Low rates of replication errors in chromosomal genes of Sulfolobus spp. demonstrate that these extreme thermoacidophiles can maintain genome integrity in environments with high temperature and low pH. In contrast to this genetic stability, we observed unusually frequent mutation of the -D-glycosidase gene (lacS) of a shuttle plasmid (pJlacS) propagated in Sulfolobus acidocaldarius. The resulting Lac ؊ mutants also grew faster than the Lac ؉ parent, thereby amplifying the impact of the frequent lacS mutations on the population. We developed a mutant accumulation assay and corrections for the effects of copy number and differential growth for this system; the resulting measurements and calculations yielded a corrected rate of 5.1 ؋ 10 ؊4 mutational events at the lacS gene per plasmid replication. Analysis of independent lacS mutants revealed three types of mutations: (i) G·C-to-A·T transitions, (ii) slipped-strand events, and (iii) deletions. These mutations were frequent in plasmid-borne lacS expressed at a high level but not in single-copy lacS in the chromosome or at lower levels of expression in a plasmid. Substitution mutations arose at only two of 12 potential priming sites of the DNA primase of the pRN1 replicon, but nearly all these mutations created nonsense (chain termination) codons. The spontaneous mutation rate of plasmid-borne lacS was 175-fold higher under high-expression than under low-expression conditions. The results suggest that important DNA repair or replication fidelity functions are impaired or overwhelmed in pJlacS, with results analogous to those of the "transcription-associated mutagenesis" seen in bacteria and eukaryotes.T he universal need of organisms to replicate genomes accurately, and in coordination with cell division, has special significance for "extreme" or "hyper-" thermophiles, which grow optimally at temperatures that kill mesophilic organisms and denature their macromolecules (1). The hyperthermophilic archaea which colonize terrestrial and marine hydrothermal systems represent diverse and ancient lineages, and all grow optimally at temperatures that accelerate DNA decomposition reactions by orders of magnitude relative to those in mesophiles (2). The idea that these archaea should have effective strategies of genome protection which compensate for diverse damaging effects of high temperature thus seems logical and is supported by the low rates of replication errors measured in several Sulfolobus isolates (3, 4). The extreme phylogenetic divergence separating archaea from bacteria and eukaryotes (5) further suggests that the strategies which preserve genome integrity in hyperthermophilic archaea may include molecular features not identified in model organisms. This idea remains consistent with the unusual gene inventories and certain biochemical features of DNA metabolism in these archaea (6). The mechanisms that maintain genomic integrity in hyperthermophilic archaea remain challenging to identify in vivo, however. Recent studies, for example, found that several putative ...