Sulfolobus acidocaldarius is an aerobic thermoacidophilic crenarchaeon which grows optimally at 80°C and pH 2 in terrestrial solfataric springs. Here, we describe the genome sequence of strain DSM639, which has been used for many seminal studies on archaeal and crenarchaeal biology. The circular genome carries 2,225,959 bp (37% G؉C) with 2,292 predicted protein-encoding genes. Many of the smaller genes were identified for the first time on the basis of comparison of three Sulfolobus genome sequences. Of the protein-coding genes, 305 are exclusive to S. acidocaldarius and 866 are specific to the Sulfolobus genus. Moreover, 82 genes for untranslated RNAs were identified and annotated. Owing to the probable absence of active autonomous and nonautonomous mobile elements, the genome stability and organization of S. acidocaldarius differ radically from those of Sulfolobus solfataricus and Sulfolobus tokodaii. The S. acidocaldarius genome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange in S. acidocaldarius. Moreover, it contains genes for a characteristic restriction modification system, a UV damage excision repair system, thermopsin, and an aromatic ring dioxygenase, all of which are absent from genomes of other Sulfolobus species. However, it lacks genes for some of their sugar transporters, consistent with it growing on a more limited range of carbon sources. These results, together with the many newly identified protein-coding genes for Sulfolobus, are incorporated into a public Sulfolobus database which can be accessed at http://dac.molbio.ku.dk/dbs/Sulfolobus.Sulfolobus acidocaldarius strain DSM639, the type strain of the archaeal genus Sulfolobus, was the first hyperthermoacidophile to be characterized from terrestrial solfataras by Brock et al. (12). It grows optimally at 75 to 80°C and pH 2 to 3, under strictly aerobic conditions, on complex organic substrates, including yeast extract, tryptone, and Casamino Acids and a limited number of sugars.Many of the seminal studies on archaea and crenarchaea were performed on S. acidocaldarius. Thus, S. acidocaldarius was employed to demonstrate the similarity of the archaeal and eukaryal transcription apparatuses (6, 36, 46). Moreover, its sensitivity to a wide range of ribosomal antibiotics (1) and ease of transformation (3) have rendered S. acidocaldarius a focus for in vivo genetic studies. Proteins responsible for chromatin folding (Sac7c) and the highly abundant Sac10b (Alba) protein, implicated in the regulation of chromatin and/or cellular RNAs in Sulfolobus (7, 30), were first characterized for this organism (29).S. acidocaldarius has also been used for studying genetic fidelity at high temperatures and is the only hyperthermophilic archaeon for which the rate and type of spontaneous mutation have been quantified in vivo (26). Its relatively low mutation rate, despite its high-temperature environment, has stimulated a strong interest in its efficient repair systems. It ...