Archaeal transcriptional machinery is similar to that of eukaryotes. We studied the fates of various components of the Sulfolobus solfataricus transcriptional apparatus under different stresses and found that in cells incubated at 90°C for 1 h, transcription factor E (TFE) is selectively depleted, but its mRNA levels are increased. We discuss the implications of these findings.The archaeal transcriptional apparatus closely resembles the eukaryotic RNA polymerase II system (11). Biochemical studies have shown that the core components of the Sulfolobus transcriptional machinery are comprised of a TATA-binding protein (TBP), transcription factor B-1 (TFB1), and a 13-subunit RNA polymerase and that all three components are essential for accurate and efficient transcription from a variety of promoters (2,9,16,20,25,28,35). TBP and TFB1 bind sequence specifically to the A box and BRE, respectively, and the resulting ternary complex recruits RNA polymerase (1,3,4,29). The Sulfolobus solfataricus genome also encodes other proteins implicated in transcription, such as transcription factor E (TFE), TBP-interacting protein 49 (TIP-49), and two TFB1 paralogs, TFB2 and TFB3 (6), but their respective roles in this process are less well understood.In eukaryotes, TFIIE serves as a general transcription factor (GTF), composed of ␣ and ␤ subunits, that is essential for recruiting TFIIH (23). Deletion analysis of TFIIE␣ has demonstrated that its 20-kDa N-terminal region is required for it to maintain function (21) and that this region is conserved in archaeal TFE (2, 15). Archaeal TFE contains a winged helixturn-helix structure in its N-terminal region, which, along with other surfaces that mediate protein-protein interactions, is conserved in TFIIE␣ (24). Like TFIIE␣, archaeal TFE also interacts with TBP and RNA polymerase (2, 37). Additionally, there appears to be functional interdependence between archaeal TFE and TFB, since mutations in one can be complemented by the other (34). Biochemical studies have found that TFE associates with the RNA polymerase, stimulates transcription from some promoters, and is a part of both initiation and elongation complexes (2,14,34). Taken together, these findings suggest that, like eukaryotic TFIIE, archaeal TFE is also a GTF that is essential for gene transcription. No homolog of any of the TFIIH subunits has been found in archaea.The heat shock response is widespread in organisms belonging to all three domains of life and allows cells to cope with thermal stress (8). In the euryarchaeote Pyrococcus furiosus, heat shock is sensed directly by the negatively acting transcription factor Phr, which dissociates from the DNA at elevated temperatures, allowing heat shock genes to be transcribed (33). While the mechanism through which heat shock is sensed in crenarchaeotes remains unknown, transient exposure of Sulfolobus shibatae to temperatures between 85 and 90°C rapidly culminates in the accumulation of heat shock proteins TF55␣ and -␤, which, together with TF55␥, assemble into rosettasomes (18,1...