title: 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.
authors: BioPAD Metagenomics Platform, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa.
authors: Kamini
authors: K
authors: Gounder
authors: Elzbieta
authors: E
authors: Brzuszkiewicz
authors: Heiko
authors: H
authors: Liesegang
authors: Antje
authors: A
authors: Wollherr
authors: Rolf
authors: R
authors: Daniel
authors: Gerhard
authors: G
authors: Gottschalk
authors: Oleg
authors: O
authors: Reva
authors: Benjamin
authors: B
authors: Kumwenda
authors: Malay
authors: M
authors: Srivastava
authors: Carlos
authors: C
authors: Bricio
authors: José
authors: J
authors: Berenguer
authors: Esta
authors: E
authors: van Heerden
authors: Derek
authors: D
authors: Litthauer
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D002876:Chromosomes, Bacterial; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics; D015321:Gene Rearrangement; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D026801:Synteny; D013824:Thermus / Q000235:genetics* / Q000378:metabolism; D016963:Thermus thermophilus / Q000235:genetics
chemical_list: D004269:DNA, Bacterial