title: Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1.
abstract: BACKGROUND
  Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life.
  
  
  RESULTS
  We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres.
  
  
  CONCLUSIONS
  Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.
authors.affiliation: Department of Microbiology, University of Hawai'i, 2538 The Mall, Honolulu, HI 96822, USA. jsaw@lanl.gov
authors.forename: Jimmy H
authors.initials: JH
authors.lastname: Saw
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Mountain
authors.forename: Lu
authors.initials: L
authors.lastname: Feng
authors.forename: Marina V
authors.initials: MV
authors.lastname: Omelchenko
authors.forename: Shaobin
authors.initials: S
authors.lastname: Hou
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Saito
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Stott
authors.forename: Dan
authors.initials: D
authors.lastname: Li
authors.forename: Guang
authors.initials: G
authors.lastname: Zhao
authors.forename: Junli
authors.initials: J
authors.lastname: Wu
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Galperin
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.forename: Yuri I
authors.initials: YI
authors.lastname: Wolf
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Rigden
authors.forename: Peter F
authors.initials: PF
authors.lastname: Dunfield
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Maqsudul
authors.initials: M
authors.lastname: Alam
mesh_terms: D001406:Bacillaceae / Q000737:chemistry* / Q000235:genetics / Q000502:physiology*; D001426:Bacterial Proteins / Q000032:analysis*; D005580:Fossils; D016680:Genome, Bacterial; D006358:Hot Temperature; D009520:New Zealand; D012822:Silicon Dioxide; D014871:Water Microbiology
chemical_list: D001426:Bacterial Proteins; D012822:Silicon Dioxide