Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01
Van Heerden, Esta
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AbstractBACKGROUND: 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
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
JB: Bilateral, South Africa/Spain collaborative project (HS2007-0013)
Gounder et al.: Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. BMC Genomics 2011 12:577.