title: Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.
abstract: We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15 degrees -98 degrees C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60 degrees C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Neil F W
authors.initials: NF
authors.lastname: Saunders
authors.forename: Torsten
authors.initials: T
authors.lastname: Thomas
authors.forename: Paul M G
authors.initials: PM
authors.lastname: Curmi
authors.forename: John S
authors.initials: JS
authors.lastname: Mattick
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Kuczek
authors.forename: Rob
authors.initials: R
authors.lastname: Slade
authors.forename: John
authors.initials: J
authors.lastname: Davis
authors.forename: Peter D
authors.initials: PD
authors.lastname: Franzmann
authors.forename: David
authors.initials: D
authors.lastname: Boone
authors.forename: Karl
authors.initials: K
authors.lastname: Rusterholtz
authors.forename: Robert
authors.initials: R
authors.lastname: Feldman
authors.forename: Chris
authors.initials: C
authors.lastname: Gates
authors.forename: Shellie
authors.initials: S
authors.lastname: Bench
authors.forename: Kevin
authors.initials: K
authors.lastname: Sowers
authors.forename: Kristen
authors.initials: K
authors.lastname: Kadner
authors.forename: Andrea
authors.initials: A
authors.lastname: Aerts
authors.forename: Paramvir
authors.initials: P
authors.lastname: Dehal
authors.forename: Chris
authors.initials: C
authors.lastname: Detter
authors.forename: Tijana
authors.initials: T
authors.lastname: Glavina
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Paul
authors.initials: P
authors.lastname: Richardson
authors.forename: Frank
authors.initials: F
authors.lastname: Larimer
authors.forename: Loren
authors.initials: L
authors.lastname: Hauser
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.forename: Ricardo
authors.initials: R
authors.lastname: Cavicchioli
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D001482:Base Composition; D003080:Cold Temperature; D004268:DNA-Binding Proteins / Q000235:genetics; D019766:Genes, Archaeal / Q000235:genetics; D020745:Genome, Archaeal; D019638:Methanomicrobiaceae / Q000235:genetics*; D017019:Methanosarcinaceae / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics; D017386:Sequence Homology, Amino Acid
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D016601:RNA-Binding Proteins; C077188:cold-shock protein CspB, Bacteria; D012343:RNA, Transfer