Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.

@article{citeulike:1090867, 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.}, address = {School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.}, author = {Saunders, N. F. and Thomas, T. and Curmi, P. M. and Mattick, J. S. and Kuczek, E. and Slade, R. and Davis, J. and Franzmann, P. D. and Boone, D. and Rusterholtz, K. and Feldman, R. and Gates, C. and Bench, S. and Sowers, K. and Kadner, K. and Aerts, A. and Dehal, P. and Detter, C. and Glavina, T. and Lucas, S. and Richardson, P. and Larimer, F. and Hauser, L. and Land, M. and Cavicchioli, R. }, citeulike-article-id = {1090867}, doi = {10.1101/gr.1180903}, issn = {1088-9051}, journal = {Genome Res}, keywords = {antarctic, bioinformatics, genomics, methanococcoides, methanogenium, psychrophily}, month = {July}, number = {7}, pages = {1580--1588}, posted-at = {2008-05-11 10:24:46}, priority = {2}, title = {Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii.}, url = {http://dx.doi.org/10.1101/gr.1180903}, volume = {13}, year = {2003} }

TY - JOUR ID - citeulike:1090867 TI - Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. JF - Genome Res VL - 13 IS - 7 SP - 1580 EP - 1588 AD - School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia. SN - 1088-9051 N2 - 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. KW - antarctic KW - bioinformatics KW - genomics KW - methanococcoides KW - methanogenium KW - psychrophily AU - Saunders, NF AU - Thomas, T AU - Curmi, PM AU - Mattick, JS AU - Kuczek, E AU - Slade, R AU - Davis, J AU - Franzmann, PD AU - Boone, D AU - Rusterholtz, K AU - Feldman, R AU - Gates, C AU - Bench, S AU - Sowers, K AU - Kadner, K AU - Aerts, A AU - Dehal, P AU - Detter, C AU - Glavina, T AU - Lucas, S AU - Richardson, P AU - Larimer, F AU - Hauser, L AU - Land, M AU - Cavicchioli, R PY - 2003/07// UR - http://dx.doi.org/10.1101/gr.1180903 ER -