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Journal of Bacteriology, June 2006, p. 4198-4206, Vol. 188, No. 12
0021-9193/06/$08.00+0     doi:10.1128/JB.00061-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Mutations and Rearrangements in the Genome of Sulfolobus solfataricus P2{dagger}

Peter Redder* and Roger A. Garrett

Danish Archaea Centre, Institute for Molecular Biology and Physiology, Copenhagen University, Sølvgade 83H, DK-1307 Copenhagen K, Denmark

Received 13 January 2006/ Accepted 26 March 2006

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.

* Corresponding author. Present address: Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, 25, rue Dr. Roux, 75724 Paris Cedex 15, France. Phone: (33)140613722. Fax: (33)145688834. E-mail: predder{at}pasteur.fr.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, June 2006, p. 4198-4206, Vol. 188, No. 12
0021-9193/06/$08.00+0     doi:10.1128/JB.00061-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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