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...
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Cold Spring Harbor Laboratory Press
2003
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Online Access: | https://espace.library.uq.edu.au/view/UQ:66250/UQ66250_OA.pdf https://espace.library.uq.edu.au/view/UQ:66250 |
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ftunivqespace:oai:espace.library.uq.edu.au:UQ:66250 2023-05-15T13:47:31+02:00 Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii Saunders, Neil F. W. Thomas, Torsten Curmi, Paul M. G. Mattick, John S. Kuczek, Elizabeth Slade, Rob Davis, John Franzmann, Peter D. Boone, David Rusterholtz, Karl Feldman, Robert Gates, Chris Bench, Shellie Sowers, Kevin Kadner, Kristen Aerts, Andrea Dehal, Paramvir Detter, Chris Glavina, Tijana Lucas, Susan Richardson, Paul Larimer, Frank Hauser, Loren Land, Miriam Cavicchioli, Ricardo 2003-01-01 https://espace.library.uq.edu.au/view/UQ:66250/UQ66250_OA.pdf https://espace.library.uq.edu.au/view/UQ:66250 eng eng Cold Spring Harbor Laboratory Press doi:10.1101/gr.1180903 issn:1088-9051 issn:1549-5469 Biotechnology & Applied Microbiology Genetics & Heredity Rna Secondary Structures Cold-shock Domain Elongation-factor-2 Proteins Thermophilic Methanogens Sp Nov ; Posttranscriptional Modification H-2-using Methanogen Ace Lake Identification Sequence 1311 Genetics 2716 Genetics (clinical) Journal Article 2003 ftunivqespace https://doi.org/10.1101/gr.1180903 2020-12-07T23:21:53Z 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 Gin and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15degrees-98degreesC) were used to generate IIII modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gin, 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 60degreesC, 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 Article in Journal/Newspaper Antarc* Antarctic The University of Queensland: UQ eSpace Ace Lake ENVELOPE(78.188,78.188,-68.472,-68.472) Antarctic The Antarctic Genome Research 13 7 1580 1588 |
institution |
Open Polar |
collection |
The University of Queensland: UQ eSpace |
op_collection_id |
ftunivqespace |
language |
English |
topic |
Biotechnology & Applied Microbiology Genetics & Heredity Rna Secondary Structures Cold-shock Domain Elongation-factor-2 Proteins Thermophilic Methanogens Sp Nov ; Posttranscriptional Modification H-2-using Methanogen Ace Lake Identification Sequence 1311 Genetics 2716 Genetics (clinical) |
spellingShingle |
Biotechnology & Applied Microbiology Genetics & Heredity Rna Secondary Structures Cold-shock Domain Elongation-factor-2 Proteins Thermophilic Methanogens Sp Nov ; Posttranscriptional Modification H-2-using Methanogen Ace Lake Identification Sequence 1311 Genetics 2716 Genetics (clinical) Saunders, Neil F. W. Thomas, Torsten Curmi, Paul M. G. Mattick, John S. Kuczek, Elizabeth Slade, Rob Davis, John Franzmann, Peter D. Boone, David Rusterholtz, Karl Feldman, Robert Gates, Chris Bench, Shellie Sowers, Kevin Kadner, Kristen Aerts, Andrea Dehal, Paramvir Detter, Chris Glavina, Tijana Lucas, Susan Richardson, Paul Larimer, Frank Hauser, Loren Land, Miriam Cavicchioli, Ricardo Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
topic_facet |
Biotechnology & Applied Microbiology Genetics & Heredity Rna Secondary Structures Cold-shock Domain Elongation-factor-2 Proteins Thermophilic Methanogens Sp Nov ; Posttranscriptional Modification H-2-using Methanogen Ace Lake Identification Sequence 1311 Genetics 2716 Genetics (clinical) |
description |
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 Gin and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15degrees-98degreesC) were used to generate IIII modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gin, 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 60degreesC, 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 |
format |
Article in Journal/Newspaper |
author |
Saunders, Neil F. W. Thomas, Torsten Curmi, Paul M. G. Mattick, John S. Kuczek, Elizabeth Slade, Rob Davis, John Franzmann, Peter D. Boone, David Rusterholtz, Karl Feldman, Robert Gates, Chris Bench, Shellie Sowers, Kevin Kadner, Kristen Aerts, Andrea Dehal, Paramvir Detter, Chris Glavina, Tijana Lucas, Susan Richardson, Paul Larimer, Frank Hauser, Loren Land, Miriam Cavicchioli, Ricardo |
author_facet |
Saunders, Neil F. W. Thomas, Torsten Curmi, Paul M. G. Mattick, John S. Kuczek, Elizabeth Slade, Rob Davis, John Franzmann, Peter D. Boone, David Rusterholtz, Karl Feldman, Robert Gates, Chris Bench, Shellie Sowers, Kevin Kadner, Kristen Aerts, Andrea Dehal, Paramvir Detter, Chris Glavina, Tijana Lucas, Susan Richardson, Paul Larimer, Frank Hauser, Loren Land, Miriam Cavicchioli, Ricardo |
author_sort |
Saunders, Neil F. W. |
title |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_short |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_full |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_fullStr |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_full_unstemmed |
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii |
title_sort |
mechanisms of thermal adaptation revealed from the genomes of the antarctic archaea methanogenium frigidum and methanococcoides burtonii |
publisher |
Cold Spring Harbor Laboratory Press |
publishDate |
2003 |
url |
https://espace.library.uq.edu.au/view/UQ:66250/UQ66250_OA.pdf https://espace.library.uq.edu.au/view/UQ:66250 |
long_lat |
ENVELOPE(78.188,78.188,-68.472,-68.472) |
geographic |
Ace Lake Antarctic The Antarctic |
geographic_facet |
Ace Lake Antarctic The Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
doi:10.1101/gr.1180903 issn:1088-9051 issn:1549-5469 |
op_doi |
https://doi.org/10.1101/gr.1180903 |
container_title |
Genome Research |
container_volume |
13 |
container_issue |
7 |
container_start_page |
1580 |
op_container_end_page |
1588 |
_version_ |
1766247261518430208 |