Mutations and Rearrangements in the Genome ofSulfolobus solfataricusP2

Abstract

The genome of Sulfolobus solfataricus P2 carries a larger number of transposable elements than any other sequenced genome from an archaeon or bacterium and, as a consequence, may be particularly susceptible to rearrangement and change. In order to gain more insight into the natures and frequencies of different types of mutation and possible rearrangements that can occur in the genome, the pyrEF locus was examined for mutations that were isolated after selection with 5-fluoroorotic acid. About two-thirds of the 130 mutations resulted from insertions of mobile elements, including insertion sequence (IS) elements and a single nonautonomous mobile element, SM2. For each of these, the element was identified and shown to be present at its original genomic position, consistent with a progressive increase in the copy numbers of the mobile elements. In addition, several base pair substitutions, as well as small deletions, insertions, and a duplication, were observed, and about one-fifth of the mutations occurred elsewhere in the genome, possibly in an orotate transporter gene. One mutant exhibited a 5-kb genomic rearrangement at the pyrEF locus involving a two-step IS element-dependent reaction, and its boundaries were defined using a specially developed "in vitro library" strategy. Moreover, while searching for the donor mobile elements, evidence was found for two major changes that had occurred in the genome of strain P2, one constituting a single deletion of about 4% of the total genome (124 kb), while the other involved the inversion of a 25-kb region. Both were bordered by IS elements and were inferred to have arisen through recombination events. The results underline the caution required in working experimentally with an organism such as S. solfataricus with a continually changing genome.

Unveiling Cell Surface and Type IV Secretion Proteins Responsible for Archaeal Rudivirus Entry

“…2A). These results are consistent with the previous reports demonstrating high transposition activity in S. solfataricus and its contribution to chromosomal plasticity (18)(19)(20). Following the procedure described above, SIRV2-resistant cultures were generated for each of the pyrEF mutants.…”

“…The stability of the transposon insertions in the pyrEF genes was tested for each of the 10 pyrEF mutants (Sens1 to Sens10) and their corresponding SIRV2-resistant colonies (Res1 to Res10) by growing them in rich media containing uracil (17) for 3 days without transfer, prior to total DNA extraction and PCR amplification of the pyrEF regions. Each transposon insertion appeared to be stable, because no wildtype PCR bands were observed, except a weak wild-type band produced in Sens2, consistent with the undetectable reversion rates for Sulfolobus transposons recorded earlier (19,20). Since Res2 did not generate the wild-type band, the extra PCR product in Sens2 was probably due to a minor contamination of the colony by wild-type cells (Fig.…”

Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota

“…Sulfolobus acidocaldarius, Sulfolobus solfataricus), several strains deposited in public culture collections (including the type strains) have lost the ability to grow autotrophically after continuous laboratory cultivation in nutrient-rich media (Huber et al, 1989;Huber & Prangishvili, 2006). This is consistent with the presence of a large number of transposable elements in the genomes of some Sulfolobales and underlines the caution required in working experimentally with these organisms (Redder & Garrett, 2006). Nevertheless, very closely related strains have been isolated which are still able to grow strictly chemolithoautotrophically (e.g.…”

The Rate and Character of Spontaneous Mutation in Thermus thermophilus

“…On average, 20% of the FOA-resistant colonies from selection plates scored as prototrophs (i.e., did not require uracil for growth). In S. solfataricus strain P2 and H. volcanii, all such FOA-resistant uracil prototrophs were confirmed to have intact pyrE and pyrF genes (Redder and Garrett 2006;Mackwan et al 2007). Therefore, we based our mutation-rate calculations only on pyrimidineauxotrophic mutations that could be localized to pyrE or pyrF by DNA sequencing (see below).…”