Sat, 26 Jul 2008 08:35:58 BST CiteULike: neils Land http://www.citeulike.org/user/neils/author/Land CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/1090867 <i>Genome Res, Vol. 13, No. 7. (July 2003), pp. 1580-1588.</i><br /><br />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. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. NF Saunders T Thomas PM Curmi JS Mattick E Kuczek R Slade J Davis PD Franzmann D Boone K Rusterholtz R Feldman C Gates S Bench K Sowers K Kadner A Aerts P Dehal C Detter T Glavina S Lucas P Richardson F Larimer L Hauser M Land R Cavicchioli doi:10.1101/gr.1180903 Genome Res, Vol. 13, No. 7. (July 2003), pp. 1580-1588. 2007-02-06T16:51:44-00:00 2003 Genome Res 1088-9051 13 7 1580 1588 antarctic bioinformatics genomics methanococcoides methanogenium psychrophily http://www.citeulike.org/user/neils/article/2761221 <i>BMC Genomics, Vol. 9, No. 1. (2008)</i><br /><br />BACKGROUND:The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles.RESULTS:Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins wheras most other bacteria have three to four, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of aorphana hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. CONCLUSIONS:The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Potentially unique operons have been identified. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures. Genomics of an extreme psychrophile, Psychromonas ingrahamii Monica Riley James Staley Antoine Danchin Tingzhang Wang Thomas Brettin Loren Hauser Miriam Land Linda Thompson doi:10.1186/1471-2164-9-210 BMC Genomics, Vol. 9, No. 1. (2008) 2008-05-06T13:58:51-00:00 2008 BMC Genomics 9 1 bacteria genome genomics psychromonas psychrophily