Sat, 26 Jul 2008 08:34:30 BST CiteULike: neils Mattick http://www.citeulike.org/user/neils/author/Mattick 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/2229597 <i>Proc Natl Acad Sci U S A (9 January 2008)</i><br /><br />A major proportion of the mammalian transcriptome comprises long RNAs that have little or no protein-coding capacity (ncRNAs). Only a handful of such transcripts have been examined in detail, and it is unknown whether this class of transcript is generally functional or merely artifact. Using in situ hybridization data from the Allen Brain Atlas, we identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain and found that the majority were associated with specific neuroanatomical regions, cell types, or subcellular compartments. Examination of their genomic context revealed that the ncRNAs were expressed from diverse places including intergenic, intronic, and imprinted loci and that many overlap with, or are transcribed antisense to, protein-coding genes of neurological importance. Comparisons between the expression profiles of ncRNAs and their associated protein-coding genes revealed complex relationships that, in combination with the specific expression profiles exhibited at both regional and subcellular levels, are inconsistent with the notion that they are transcriptional noise or artifacts of chromatin remodeling. Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs. Specific expression of long noncoding RNAs in the mouse brain. Tim R Mercer Marcel E Dinger Susan M Sunkin Mark F Mehler John S Mattick doi:10.1073/pnas.0706729105 Proc Natl Acad Sci U S A (9 January 2008) 2008-01-14T09:31:04-00:00 2008 Proc Natl Acad Sci U S A 1091-6490 bioinformatics brain expression mice ncrna rna