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CONTENTS CONTENTS EXTREMOPHILES Extremophiles - Volume 1 No. of Pages: 396 ISBN: 978-1-905839-93-3 (eBook) ISBN: 978-1-84826-993-4 (Print Volume) Extremophiles - Volume 2 No. of Pages: 392 ISBN: 978-1-905839-94-0 (eBook) ISBN: 978-1-84826-994-1 (Print Volume) Extremophiles - Volume 3 No. of Pages: 364 ISBN: 978-1-905839-95-7 (eBook) ISBN: 978-1-84826-995-8 (Print Volume) For more information of e-book and Print Volume(s) order, please click here Or contact : [email protected] ©Encyclopedia of Life Support Systems (EOLSS) EXTREMOPHILES CONTENTS VOLUME I Extremophiles: Basic Concepts 1 Charles Gerday, Laboratory of Biochemistry, University of Liège, Belgium 1. Introduction 2. Effects of Extreme Conditions on Cellular Components 2.1. Membrane Structure 2.2. Nucleic Acids 2.2.1. Introduction 2.2.2. Desoxyribonucleic Acids 2.2.3. Ribonucleic Acids 2.3. Proteins 2.3.1. Introduction 2.3.2. Thermophilic Proteins 2.3.2.1. Enthalpically Driven Stabilization Factors: 2.3.2.2. Entropically Driven Stabilization Factors: 2.3.3. Psychrophilic Proteins 2.3.4. Halophilic Proteins 2.3.5. Piezophilic Proteins 2.3.5.1. Interaction with Other Proteins and Ligands: 2.3.5.2. Substrate Binding and Catalytic Efficiency: 2.3.6. Alkaliphilic Proteins 2.3.7. Acidophilic Proteins 3. Conclusions Extremophiles: Overview of the Biotopes 43 Michael Gross, University of London, London, UK 1. Introduction 2. Extreme Temperatures 2.1. Terrestrial Hot Springs 2.2. Hot Springs on the Ocean Floor and Black Smokers 2.3. Life at Low Temperatures 3. High Pressure 3.1. The Deep Sea 3.2. The Deep Subsurface 4. Chemical Stress Factors 4.1. High-Salinity Biotopes 4.2. Life at Extreme pH 4.3. Hydrophobic Environments 5. Other Extremes 5.1. Resistance to Drought and Radiation 5.2. Yet to be Discovered 6. Extremophiles and the Evolution of Life 6.1. Primeval Earth as an Extreme Habitat 6.2. Archaea: A New, Very Old Domain of Life 6.3. Does Life Come out of the Heat? Phylogeny of Extremophiles 71 Nicolas Glansdorff, Vrije Universiteit Brussel, Brussels, Belgium Ying Xu, Vrije Universiteit Brussel, Brussels, Belgium ©Encyclopedia of Life Support Systems (EOLSS) i EXTREMOPHILES 1. Introduction 2. The Structure of the Tree of Life 2.1. The Last Common Ancestor (LCA) and the Three Domains 2.2. The Root of the Tree of Life 3. Was the LCA a Hyperthermophile? 4. Was the LCA a Prokaryote? 5. The Origin of Prokaryotes and of Hyperthermophily 6. Thermophilic Prokaryotes 7. Piezophilic Prokaryotes 8. Psychrophilic Prokaryotes 9. Extreme Halophiles 10. Concluding Remarks Survival Strategies and Membrane Properties of Extremophiles 98 Wil N. Konings, University of Groningen, The Netherlands Sonja-Verena Albers, University of Groningen, The Netherlands Sonja M. Koning, University of Groningen, The Netherlands Arnold J.M. Driessen, University of Groningen, The Netherlands 1. Introduction 2. Composition of the Membrane 3. Bioenergetics 4. Bioenergetic Problems of Extremophiles 4.1. Temperature 4.2. Salt 4.3. pH 5. Transport of Solutes in Extremophiles 5.1. Secondary Transporters 5.2. ABC Transporters 5.2.1. Solute-Binding Proteins 5.2.2. ATP-Binding Domains 5.3. Distribution of Transporters 6. Conclusions Thermophily 117 Gudmundur O. Hreggvidsson, University of Iceland and Prokaria Ltd, Reykjavik, Iceland Jakob K. Kristjansson, University of Iceland and Prokaria Ltd, Reykjavik, Iceland 1. Introduction 1.1. Thermophily and Geochemical History 1.2. Definitions and Terminology 2. Habitats and Ecology 2.1. Diversity of Thermal Environments 2.2. Energy Sources and Physiology 2.3. Development of Isolation Methods 2.4. Culture-Independent Studies of Thermophilic Communities 3. Thermophile Diversity and Population Structure 3.1. Phylogeny and Species 3.2. Main Thermophilic Bacterial Phyla 3.2.1. Thermophilic Cyanobacteria 3.2.2. The Genus Thermus 3.2.3. The Order Aquificales 4. Archaea 5. Distribution and Speciation of Thermophiles 5.1. Global Distribution of Thermophiles 5.2. Dispersal of Thermophiles ©Encyclopedia of Life Support Systems (EOLSS) ii EXTREMOPHILES 5.3. Evolution and Speciation of Thermophiles 5.4. Lateral Gene Transfer in Thermophiles 6. Conclusion Hyperthermophilic Microorganisms 158 Karl O. Stetter, Universität Regensburg, Lehrstuhl für Mikrobiologie, Universitätsstraße 31, D-93053 Regensburg, Germany 1. Introduction 2. Biotopes of Hyperthermophiles 2.1. Terrestrial Biotopes 2.2. Marine Biotopes 3. Phylogeny of Hyperthermophiles 4. Taxonomy of Hyperthermophiles 5. Sampling and Isolation of Hyperthermophiles 6. Strategies of Life and Environmental Adaptations of Hyperthermophiles 6.1. General Metabolic Potentialities 6.2. Physiological Properties of the Different Groups of Hyperthermophiles 6.2.1. Terrestrial Hyperthermophiles 6.2.2. Marine Hyperthermophiles 7. Distribution of Species and Complexity in Hyperthermophilic Ecosystems 8. Basis of Heat Stability and the Upper Temperature Limit for Life 9. Conclusions: hyperthermophiles in the history of life Strategies of Hyperthermophiles in Nucleic Acids Adaptation to High Temperature 189 Patrick Forterre, Universite de Paris-Sud, France 1. Introduction 2. The General Problem of Nucleic Acid Stability at High Temperature 3. Thermoprotection of RNA in Hyperthermophiles 3.1. Protection of RNA against Thermodenaturation 3.2. The Problem of RNA Thermodegradation 3.3. Hyperthermophiles and the Possibility of a Very Hot RNA World 4. Thermoprotection of DNA in Hyperthermophiles 4.1. Effect of Temperature on the DNA Secondary and Tertiary Structures 4.2. Effect of Temperature on the DNA Chemical Integrity 4.2.1. Depurination 4.2.2. DNA—Cytosine Deamination 4.3. DNA Repair in Hyperthermophiles 4.4. Reverse Gyrase 5. Conclusion Thermostability and Thermoactivity of Extremozymes 209 Michael John Danson, University of Bath, UK David W. Hough, University of Bath, UK 1. Introduction 2. Enzyme Stability 2.1. Thermodynamic Stability 2.2. Kinetic Stability 2.3. Thermostability 3. The Structural Basis of Thermostability 3.1. Conformational Flexibility and Loop Regions 3.2. Increased Hydrophobicity 3.3. Ionic Interactions and Networks ©Encyclopedia of Life Support Systems (EOLSS) iii EXTREMOPHILES 3.4. Packing Density and Other Electrostatic Interactions 3.5. Other Structural Features 3.6. Oligomeric Enzymes and Subunit Interactions 3.7. Thermolabile Amino Acids 4. Observations from Nature 4.1. Systematic Structural Comparisons 4.2. Specific Enzyme Studies 4.3. Citrate Synthase: an Homologous Series Spanning the Biological Temperature Range 5. Lessons From Directed Evolution 5.1. Thermal Adaptation of Enzyme Stability 5.2. Adaptation of Catalytic Activity 5.3. Flexibility and Stability 6. Intrinsic versus Extrinsic Factors in Enzyme Thermostability 7. Thermoactivity 7.1. Catalytic Activity at Physiological Temperatures 7.2. The Temperature Optimum of an Enzyme 8. Concluding Remarks Unique Aspects of the Hyperthermophile Proteome 239 James F. Holden, University of Georgia, Athens, Georgia, USA Michael W. W. Adams, University of Georgia, Athens, Georgia, USA 1. Introduction 2. Systematics of the Order Thermococcales 2.1. Phylogeny 2.2. Growth Characteristics 2.3. Habitats 3. Characterized Enzymes and Proteins 3.1. Oxidoreductases (EC 1.-.-.-) 3.2. Transferases (EC 2.-.-.-) 3.3. Hydrolases (EC 3.-.-.-) 3.3.1. Esterases (EC 3.1.-.-) 3.3.2. Glycosylases (EC 3.2.-.-) 3.3.3. Peptidases (EC 3.4.-.-) 3.3.4. Other Hydrolases 3.4. Lyases (EC 4.-.-.-) 3.5. Isomerases (EC 5.-.-.-) 3.6. Ligases (EC 6.-.-.-) 3.7. Other Proteins 4. Starch Catabolism 5. Functional and Structural Genomics 6. Conclusions Compatible Solutes in Microorganisms that Grow at High Temperature 265 Milton S. da Costa, Universidade de Coimbra, Coimbra, Portugal Helena Santos, Universidade Nova de Lisboa, Oeiras, Portugal 1. Introduction 2. Strategies for Osmotic Adaptation in Microorganisms 3. Compatible Solutes of Organisms that Live at High Temperatures 4. The Distribution of Compatible Solutes Within the Tree of Life 5. Reflections on the Physiological Role of Compatible Solutes in Thermoadaptation 6. The Effect of Hypersolutes on Protein Stability 6.1. The Effect of Mannosylglycerate on the Stabilization of Enzymes 6.2. The Effect of Di-myo-Inositol-Phosphate on the Stabilization of Enzymes 6.3. Stabilization of Proteins and Enzymes by Diglycerol Phosphate ©Encyclopedia of Life Support Systems (EOLSS) iv EXTREMOPHILES 6.4. Stabilization of Enzymes by Cyclic 2,3-Bisphosphoglycerate 7. Pathways for the Synthesis of Compatible Solutes in Thermophiles and Hyperthermophiles 8. Concluding Remarks Heat-Shock Response in Thermophilic Microorganisms 282 Mose Rossi, Istituto di Biochimica delle Proteine ed Enzimologia, Napoli, Italy and Università “Federico II”, Napoli, Italy Annamaria Guagliardi, Università “Federico II”, Napoli, Italy 1. Introduction 1.1. The Concept of Molecular Chaperone 2. Even Extreme Thermophiles Display Heat-Shock Response 3. Archaeal Chaperonins 3.1. Chaperonin-Assisted In Vitro Folding of Denatured Proteins 3.2. Chaperonin-Mediated Prevention of Native Protein Denaturation 3.3. Chaperonin-Dependent Formation of Filaments 4. Archaeal Chaperonins Are Biotechnological Tools 5. Perspectives Thermoactive Enzymes in Biotechnological Applications 294 Costanzo Bertoldo, Technical University Hamburg-Harburg, Hamburg, Germany Garabed Antranikian, Technical University Hamburg-Harburg, Hamburg, Germany 1. Introduction 2. Extreme Environments as a Source of Novel Thermoactive Enzymes 2.1. Biology at the Boiling Point of Water 2.2. 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    Proc. Natl. Acad. Sci. USA Vol. 92, pp. 12285-12289, December 1995 Biochemistry Intercellular mobility and homing of an archaeal rDNA intron confers a selective advantage over intron- cells of Sulfolobus acidocaldarius CLAus AAGAARD, JACOB Z. DALGAARD*, AND ROGER A. GARRETr Institute of Molecular Biology, Copenhagen University, S0lvgade 83 H, 1307 Copenhagen K, Denmark Communicated by Carl R. Woese, University of Illinois at Urbana-Champaign, Urbana, IL, August 28, 1995 ABSTRACT Some intron-containing rRNA genes of ar- experiments suggest, but do not establish, that the intron is chaea encode homing-type endonucleases, which facilitate mobile between yeast cells. intron insertion at homologous sites in intron- alleles. These To test whether the archaeal introns constitute mobile archaeal rRNA genes, in contrast to their eukaryotic coun- elements, we electroporated the intron-containing 23S rRNA terparts, are present in single copies per cell, which precludes gene from the archaeal hyperthermophile Desulfurococcus intron homing within one cell. However, given the highly mobilis on nonreplicating bacterial vectors into an intron- conserved nature of the sequences flanking the intron, hom- culture of Sulfolobus acidocaldarius. In the presence of I-Dmo ing may occur in intron- rRNA genes of other archaeal cells. I, the endonuclease encoded by the D. mobilis intron (20), the To test whether this occurs, the intron-containing 23S rRNA intron was shown to home in the chromosomal DNA of intron- gene of the archaeal hyperthermophile Desulfurococcus mobi- cells of S. acidocaldarius. Moreover, using a double drug- lis, carried on nonreplicating bacterial vectors, was electro- resistant mutant (21), it was demonstrated that the intron can porated into an intron- culture of Sulfolobus acidocaldarius.
  • 2I52 Lichtarge Lab 2006

    2I52 Lichtarge Lab 2006

    Pages 1–11 2i52 Evolutionary trace report by report maker February 25, 2010 4.3.3 DSSP 10 4.3.4 HSSP 10 4.3.5 LaTex 10 4.3.6 Muscle 10 4.3.7 Pymol 10 4.4 Note about ET Viewer 10 4.5 Citing this work 10 4.6 About report maker 11 4.7 Attachments 11 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2i52): Title: Crystal structure of protein pto0218 from picrophilus torridus, pfam duf372 Compound: Mol id: 1; molecule: hypothetical protein; chain: a, b, CONTENTS c, d, e, f; engineered: yes Organism, scientific name: Picrophilus Torridus; 1 Introduction 1 2i52 contains a single unique chain 2i52F (119 residues long) and its homologues 2i52A, 2i52D, 2i52C, 2i52E, and 2i52B. 2 Chain 2i52F 1 2.1 Q6L2J9 overview 1 2.2 Multiple sequence alignment for 2i52F 1 2.3 Residue ranking in 2i52F 1 2.4 Top ranking residues in 2i52F and their position on the structure 1 2 CHAIN 2I52F 2.4.1 Clustering of residues at 25% coverage. 1 2.4.2 Overlap with known functional surfaces at 2.1 Q6L2J9 overview 25% coverage. 2 From SwissProt, id Q6L2J9, 97% identical to 2i52F: Description: Hypothetical protein. 3 Notes on using trace results 9 Organism, scientific name: Picrophilus torridus. 3.1 Coverage 9 Taxonomy: Archaea; Euryarchaeota; Thermoplasmata; Thermoplas- 3.2 Known substitutions 9 matales; Picrophilaceae; Picrophilus. 3.3 Surface 9 3.4 Number of contacts 9 3.5 Annotation 9 3.6 Mutation suggestions 9 2.2 Multiple sequence alignment for 2i52F 4 Appendix 9 For the chain 2i52F, the alignment 2i52F.msf (attached) with 30 4.1 File formats 9 sequences was used.