title: Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species.
abstract: BACKGROUND
  Bacteria 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.
  
  
  RESULTS
  Using 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.
  
  
  CONCLUSIONS
  Global 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.
authors.affiliation: Department of Biochemistry, Bioinformatics and Computational Biology Unit, University of Pretoria, Pretoria, South Africa. benjkum@gmail.com.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Kumwenda
authors.forename: Derek
authors.initials: D
authors.lastname: Litthauer
authors.forename: Oleg
authors.initials: O
authors.lastname: Reva
mesh_terms: D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D019143:Evolution, Molecular; D023061:Gene Order; D015321:Gene Rearrangement; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D007218:Industrial Microbiology; D053858:Metabolic Networks and Pathways; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics*; D013824:Thermus / Q000145:classification / Q000235:genetics*