Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.
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.
Saunders
Neil F W
NF
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
Thomas
Torsten
T
Curmi
Paul M G
PM
Mattick
John S
JS
Kuczek
Elizabeth
E
Slade
Rob
R
Davis
John
J
Franzmann
Peter D
PD
Boone
David
D
Rusterholtz
Karl
K
Feldman
Robert
R
Gates
Chris
C
Bench
Shellie
S
Sowers
Kevin
K
Kadner
Kristen
K
Aerts
Andrea
A
Dehal
Paramvir
P
Detter
Chris
C
Glavina
Tijana
T
Lucas
Susan
S
Richardson
Paul
P
Larimer
Frank
F
Hauser
Loren
L
Land
Miriam
M
Cavicchioli
Ricardo
R
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
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D016601:RNA-Binding Proteins; C077188:cold-shock protein CspB, Bacteria; D012343:RNA, Transfer