In previous studies, we characterized five histidine kinases (Hiks) and the cognate response regulators (Rres) that control the expression of ϳ70% of the hyperosmotic stress-inducible genes in the cyanobacterium Synechocystis sp. PCC 6803. In the present study, we screened a gene knock-out library of Rres by RNA slotblot hybridization and with a genome-wide DNA microarray and identified three Hik-Rre systems, namely, Hik33-Rre31, Hik10-Rre3, and Hik16-Hik41-Rre17, as well as another system that included Rre1, that were involved in perception of salt stress and transduction of the signal. We found that these Hik-Rre systems were identical to those that were involved in perception and transduction of the hyperosmotic stress signal. We compared the induction factors of the salt stress-and hyperosmotic stress-inducible genes that are located downstream of each system and found that these genes responded to the two kinds of stress to different respective extents. In addition, the Hik33-Rre31 system regulated the expression of genes that were specifically induced by hyperosmotic stress, whereas the system that included Rre1 regulated the expression of one or two genes that were specifically induced either by salt stress or by hyperosmotic stress. Our observations suggest that the perception of salt and hyperosmotic stress by the Hik-Rre systems is complex and that salt stress and hyperosmotic stress are perceived as distinct signals by the Hik-Rre systems.Responses to salt stress and hyperosmotic stress have been investigated in prokaryotes, fungi, and plants. However, there is some confusion in the literature because salt stress and hyperosmotic stress have been regarded both as equivalent and as distinct stimuli (1-4). In Arabidopsis thaliana, both salt stress due to 0.1 M NaCl and hyperosmotic stress due to 0.2 M mannitol regulate the expression of not only the same set of genes but also of different sets of genes (4). In the cyanobacterium Synechocystis sp. PCC 6803 (hereafter, Synechocystis), it is clear that there are major differences between the sets of genes that respond to salt stress due to 0.5 M NaCl and hyperosmotic stress due to 0.5 M sorbitol (3). Moreover, the cytoplasmic volume of Synechocystis decreases by ϳ70% of the original volume within 10 min when cells are exposed to 0.5 M sorbitol, but the decrease in cytoplasmic volume is only 30% with 0.5 M NaCl (3). Although the responses to hyperosmotic stress and salt stress are different in terms of gene expression and changes in cytoplasmic volume, recent studies have demonstrated that the same histidine kinases (Hiks), 1 such as Hik33, Hik34, and Hik16, might be involved in the perception of salt and hyperosmotic stress (5, 6).In Synechocystis, several Hiks that are paired with specific response regulators (Rres) have been identified as regulators of the response to hyperosmotic stress (6). A specific Hik senses hyperosmotic stress, and it seems likely that the signal is transferred to the cognate Rre by transfer of a phosphate group from the histidine...