Collective transcriptional analysis of heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus was examined by using a targeted cDNA microarray in conjunction with Northern analyses. Differential gene expression suggests that P. furiosus relies on a cooperative strategy of rescue (thermosome [Hsp60], small heat shock protein [Hsp20], and two VAT-related chaperones), proteolysis (proteasome), and stabilization (compatible solute formation) to cope with polypeptide processing during thermal stress.Information gleaned from genome sequence data indicates that heat shock response in hyperthermophilic archaea has several distinguishing features. For example, hyperthermophilic archaea lack Hsp70 (DnaK), Hsp40 (DnaJ), and GrpE, all of which are centrally important in the heat shock response of most known microorganisms (26). Also, the major chaperonin found thus far in thermophilic archaea, an Hsp60 homolog referred to as the thermosome, is more closely related to chaperonins associated with the eukaryotic cytosol (TriCC/CCT complex) than to the bacterial GroEL/ES system (19, 32). Energy-dependent proteolysis plays a major role during heat shock in bacteria in which genes encoding ATP-dependent proteases, such as lon, clp, and hfl, are linked to heat shock promoters (13). However, based on available genome sequence data, hyperthermophilic archaea lack the Clp and HflB (FtsH) family of proteins and have a different version of the Lon protease (43). Hyperthermophilic archaea, which typically have proteasomes, lack the eukaryotic ubiquitination pathway for selective protein degradation by the proteasome and, therefore, seem to modulate proteolysis at the protease level. Another interesting feature of hyperthermophilic archaeal heat shock response is the induced formation of unique compatible solutes that have been proposed to stabilize intracellular proteins against thermal denaturation (33). Whether compatible solutes reduce the need for protein turnover mechanisms is not known.The relative contributions to the collective response of chaperones, chaperonins, proteases, and compatible solutes during heat shock in hyperthermophilic archaea have yet to be examined. Here, the heat shock response of the hyperthermophilic archaeon Pyrococcus furiosus (9) was investigated by using Northern analyses in conjunction with a targeted cDNA microarray, based on genes encoding the thermosome, molecular chaperones, proteases, glycoside hydrolases, and other relevant cellular functions expected to be affected during thermal stress.Experimental approach and data analysis. Relevant open reading frames (ORFs) were located from the P. furiosus genome at NCBI (http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez /framik?dbϭgenome&gi ϭ 228) and BLAST searches of prokaryotic genomes found at The Institute for Genomic Research (www.TIGR.org). SCANPROSITE (http://expasy.cbr .nrc.ca/tools/scnpsit1.html) and PFAM HMM (Ͼhttp://pfam .wustl.edu/hmmsearch.shtml) search tools were used to verify the presence of putative catalytic domains. ORF fra...