Synechococcus sp. strain PCC 7942 has a second clpB gene that encodes a 97-kDa protein with novel features. ClpBII is the first ClpB not induced by heat shock or other stresses; it is instead an essential, constitutive protein. ClpBII is unable to complement ClpBI function for acquired thermotolerance. No truncated ClpBII version is normally produced, unlike other bacterial forms, while ectopic synthesis of a putative truncated ClpBII dramatically decreased cell viability.In response to rising growth temperatures, all organisms synthesize heat shock proteins (HSPs). Many of these inducible polypeptides are members of larger families based on similar size and sequence homology, and most include proteins synthesized constitutively under nonstress conditions. Members of most HSP families function as molecular chaperones in assisting the folding, assembly, and translocation of other proteins during normal and adverse growth regimens. One relatively new family of chaperones is HSP100/Clp. It can be divided into two basic groups, with proteins in the first (ClpA to -E) having two distinct ATP-binding domains (ATP-1 and ATP-2) while proteins in the second (ClpX and -Y) possess only one such domain (21). The main HSP of this chaperone family is ClpB, and most organisms produce at least two different types. Separate nuclear clpB genes in eukaryotes encode mitochondrial (78-kDa [11]) and cytosolic (100-to 110-kDa [19]) proteins, while plants have another ClpB isomer localized in chloroplasts (10). In contrast, a single gene in eubacteria encodes two differently sized proteins (ca. 79 and 93 kDa) via dual translational initiation sites within the clpB transcript (5, 23).ClpB is essential for resistance to high-temperature stress. The cytosolic ClpB in Saccharomyces cerevisiae and plants confers acquired thermotolerance (9,18,19), which is commonly defined as the resistance developed by an organism to withstand an otherwise lethal temperature treatment by being preexposed to a nonlethal high temperature. Similarly, the heat shock-inducible ClpBI protein from the cyanobacterium Synechococcus sp. strain PCC 7942 (Synechococcus) is also crucial for thermotolerance (5), a role that can be complemented by Escherichia coli ClpB (6). In the case of ClpBI, both the fulllength and truncated forms of the protein contribute to the thermotolerance acquired by Synechococcus (3).Mechanistically, ClpB functions to dissolve inactive protein aggregates that accumulate at high temperatures (16). In both bacteria and eukaryotes, ClpB cooperates with the DnaKDnaJ-GrpE proteins in a bichaperone network to prevent and revert protein aggregates during heat shock (7,13,14). ClpB apparently dissolves large, stable heat-inactivated proteins by directly binding to aggregates and exposing hydrophobic surfaces within the polypeptides by ATP-induced structural changes in the ClpB protein (4, 8).All ClpB proteins studied to date are strongly induced by high temperatures, and most are vital for heat tolerance. Under nonstressed conditions, however, ClpB i...