Previously, it was shown that transcription of the small heat-shock protein gene, hspA, from the thermophilic cyanobacterium Synechococcus vulcanus is transiently heat-inducible at a vegetative promoter that lacks any known regulatory DNA elements. A novel regulatory mechanism that suppresses the expression of hspA under non-heat-shock condition has been postulated. In this study, it is demonstrated that a protein(s) in the extract of unstressed cells of the thermophilic cyanobacterium Thermosynechococcus elongatus, a cyanobacterium closely related to S. vulcanus, specifically binds to a 5'-untranslated region of the hspA gene. An AT-rich imperfect inverted-repeat sequence (ACAAgcAAA-TTTagTTGT) as a target for a putative DNA-binding protein has been identified. The DNA-binding activity in the cell as well as in the cell extract was lost much more quickly at a heat-shock temperature than a normal growth temperature. In a cell, the activity was restored within 45 min after a heat-shock by the heat-induced synthesis and stabilization of a DNA-binding protein. It is proposed that the inverted repeat is a specific target for a DNA-binding protein and that it plays a role in the regulation of the cyanobacterial hspA gene expression. (C) 2002 Elsevier Science (USA). All rights reserved.