Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01

Abstract

BACKGROUND: Many strains of Thermus have been isolated from hot environments around the world. Thermus
 scotoductus SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The
 isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors
 and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The
 genomes from two different Thermus thermophilus strains have been completed. This paper represents the
 completed genome from a second Thermus species - T. scotoductus.
 RESULTS: The genome of Thermus scotoductus SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid
 which, together are about 11% larger than the Thermus thermophilus genomes. The T. thermophilus megaplasmid
 genes are part of the T. scotoductus chromosome and extensive rearrangement, deletion of nonessential genes and
 acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of T.
 scotoductus and T. thermophilus. At least nine large inserts of which seven were identified as alien, were found, the
 most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which
 appear to have been acquired from Meiothermus ruber. The majority of acquired genes are from closely related
 species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a
 thermophilic or hyperthermophilic lifestyle. The natural competence of Thermus scotoductus was confirmed
 experimentally as expected as most of the proteins of the natural transformation system of Thermus thermophilus
 are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and
 anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a
 wide variety of compounds are indicative of an oligotrophic lifestyle.
 CONCLUSIONS: The genome of Thermus scotoductus SA-01 shows remarkable plasticity with the loss, acquisition and
 rearrangement of large portions of its genome compared to Thermus thermophilus. Its ability to naturally take up
 foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population
 which acted as source of nutrients. The genome of Thermus scotoductus illustrates how rapid adaptation can be
 achieved by a highly dynamic and plastic genome.

Funding for the project was provided by:
 DL and EvH: The Advanced Biomolecular Research Cluster of the Strategic
 Academic Cluster Initiative of the University of the Free State, the National
 Research Foundation (South Africa) HICD - Institutional Research
 Development Programme(IRDP - RNAs) (Grant number 62692), the SA/
 Germany Agreement on Cooperation in Science and Technology (UID
 69440) and the Technology Innovation Agency/University of the Free State
 Metagenomics Platform.
 OR and BK: The Southern African Biochemistry and Informatics for Natural
 Products Network (SABINA), the National Research Foundation (South Africa)
 grant for National Bioinformatics and Functional Genomics Programme
 (Grant number 71261).
 RD: The Bundesministerium für Bildung und Forschung (grant number SUA
 08/12)
 JB: Bilateral, South Africa/Spain collaborative project (HS2007-0013)

http://www.biomedcentral.com/1471-2164/12/577

nf2012