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Acclimation of living organisms to cold stress begins with the perception and transduction of the cold signal. However, traditional methods failed to identify the sensors and transducers of cold stress. Therefore, we combined systematic mutagenesis of potential sensors and transducers with DNA microarray analysis in an attempt to identify these components in the cyanobacterium Synechocystis sp. PCC 6803. We identified histidine kinase Hik33 as a potential cold sensor and found that Hik33 participates in the regulation of the expression of more than 60% of the cold-inducible genes. Further study revealed that Hik33 is also involved in the perception of hyperosmotic stress and salt stress and transduction of the signals. Complexity of responses to cold and other environmental stresses is discussed.