Abstract
BackgroundBacteria of genus Thermus inhabit both man-made and natural thermal environments. Several Thermus species have shown biotechnological potential such as reduction of heavy metals which is essential for eradication of heavy metal pollution; removing of organic contaminants in water; opening clogged pipes, controlling global warming among many others. Enzymes from thermophilic bacteria have exhibited higher activity and stability than synthetic or enzymes from mesophilic organisms.ResultsUsing Meiothermus silvanus DSM 9946 as a reference genome, high level of coordinated rearrangements has been observed in extremely thermophilic Thermus that may imply existence of yet unknown evolutionary forces controlling adaptive re-organization of whole genomes of thermo-extremophiles. However, no remarkable differences were observed across species on distribution of functionally related genes on the chromosome suggesting constraints imposed by metabolic networks. The metabolic network exhibit evolutionary pressures similar to levels of rearrangements as measured by the cross-clustering index. Using stratigraphic analysis of donor-recipient, intensive gene exchanges were observed from Meiothermus species and some unknown sources to Thermus species confirming a well established DNA uptake mechanism as previously proposed.ConclusionGlobal genome rearrangements were found to play an important role in the evolution of Thermus bacteria at both genomic and metabolic network levels. Relatively higher level of rearrangements was observed in extremely thermophilic Thermus strains in comparison to the thermo-tolerant Thermus scotoductus. Rearrangements did not significantly disrupt operons and functionally related genes. Thermus species appeared to have a developed capability for acquiring DNA through horizontal gene transfer as shown by the donor-recipient stratigraphic analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-813) contains supplementary material, which is available to authorized users.
Highlights
Bacteria of genus Thermus inhabit both man-made and natural thermal environments
Identification of orthologous genes To identify orthologous genes for investigating possible gene exchanges among various bacteria species, a BLASTp search was done in a pair-wise manner for all coding sequences of 10 sampled genomes: Thermus thermophilus HB8 and HB27, T. scotoductus SA-01, T. aquaticus Y51MC23, T. igniterrae ATCC 700962, T. oshimai JL-2, Thermus sp
In the further study we focused on comparison of M. silvanus DSM 9946, T. scotoductus SA-01, T. thermophilus HB8 and HB27 as representatives of thermo-tolerant and extremely thermophilic organisms
Summary
Bacteria of genus Thermus inhabit both man-made and natural thermal environments. Genomic recombinations are involved in evolution and speciation of organisms in addition to other mechanisms such as mutations, natural selection and horizontal gene transfer [11]. The extent to which thermal environments affect genome rearrangements on the chromosome or exert evolutionary pressure on the metabolic network is not clear. Both the retrograde and patchwork theories attempt to explain the evolution of metabolic networks based on gene and operon duplication linking distribution of genes on the chromosome which may be affected by rearrangements and on the structure of the metabolic network [12]. Whilst prior work by Gouder et al [15] performed a comprehensive analysis of genomic islands possibly acquired through natural transformations, and their functional contribution in Thermus species, this work investigated movement of genomic islands and the ability for Thermus species to acquire external DNA
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