Spontaneous mutations in the orotate:phosphoribosyl transferase (pyrE2) gene of the halophilic archaeon Haloferax volcanii were selected by 5-fluoroorotic acid plus uracil at a rate of $2 3 10 À8 /cell division in fluctuation and null-fraction tests but $6 3 10 À8 /cell division in mutation-accumulation tests. The corresponding genomic mutation rates were substantially lower than those observed for other mesophilic microbial DNA genomes on the basis of similar target genes. The mutational spectrum was dominated by indels adding or deleting multiples of 3 bp. Properties of the organism contributing to this unusual mutational pattern may include phenotypic lag caused by a high chromosomal copy number and efficient promotion of strand misalignments by short direct repeats.A NALYSES of spontaneous mutation in diverse micro-organisms have provided important insights into the fundamental forces and molecular mechanisms determining genetic fidelity. In most of these studies, a selection is used to quantify the rate of forward (i.e., inactivating) mutations in one or more chromosomal genes. Sequencing of representative mutants then reveals a spectrum of mutation, which enables the efficiency of mutation detection and other parameters to be estimated. Such analyses have shown that all mesophilic micro-organisms examined (including DNA viruses) share two mutational characteristics: (i) the rates of mutation per genome fall near 0.003/replication, despite large differences in mutation rates per base pair (Drake 1991;Drake et al. 1998;Drake and Hwang 2005), and (ii) $70% of the observed mutations are base-pair substitutions (BPSs) (Grogan et al. 2001). However, extending this analysis to an archaeon from a geothermal environment revealed an apparently lower genomic rate (#0.0018) and a lower proportion of BPSs (33%) (Grogan et al. 2001). These results suggest that basic mutational properties of micro-organisms may adapt to unusual environmental conditions.Halophilic archaea grow optimally at moderate temperatures in 1-4 m salt (Rodriquez-Valera 1995). They cope with these environments by maintaining high intracellular concentrations of potassium and chloride (Lanyi 1974), which can be expected to exert molecular stresses on genetic processes. Certain genetic methods have been developed for Halobacterium salinarum and Haloferax volcanii (Allers and Mevarech 2005; Soppa 2006), and various systems for repairing DNA damage have been reported in these two species (McCready 1996;Baliga et al. 2004;Kottemann et al. 2005), but neither halophile has been evaluated for the accuracy of genome replication. In this study, we demonstrated the ability of 5-fluoroorotic acid (FOA) to select spontaneous orotate:phosphoribosyl transferase (OPRTase) mutants of H. volcanii. We measured the rate of spontaneous mutation in the corresponding pyrE2 gene, analyzed a number of mutants by DNA sequencing, and evaluated the implications for genomic mutation in this organism.The H. volcanii wild-type strain DS70 (Wendoloski et al. 2001) was cul...

Selection of spontaneous, loss-of-function mutations at two chromosomal loci (pyrF and pyrE) enabled the first molecular-level analysis of replication fidelity in the extremely thermophilic bacterium Thermus thermophilus. Two different methods yielded similar mutation rates, and mutational spectra determined by sequencing of independent mutants revealed a variety of replication errors distributed throughout the target genes. The genomic mutation rate estimated from these targets, 0.00097 6 0.00052 per replication, was lower than corresponding estimates from mesophilic microorganisms, primarily because of a low rate of base substitution. However, both the rate and spectrum of spontaneous mutations in T. thermophilus resembled those of the thermoacidophilic archaeon Sulfolobus acidocaldarius, despite important molecular differences between these two thermophiles and their genomes.