title: The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation.
abstract: Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five-tiered evidence rating (ER) system that ranked annotations from ER1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea, which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino-acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall, membrane, envelope biogenesis COG genes are overrepresented. Likewise, signal transduction (COG category T) genes are overrepresented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two overrepresented COG categories appear to have been acquired from epsilon- and delta-Proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they have an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it adapted from a marine to an Antarctic lake environment.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Allen
authors.forename: Federico M
authors.initials: FM
authors.lastname: Lauro
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Williams
authors.forename: Dominic
authors.initials: D
authors.lastname: Burg
authors.forename: Khawar S
authors.initials: KS
authors.lastname: Siddiqui
authors.forename: Davide
authors.initials: D
authors.lastname: De Francisci
authors.forename: Kevin W Y
authors.initials: KW
authors.lastname: Chong
authors.forename: Oliver
authors.initials: O
authors.lastname: Pilak
authors.forename: Hwee H
authors.initials: HH
authors.lastname: Chew
authors.forename: Matthew Z
authors.initials: MZ
authors.lastname: De Maere
authors.forename: Lily
authors.initials: L
authors.lastname: Ting
authors.forename: Marilyn
authors.initials: M
authors.lastname: Katrib
authors.forename: Charmaine
authors.initials: C
authors.lastname: Ng
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Sowers
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Galperin
authors.forename: Iain J
authors.initials: IJ
authors.lastname: Anderson
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Eileen
authors.initials: E
authors.lastname: Dalin
authors.forename: Michele
authors.initials: M
authors.lastname: Martinez
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Loren
authors.initials: L
authors.lastname: Hauser
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.forename: Torsten
authors.initials: T
authors.lastname: Thomas
authors.forename: Ricardo
authors.initials: R
authors.lastname: Cavicchioli
mesh_terms: D000220:Adaptation, Biological; D003080:Cold Temperature; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D019766:Genes, Archaeal; D020745:Genome, Archaeal; D017019:Methanosarcinaceae / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
chemical_list: D019641:DNA, Archaeal