The clpP multigene family for the ATP-dependent Clp protease in the cyanobacterium Synechococcus

In the cyanobacterium Synechococcus sp. strain PCC 7942 a multigene family of three different isozymes encodes the proteolytic subunit CIpP of the ATP-dependent CIp protease. In contrast to the monocistronic cIpPI gene, cIpPII and cIpPIII are part of two bicistronic operons with cIpX and cIpR, respectively. Unlike most bacterial Clip proteins, the Synechococcus CIpP2, CIpP3, CIpR and CIpX proteins were not highly inducible by high temperatures, or by other stresses such as cold, high light or oxidation, although slower gradual rises occurred for all four proteins during high light, and for CIpP3, CIpR and CIpX at low temperature. Attempts to inactivate the cIpPII, cIpIII, cIpR or cIpX genes were only successful for cIpPII, suggesting the others are essential for Synechococcus cell viability. The DeltacIpPII mutant exhibited no significant phenotypic changes from the wild-type, including no change in CIpX content. Despite the apparent bicistronic arrangement of both cIpPII-cIpX and cIpR-cIpPIII, all four genes primarily produce monocistronic transcripts, although pollycistronic transcripts were detected. Mapping of 5' ends for the cIpX and cIpPIII monocistronic transcripts revealed promoters situated within the 3' region of cIpPII and cIpR, respectively. Transcriptional and translational studies further showed differences in the expression and regulation between the cIpP-cIpR-cIpX genes. Inactivation of cIpPI caused a significant decrease in CIpP2 protein concomitant to small increases in both CIpP3 and CIpR. Inactivation of cIpPII resulted in a large rise in cIpPI transcripts but to a lesser extent in CIpP1 protein. Similar small increases in CIpP3, CIpR and CIpX proteins also occurred in DeltacIpPII. These results highlight the regulatory complexity of these multiple cIp genes and their functional importance in cyanobacteria.