title: Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4.
abstract: Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows non-fermentatively in a pH range from 7.5 to above 11.4 and can withstand large sudden increases in external pH. It is a model organism for studies of bioenergetics at high pH, at which energy demands are higher than at neutral pH because both cytoplasmic pH homeostasis and ATP synthesis require more energy. The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at which the pH homeostasis capacity is exceeded, and manages other stresses that are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses. The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular environmental conditions. The genome also reveals a more acidic pI profile for proteins exposed on the outer surface than found in neutralophiles. A large array of transporters and regulatory genes are predicted to protect the alkaliphile from its overlapping stresses. In addition, unanticipated metabolic versatility was observed, which could ensure requisite energy for alkaliphily under diverse conditions.
authors.affiliation: Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences and Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA 15212, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Janto
authors.forename: Azad
authors.initials: A
authors.lastname: Ahmed
authors.forename: Masahiro
authors.initials: M
authors.lastname: Ito
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.forename: David B
authors.initials: DB
authors.lastname: Hicks
authors.forename: Sarah
authors.initials: S
authors.lastname: Pagni
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Fackelmayer
authors.forename: Terry-Ann
authors.initials: TA
authors.lastname: Smith
authors.forename: Joshua
authors.initials: J
authors.lastname: Earl
authors.forename: Liam D H
authors.initials: LD
authors.lastname: Elbourne
authors.forename: Karl
authors.initials: K
authors.lastname: Hassan
authors.forename: Ian T
authors.initials: IT
authors.lastname: Paulsen
authors.forename: Anne-Brit
authors.initials: AB
authors.lastname: Kolstø
authors.forename: Nicolas J
authors.initials: NJ
authors.lastname: Tourasse
authors.forename: Garth D
authors.initials: GD
authors.lastname: Ehrlich
authors.forename: Robert
authors.initials: R
authors.lastname: Boissy
authors.forename: D Mack
authors.initials: DM
authors.lastname: Ivey
authors.forename: Gang
authors.initials: G
authors.lastname: Li
authors.forename: Yanfen
authors.initials: Y
authors.lastname: Xue
authors.forename: Yanhe
authors.initials: Y
authors.lastname: Ma
authors.forename: Fen Z
authors.initials: FZ
authors.lastname: Hu
authors.forename: Terry A
authors.initials: TA
authors.lastname: Krulwich
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001407:Bacillus / Q000235:genetics* / Q000502:physiology; D001426:Bacterial Proteins / Q000737:chemistry; D002473:Cell Wall / Q000502:physiology; D003593:Cytoplasm / Q000737:chemistry; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics; D004734:Energy Metabolism; D016680:Genome, Bacterial; D006863:Hydrogen-Ion Concentration; D007438:Introns; D058977:Molecular Sequence Annotation; D018384:Oxidative Stress; D010766:Phosphorylation; D010957:Plasmids / Q000235:genetics; D018741:Replication Origin; D012964:Sodium / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D012964:Sodium