Sat, 05 Jul 2008 03:29:10 BST CiteULike: neils adaptation http://www.citeulike.org/user/neils/tag/adaptation CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2644009 <i>Genome Biology, Vol. 9, No. 4. (2008)</i><br /><br />BACKGROUND:Halophilic prokaryotes are adapted to thrive in extreme conditions of salinity. Identification and analysis of distinct macromolecular characteristics of halophiles provide insight into the factors responsible for their adaptation to high-salt environment. The current report presents an extensive and systematic comparative analysis of genome and proteome composition of halophilic and non-halophilic microorganisms, with a view to identify such macromolecular signatures of haloadaptation. RESULTS:Comparative analysis of genome and proteome of halophiles and non-halophiles reveal some common trends in halophiles that transcend the boundary of phylogenetic relationship and the genomic GC-content of the species. At the protein level, halophilic species are characterized by low hydrophobicity; overrepresentation of acidic residues, especially Asp; underrepresentation of Cys; lower propensities for helix formation and higher propensities for coil structure. At the DNA level, the dinucleotide abundance profiles of halophilic genomes bear some common characteristics, which are quite distinct from those of non-halophiles and hence, may be regarded as specific genomic signatures for salt-adaptation. The synonymous codon usage in halophiles also exhibit similar patterns regardless of their long-term evolutionary history. CONCLUSION:The generality of molecular signatures for environmental adaptation of extreme salt-loving organisms, demonstrated in the present study, advocates for convergent evolution of halophilic species towards specific genome and amino acid composition, irrespective of their varying GC-bias and widely disparate taxonomic positions. The adapted features of halophiles seem to be related to physical principles governing DNA and protein stability, in response to the extreme environmental conditions in which they thrive. Molecular Signature of Hypersaline Adaptation: Insights from Genome and Proteome Composition of Halophilic Prokaryotes Sandip Paul Sumit Bag Sabyasachi Das Eric Harvill Chitra Dutta doi:10.1186/gb-2008-9-4-r70 Genome Biology, Vol. 9, No. 4. (2008) 2008-04-09T08:46:48-00:00 2008 Genome Biology 9 4 adaptation bioinformatics comparative genomics halophile prokaryotes proteomics http://www.citeulike.org/user/neils/article/2322446 <i>J. Proteome Res. (2 February 2008)</i><br /><br />Abstract: We have performed a comprehensive characterization of global molecular changes for a model organism Pyrococcus furiosus using transcriptomic (DNA microarray), proteomic, and metabolomic analysis as it undergoes a cold adaptation response from its optimal 95 to 72 °C. Metabolic profiling on the same set of samples shows the down-regulation of many metabolites. However, some metabolites are found to be strongly up-regulated. An approach using accurate mass, isotopic pattern, database searching, and retention time is used to putatively identify several metabolites of interest. Many of the up-regulated metabolites are part of an alternative polyamine biosynthesis pathway previously established in a thermophilic bacterium Thermus thermophilus. Arginine, agmatine, spermidine, and branched polyamines N4-aminopropylspermidine and N4-(N-acetylaminopropyl)spermidine were unambiguously identified based on their accurate mass, isotopic pattern, and matching of MS/MS data acquired under identical conditions for the natural metabolite and a high purity standard. Both DNA microarray and semiquantitative proteomic analysis using a label-free spectral counting approach indicate the down-regulation of a large majority of genes with diverse predicted functions related to growth such as transcription, amino acid biosynthesis, and translation. Some genes are, however, found to be up-regulated through the measurement of their relative mRNA and protein levels. The complimentary information obtained by the various omics techniques is used to catalogue and correlate the overall molecular changes. Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile Sunia Trauger Ewa Kalisak Jaroslaw Kalisiak Hirotoshi Morita Michael Weinberg Angeli Menon Poole Michael Adams Gary Siuzdak doi:10.1021/pr700609j J. Proteome Res. (2 February 2008) 2008-02-02T07:59:47-00:00 2008 J. Proteome Res. adaptation metabolomics proteomics pyrococcus thermophily transcriptomics http://www.citeulike.org/user/neils/article/2288272 <i>Nucleic Acids Res, Vol. 29, No. 7. (1 April 2001), pp. 1608-1615.</i><br /><br />The global amino acid compositions as deduced from the complete genomic sequences of six thermophilic archaea, two thermophilic bacteria, 17 mesophilic bacteria and two eukaryotic species were analysed by hierarchical clustering and principal components analysis. Both methods showed an influence of several factors on amino acid composition. Although GC content has a dominant effect, thermophilic species can be identified by their global amino acid compositions alone. This study presents a careful statistical analysis of factors that affect amino acid composition and also yielded specific features of the average amino acid composition of thermophilic species. Moreover, we introduce the first example of a 'compositional tree' of species that takes into account not only homologous proteins, but also proteins unique to particular species. We expect this simple yet novel approach to be a useful additional tool for the study of phylogeny at the genome level. Identification of thermophilic species by the amino acid compositions deduced from their genomes. DP Kreil CA Ouzounis Nucleic Acids Res, Vol. 29, No. 7. (1 April 2001), pp. 1608-1615. 2008-01-25T06:47:14-00:00 2001 Nucleic Acids Res 1362-4962 29 7 1608 1615 adaptation composition for-thuber genomics mesophily thermal thermophily http://www.citeulike.org/user/neils/article/822430 <i>PNAS, Vol. 96, No. 7. (30 March 1999), pp. 3578-3583.</i><br /><br />10.1073/pnas.96.7.3578 Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species Paul Haney Jonathan Badger Gerald Buldak Claudia Reich Carl Woese Gary Olsen doi:10.1073/pnas.96.7.3578 PNAS, Vol. 96, No. 7. (30 March 1999), pp. 3578-3583. 2006-08-30T23:15:59-00:00 1999 PNAS 96 7 3578 3583 adaptation for-thuber genomics hyperthermophily mesophily methanococcus methanogen thermal http://www.citeulike.org/user/neils/article/2288264 <i>Protein Eng., Vol. 14, No. 3. (1 March 2001), pp. 141-148.</i><br /><br />A systematic comparative analysis of 21 psychrophilic enzymes belonging to different structural families from prokaryotic and eukaryotic organisms is reported. The sequences of these enzymes were multiply aligned to 427 homologous proteins from mesophiles and thermophiles. The net flux of amino acid exchanges from meso/thermophilic to psychrophilic enzymes was measured. To assign the observed preferred exchanges to different structural environments, such as secondary structure, solvent accessibility and subunit interfaces, homology modeling was utilized to predict the secondary structure and accessibility of amino acid residues for the psychrophilic enzymes for which no experimental three-dimensional structure is available. Our results show a clear tendency for the charged residues Arg and Glu to be replaced at exposed sites on alpha-helices by Lys and Ala, respectively, in the direction from `hot' to `cold' enzymes. Val is replaced by Ala at buried regions in alpha-helices. Compositional analysis of psychrophilic enzymes shows a significant increase in Ala and Asn and a decrease in Arg at exposed sites. Buried sites in beta-strands tend to be depleted of Val. Possible implications of the observed structural variations for protein stability and engineering are discussed. 10.1093/protein/14.3.141 Structural adaptation of enzymes to low temperatures Giulio Gianese Patrick Argos Stefano Pascarella doi:10.1093/protein/14.3.141 Protein Eng., Vol. 14, No. 3. (1 March 2001), pp. 141-148. 2008-01-25T06:43:02-00:00 2001 Protein Eng. 14 3 141 148 adaptation enzymes for-thuber psychrophily structure thermal