Sun, 27 Jul 2008 07:19:53 BST CiteULike: neils's Richardson http://www.citeulike.org/user/neils/author/Richardson CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2873245 <i>Proceedings of the National Academy of Sciences of the United States of America (5 June 2008)</i><br /><br />The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, "Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form. A korarchaeal genome reveals insights into the evolution of the Archaea. James G Elkins Mircea Podar David E Graham Kira S Makarova Yuri Wolf Lennart Randau Brian P Hedlund Céline Brochier-Armanet Victor Kunin Iain Anderson Alla Lapidus Eugene Goltsman Kerrie Barry Eugene V Koonin Phil Hugenholtz Nikos Kyrpides Gerhard Wanner Paul Richardson Martin Keller Karl O Stetter doi:10.1073/pnas.0801980105 Proceedings of the National Academy of Sciences of the United States of America (5 June 2008) 2008-06-08T07:53:47-00:00 2008 Proceedings of the National Academy of Sciences of the United States of America 1091-6490 archaea evolution genome koryarchaeota koryarchaeum 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/2475666 <i>Nature, Vol. 452, No. 7183. (6 March 2008), pp. 88-92.</i> The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis F Martin A Aerts D Ahren A Brun EGJ Danchin F Duchaussoy J Gibon A Kohler E Lindquist V Pereda A Salamov HJ Shapiro J Wuyts D Blaudez M Buee P Brokstein B Canback D Cohen PE Courty PM Coutinho C Delaruelle JC Detter A Deveau S Difazio S Duplessis L Fraissinet-Tachet E Lucic P Frey-Klett C Fourrey I Feussner G Gay J Grimwood PJ Hoegger P Jain S Kilaru J Labbe YC Lin V Legue F Le Tacon R Marmeisse D Melayah B Montanini M Muratet U Nehls H Niculita-Hirzel Oudot-Le Secq M Peter H Quesneville B Rajashekar M Reich N Rouhier J Schmutz T Yin M Chalot B Henrissat U Kues S Lucas Y Van de Peer GK Podila A Polle PJ Pukkila PM Richardson P Rouze IR Sanders JE Stajich A Tunlid G Tuskan IV Grigoriev doi:10.1038/nature06556 Nature, Vol. 452, No. 7183. (6 March 2008), pp. 88-92. 2008-03-05T22:42:12-00:00 2008 Nature 452 7183 88 92 Nature Publishing Group bioinformatics genome laccaria mycorrhizae sequence symbiosis