© 1995 • 1037 pp., illus., appendices, index
Cloth (three-book set) • ISBN  0-87969-397-5

Foreword by Carl R. Woese, University of Illinois

The use of ribosomal RNA sequences as molecular chronometers has led to the recognition of a group of prokaryotes, the Archaea, that are phylogenetically distinct from both bacteria and eukaryotes. Although the Archaea are prokaryotes, lacking a nuclear membrane and possessing a single circular chromosome, they possess several molecular properties with similarity to the eukaryotes such as transcription signals, transcription factors, chaperones, and histones. Their unique phylogeny is underscored by a predilection for extreme environments which include high temperature, high salt, and strictly anaerobic conditions and the adaptive strategies that they have evolved to survive in these environments. These unique biomolecular adaptations have recently generated interest in the areas of genetic variability and genome evolution, extremely thermostable enzymes, such as DNA polymerases for PCR, methanogenesis as an alternative fuel source, anaerobic bioremediation, and use of bacteriorhodopsin for production of a biocomputer chip or a model for transmembrane ion translocation.

The Archaea occupy a pivotal phylogenetic position and offer extraordinary potential for biotechnology. One of the difficulties facing researchers, especially newcomers who wish to study the Archaea, has been the lack of a comprehensive source for the specialized techniques required. As the field has evolved, solutions to many problems have been discovered empirically and the special techniques have largely been disseminated either verbally or by means of journal articles. The protocols in these three books are selected to provide a detailed guide to experiments with the methanogenic, extremely halophilic, and thermophilic sulfur-utilizing Archaea, with overviews to highlight areas of future development. The individual protocols consist of an introduction describing the specific applications of the techniques, step-by-step procedures for applying the protocols, followed by any additional comments that will facilitate successful application of the protocol. A feature of research in this area is the interplay between microbiology, bioengineering, bio-chemistry, and molecular biology, and authors from all of these fields have been selected to provide these three concise and comprehensive resources for scientists interested in conducting research on the Archaea.

• Volume 1: Halophilic Archaea
• Volume 2: Methanogenic Archaea
• Volume 3: Thermophilic Archaea

Volume 1: Halophiles

Halophilic Archaea: An Overview (S. DasSarma)

Growth and Identification: Protocol 1. Cultivation of Halophilic Archaea (F. Rodriguez-Valera); Protocol 2. Growth of Halophilic Archaea Under Conditions of Low Oxygen Tension and High Light Intensity (M.C. Betlach, R.F. Shand); Protocol 3. Selection and Screening Methods for Halobacterial Rhodopsin Mutants (J.L. Spudich, E.N. Spudich); Protocol 4. Electron Microscopy of Halobacteria (Y. Nishiyama et al.)

Biochemistry: Protocol 5. Isoprenoids and Polar Lipids of Extreme Halophiles (M. Kates, S. Kushwaha); Protocol 6. Isolation of Purple Membranes (D. Oesterhelt); Protocol 7. Purification of Halorhodopsin from Halobacterium halobium (J.K. Lanyi); Protocol 8. Spectroscopic Assays for Sensory Rhodopsins I and II in Halobacterium salinarium Cells and Enriched Membrane Preparations (R.A. Bogomolni et al.); Protocol 9. Purification of the ATPase from Halobacterium halobium (B. Schobert); Protocol 10. Electrophoresis of Halobacterium Gas Vesicles in Phenol-Acetic Acid-Urea Gels (R.D. Simon); Protocol 11. Isolation of Halobacterial Ferredoxin (D. Oesterhelt, L. Kerscher); Protocol 12. Halophilic Proteases from Halophilic Archaea (M. Kamekura); Protocol 13. Purification of Halophilic Archaeal Ketohexokinase from Haloarcula vallismortis (V. Rangaswamy, W. Altekar); Protocol 14. Purification of Superoxide Dismutase and a Catalase-Peroxidase in a High-salt Environment (M.L. Salin, N.J. Brown-Peterson);

Molecular Biology and Genetics: Protocol 15. Purification of Halobacterium halobium DNA Polymerases (M. Kohiyama et al.); Protocol 16. Purification of DNA-dependent RNA Polymerase from Halobacterium halobium (F. Gropp, J. Leibrock); Protocol 17. Preparation of Transfer RNA, Aminoacyl-tRNA Synthetases, and tRNAs Specific for an Amino Acid from Extreme Halophiles (R. Gupta); Protocol 18. Cell-free Protein Synthesis System for Halobacterial Archaea (I. Marin et al.); Protocol 19. Isolation of Free and Membrane-bound Polysomes from Halobacterium halobium (R. Gropp); Protocol 20. Total Reconstitution of Ribosomal Subunits of Haloferax mediterranei (M.E. Sanchez, R. Amils); Protocol 21. The MPD-NaClH2O System for the Crystalization of Halophilic Proteins (S. Richard et al.); Protocol 22. Purification and Labeling of RNA from Halobacterium halobium for Identification of Regulated Genes (S. DasSarma, J.-M. Kim); Protocol 23. A Rapid Procedure for the Isolation of RNA from Haloferax volcanii (D.T. Nieuwlandt et al.); Protocol 24. Analysis of RNA Transcripts in Archaea (P.P. Dennis, J. Chow); Protocol 25. Isolation of Genomic and Plasmid DNAs from Halobacterium halobium (W.-L. Ng et al.); Protocol 26. Preparation of Intact, Agarose-embedded DNA from Halobacterium halobium and Its Digestion by Restriction Enzyme (N. Hackett); Protocol 27. Fractionation of Halobacterial DNA into FI and FII Using Affinity Chromatography on Malachite Green Bisacrylamide (F. Pfeifer); Protocol 28. Electrophoretic Mobility Shift Assays with Crude Extracts of Halobacterium halobium (N. Hackett, R. Ken); Protocol 29. Transformation of Halophilic Archaea (S.W. Cline et al.); Protocol 30. Gene Replacement in Halobacterium halobium (M. Krebs); Protocol 31. Selection for Spontaneous and Engineered Mutations in the rRNA Genes in Halophilic Archaea (A.S. Mankin)

Appendices

Volume 2: Methanogens

Methanogenic Archaea: An Overview (K.R. Sowers)

Growth and Identification: Protocol 1. Techniques for Anaerobic Growth (K.R. Sowers, K.M. Noll); Protocol 2. Growth of Methanogens on Solidified Medium (D.L. Tumbula et al.); Protocol 3. Plating Techniques for Extremely Thermophilic Methanogens (A. Rodabough et al.); Protocol 4. Growth of Methanosarcina spp. as Single Cells (K.R. Sowers); Protocol 5. Large-scale Culture Techniques (L. Daniels); Protocol 6. Large-scale Growth of Acetate- and Formate-utilizing Methanogens in a pH Auxostat (K.R. Sowers); Protocol 7. Short- and Long-term Maintenance of Stock Cultures (D.R. Boone); Protocol 8. Long-term Maintenance of Stock Cultures in Glycerol (D.L. Tumbula et al.); Protocol 9. Techniques for Monitoring Cell Growth (K.R. Sowers); Protocol 10. Immunologic Identification and Analysis (E. Conway de Macario, A.J.L. Macario); Protocol 11. Use of Fluorescent Probes for Determinative Microscopy (D.A. Stahl et al.); Protocol 12. Electron Microscopy Techniques for the Archaea (M. Firtel et al.)

Biochemistry: Protocol 13. Techniques for Anaerobic Biochemistry (K.R. Sowers); Protocol 14. Purification of Tetrahydromethanopterin-dependent Enzymes (A.A. DiMarco et al.); Protocol 15. Purification of Methylreductase and Components A2 and A3a from Methanobacterium thermoautotrophicum (C.H. Kuhner et al.); Protocol 16. Purification of Coenzymes (D.J. Stemke); Protocol 17. Purification of F420-reducing Hydrogenase from Methanobacterium formicicum (S.F. Baron, J.G. Ferry); Protocol 18. Purification of Formate Dehydrogenase from Methanobacterium formicicum (N.L. Schauer, J.G. Ferry); Protocol 19. Purification of Methanosarcina thermophila Acetate Kinase and Phosphotransacetylase Overproduced in Escherichia coli (M.T. Latimer, J.G. Ferry); Protocol 20. Purification of Carbon Monoxide Dehydrogenase from Methanosarcina thermophila (M.E. Rasche et al.); Protocol 21. Purification of Carbon Monoxide Dehydrogenase-linked Ferredoxin from Methanosarcina thermophila (A.P. Clements, J.G. Ferry); Protocol 22. Purification of Carbonic Anhydrase from Methanosarcina thermophila (B.E. Alber, J.G. Ferry); Protocol 23. Purification of Methanol-catabolizing Enzymes (J.T. Keltjens et al.); Protocol 24. Purification of Enzymes Involved in Secondary Alcohol Utilization (F. Widdel, U. Frimmer); Protocol 25. Electron Microscopy Technique for Immunocytochemical Localization of Enzymes (M. Hoppert, F. Mayer); Protocol 26. Purification of Nitrogenase (Y.-T. Chien, S.H. Zinder); Protocol 27. Preparation of Pseudomurein Endopeptidase from Methanobacterium wolfei (D. Stax et al.); Protocol 28. Preparation of Methanosarcina-disaggregating Enzyme (L. Xun et al.); Protocol 29. Purification of DNA-dependent RNA Polymerase (M. Thomm); Protocol 30. Purfication of the Histone HMf from Methanothermus fervidus (K. Sandman et al.); Protocol 31. Purification of Flagellins (K.F. Jarrell et al.); Protocol 32. Isolation and Analysis of Cell Walls (H. Konig); Protocol 33. Purification of Ether Lipids and Liposome Formation from Polar Lipid Extracts (G.D. Sprott et al.); Protocol 34. Turnover of Amino Acids Monitored by NMR Spectroscopy (M.F. Roberts); Protocol 35. Detection of Phosphorylated Small Molecules H by 31P and 13C NMR Spectroscopy (A. Gorkovenko, M.F. Roberts); Protocol 36. Extraction and Detection of Compatible Intracellular Solutes (R. Ciulla et al.)

Molecular Biology and Genetics: Protocol 37. Isolation of Chromosomal and Plasmid DNAs (K.R. Sowers); Protocol 38. Isolation of RNA (M. Thomm, H.-P. Gohl); Protocol 39. Chromosomal Mapping (J. Sitzmann, A. Klein); Protocol 40. Gene Cloning following Size Selection of Restriction Endonuclease Fragments (K. Sandman et al.); Protocol 41. Gene Selection and Cloning with Bacteriophage l Libraries (K.R. Sowers); Protocol 42. Mutagenesis of Methanococcus spp. with Ethyl Methane-sulfonate (Y.-L. Yang et al.); Protocol 43. Selection for Auxotrophic Mutants of Methanococcus (T.L. Bowen et al.); Protocol 44. Integration Vectors (A. Klein, K. Horner); Protocol 45. Transformation of Methanococcus voltae by Protoplast Regeneration (G.B. Patel et al.); Protocol 46. Transduction of Methanobacterium thermo-autotrophicum Marburg (L. Meile et al.); Protocol 47. Techniques for In Vitro Transcription Assays (M. Thomm, W. Hausner)

Appendices

Volume 3: Thermophiles

Thermophilic Archaea: An Overview (M.W.W. Adams)

Growth and Identification: Protocol 1. Isolation and Cultivation of Heterotrophic Hyperthermophiles from Deep-sea Hydrothermal Vents (H.W. Jannasch et al.); Protocol 2. Isolation, Growth, and Maintenance of Hyperthermophiles (J.A. Baross); Protocol 3. Plate Cultivation Technique for Strictly Anaerobic, Thermophilic, Sulfur-metabolizing Archaea (G. Erauso, D. Prieur); Protocol 4. Continuous Culture Techniques for Extremely Thermophilic and Hyperthermophilic Archaea (R.N. Schicho et al.); Protocol 5. High-pressure-High-temperature Cultivation of Extremely Thermophilic Archaea (C.M. Nelson, D.S. Clark); Protocol 6. Large-scale Growth of Hyperthermophiles (M.W.W. Adams); Protocol 7. Culture of Thermoplasma acidophilum (D. Searcy)

Biochemistry: Protocol 8. Solubilization from Membranes and Purification of Hydrogenases from Pyrodictium spp. (R.J. Maier et al.); Protocol 9. Purification of Hydrogenase and Ferredoxin from a Hyperthermophile (M.W.W. Adams, Z.H. Zhou); Protocol 10. Archaeal Lipid Analysis (D.B. Hedrick, D.C. White); Protocol 11. Glucose Metabolic Pathways in Thermoplasma acidophilum using 13C and 15N NMR Spectroscopy (K.J. Stevenson et al.)

Molecular Biology and Genetics: Protocol 12. Purification of Plasmids from Thermophilic and Hyperthermophilic Archaea (F. Charbonnier, P. Forterre); Protocol 13. Transfection of Sulfolobus solfataricus (C. Schleper, W. Zillig); Protocol 14. Preparation of Genomic DNA from Sulfur-dependent Hyperthermophilic Archaea (R. Vijayaragavan, M.W.W. Adams); Protocol 15. RNA Extraction from Sulfur-utilizing Thermophilic Archaea (J. DiRuggiero, F.T. Robb); Protocol 16. Reliable Amplification of Hyperthermophilic Archaeal 16S rRNA Genes by the Polymerase Chain Reaction (A.-L. Reysenbach, N.R. Pace); Protocol 17. Characterization of Archaeal Introns in the rRNA Genes of Hyperthermophiles (J.Z. Dalgaard et al.); Protocol 18. Generation of Subtraction Probes for Isolation of Specific Genes in Thermophilic Archaea (K.A. Robinson et al.); Protocol 19. Isolation of Sulfolobus acidocaldarius Mutants (D. Grogan); Protocol 20. Measurement of Mutation Rates in Sulfolobus acido-caldarius (D. Grogan); Protocol 21. Typing Marine Vent Thermophiles by DNA Polymerase Restriction Fragment Length Polymorphisms (F.B. Perler et al.); Protocol 22. Typing Hyperthermophilic Archaea Based on the 16S/23S rRNA Spacer Region (J. DiRuggiero et al.); Protocol 23. In Vitro Transcription from Natural and Mutated rDNA Promoters of the Extremely Thermophilic Archaeon Sulfolobus shibatae (J. Hain, W. Zillig)

Appendices