Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
- Neil F.W. Saunders1,
- Torsten Thomas1,10,
- Paul M.G. Curmi2,
- John S. Mattick3,
- Elizabeth Kuczek3,
- Rob Slade3,
- John Davis3,
- Peter D. Franzmann4,
- David Boone5,
- Karl Rusterholtz5,
- Robert Feldman6,
- Chris Gates6,
- Shellie Bench6,
- Kevin Sowers7,
- Kristen Kadner8,
- Andrea Aerts8,
- Paramvir Dehal8,
- Chris Detter8,
- Tijana Glavina8,
- Susan Lucas8,
- Paul Richardson8,
- Frank Larimer9,
- Loren Hauser9,
- Miriam Land9, and
- Ricardo Cavicchioli1,11
- 1 School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- 2 School of Physics, The University of New South Wales, Sydney, NSW 2052, Australia and Centre for Immunology, St. Vincent's Hospital, Sydney, NSW 2010, Australia
- 3 Australian Genome Research Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
- 4 CSIRO Land and Water, Floreat, Western Australia, 6014, Australia
- 5 Department of Biology, Portland State University, Portland, Oregon 97201 USA
- 6 Genomics Applications, Amersham Biosciences, Sunnyvale, California 94086-4520, USA
- 7 Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA
- 8 DOE Joint Genome Institute, Walnut Creek, California 94598, USA
- 9 IUT Genome Science and Technology, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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°–98°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°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.
Footnotes
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Article published online before print in June 2003.
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1180903.
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↵10 Present address: Nucleics Pty Ltd, PO Box 620, Randwick, 2031, NSW, Australia.
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↵11 Corresponding author. E-MAIL r.cavicchioli{at}unsw.edu.au; FAX 61-2-93852742.
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- Accepted April 22, 2003.
- Received January 15, 2003.
- Cold Spring Harbor Laboratory Press
