor protein SYCRP1

The target genes for SYCRP1, a cyanobacterial cAMP receptor protein, were surveyed using a DNA microarray method. Total RNAs were extracted from a wild-type strain and a sycrp1 disruptant of Synechocystis sp. PCC 6803, and the respective gene expression levels were compared. The expression levels of six genes (slr1667, slr1168, slr2015, slr2016, slr2017 and slr2018) were clearly decreased by the disruption of the sycrp1 gene. The data suggest that slr1667 and slr1668 constitute one operon and the other four genes constitute another operon. Transcription start points for the first genes of these putative operons, which are slr1667 and slr2015, were determined by primer extension experiments. Gel mobility shift assays and DNase 1 footprint analyses were carried out to explore the binding of SYCRP1 to the putative promoter regions of slr1667 and slr2015. SYCRP1 bound to the specific site in the 5' upstream region of slr1667 from positions -170 to -155 relative to the transcription start point, while it did not bind to the 5' upstream region of slr2015. It was concluded that SYCRP1 regulates the expression of the slr1667 gene directly by binding to a specific site in its promoter.