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Molecular Biology and Biotechnology of Extremophiles

Molecular Biology and Biotechnology of Extremophiles

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It is now well recognised that many environments considered by man to be extreme are colonised by micro-organisms which are specifically adapted to these ecological niches. These organisms not only survive but actively grow under such conditions. A diverse range of bacteria, cyanobacteria, algae and yeasts has now been isolated from these habitats which are extreme in terms oftemperature, pH, salinity and pressure as well as species which are resistant to radiation and toxic chemicals. Whilst originally considered to be mere 'scientific curiosities', it is now generally accepted that many have con siderable biotechnological and commercial significance. Recently the term 'extremophile' has been used to describe these organisms. Over the past twenty years extensive studies of the ecology, physiology, taxonomy and molecular biology of these micro-organisms have been undertaken. These have resulted in a complete reassessment of our concept ofmicrobial evolution. The identification ofthe Archaeobacteria as the third kingdom ofliving organisms has given considerable impetus to extremophile research and is presenting many new challenges.
1 Biochemistry and molecular biology of the extremely thermophilic archaeobacteria.- 1.1 Introduction.- 1.2 Archaeobacterial phylogeny.- 1.3 Ecology of the thermophilic Archaea.- 1.3.1 Morphology of the Archaea.- 1.3.2 Physiology and biochemistry of the Archea.- 1.3.3 Enzymes.- 1.3.4 Structural macromolecules.- 1.3.5 Lipids and lipid biosynthesis.- 1.3.6 Molecular genetics of the extremely thermophilic Archaea.- References.- 2 The molecular genetics and biotechnological application of enzymes from extremely thermophilic eubacteria.- 2.1 Introduction.- 2.2 Aerobic eubacteria.- 2.2.1 The molecular biology and genetics of Thermus.- 2.2.2 Thermus aquaticus DNA polymerase.- 2.2.3 Thermus aquaticus restriction—modification system.- 2.2.4 Expression of other genes from Thermus genomic libraries.- 2.2.5 Proteinases from Thermus spp.- 2.2.6 Genetic transfer and plasmids in Thermus.- 2.2.7 A repetitive sequence in Thermus thermophilus.- 2.2.8 Promoter regions and other control sequences in Thermus.- 2.2.9 Genes and proteins from thermophilic strains of Bacillus.- 2.2.10 ?-Amylases from Bacillus spp.- 2.2.11 Pullulanases and related enzymes from thermophilic bacilli.- 2.2.12 Other genes and genetic systems in Bacillus stearothermophilus.- 2.3 Anaerobic eubacteria.- 2.3.1 Cloning of genes involved in cellulose hydrolysis.- 2.3.2 Hemicellulose hydrolysis.- 2.3.3 Starch hydrolysis.- 2.3.4 Pullulanases.- 2.4 Other enzymes from anaerobic thermophiles.- 2.4.1 Thermotoga.- References.- 3 Biotechnological prospects for halophiles and halotolerant micro-organisms.- 3.1 Introduction.- 3.2 Micro-organisms in the food industry.- 3.2.1 Food spoilage.- 3.2.2 Fermentation products.- 3.2.3 Single-cell protein (SCP).- 3.2.4 Food colouring/flavouring.- 3.3 Production of commercially useful compounds.- 3.3.1 Biological fermentation processes at high salinities.- 3.3.2 Pharmaceutical compounds.- 3,3.3 Polymers.- 3.3.4 Enzymes.- 3.3.5 Compatible solutes.- 3.4 Future aspects.- 3.4.1 Environmental biotechnology.- 3.4.2 Agricultural aspects.- 3.4.3 Fuel from renewable sources.- References.- 4 Acidophilic bacteria: adaptations and applications.- 4.1 Introduction.- 4.2 Constraints on growth at acid pH.- 4.2.1 Chemiosmotic considerations.- 4.2.2 Considerations of the conditions in the periplasm and the implications for its processes.- 4.3 The diversity of the extreme acidophiles.- 4.3.1 Iron-and sulphur-oxidising acidophiles.- 4.3.2 Phylum-and group-specific traits?.- 4.4 The bacterial extraction of metals from mineral sulphides.- 4.4.1 Factors influencing the selection of bacteria for mineral-leaching processes.- 4.5 Molecular genetic studies of acidophiles.- 4.5.1 The development of genetic systems for acidophiles.- 4.5.2 Gene transfer.- 4.6 Concluding comments: diversity, identification and applied molecular biology.- References.- 5 Alkaliphiles: ecology and biotechnological applications.- 5.1 Introduction.- 5.1.1 Ecology and environments.- 5.1.2 Alkaliphile diversity.- 5.1.3 Alkaliphile physiology.- 5.2 Alkaliphiles and industry.- 5.2.1 Enzymes.- 5.2.2 Spirulina.- 5.2.3 Secretion vectors.- 5.2.4 Future trends.- References.- 6 Physiology and biotechnological potential of deep-sea bacteria.- 6.1 Introduction.- 6.2 Deep-sea bacteria.- 6.3 Hydrothermal vents.- 6.3.1 Distribution of vent fields and their main features.- 6.3.2 Chemical features of hydrothermal fluids and expected metabolisms.- 6.3.3 Abundance and activity of bacteria in sea water.- 6.3.4 Bacterial communities on inert surfaces and bacterial mats.- 6.4.5 Main features of mesophilic bacteria isolated from sea water and surfaces.- 6.3.6 Invertebrate-associated bacteria.- 6.4 Biotechnology of deep-sea bacteria.- References.- 7 Physiology and molecular biology of psychrophilic micro-organisms.- 7.1 What are psychrophiles and psychrotrophs?.- 7.2 Microbial types of psychrophiles.- 7.3 Ecology of psychrophiles and psychrotrophs.- 7.3.1 Food.- 7.3.2 Terrestrial and aquatic ecosystems.- 7.4 Molecular mechanisms of adaptation to low temperature.- 7.4.1 Lipids, membrances and nutrient uptake.- 7.4.2 Proteins and protein synthesis.- 7.5 Biotechnological uses and potential of psychrophiles.- References.- 8 Molecular biology and biotechnology of microbial interactions with organic and inorganic heavy metal compounds.- 8.1 Introduction.- 8.2 Physiology of metal-microbe interactions.- 8.3 Molecular biology of heavy metal tolerance.- 8.3.1 Plasmid-mediated bacterial heavy metal resistance.- 8.3.2 Metal-binding proteins of fungi.- 8.4 Biotechnological aspects of metal-microbe interactions.- 8.4.1 Microbial removal and recovery of heavy metals and radionuclides.- References.- 9 Molecular biology of radiation-resistant bacteria.- 9.1 Introduction.- 9.2 Types of radiation.- 9.3 Radiation resistance of bacterial species.- 9.4 Repair of radiation damage: mutation rates and mutagens.- 9.5 The biology of the Deinobacteriaceae.- 9.5.1 Radiobiology.- 9.5.2 Molecular description of D. radiodurans.- 9.5.3 Genome of the deinococci.- 9.5.4 Transformation of the deinococci.- 9.6 Shuttle plasmids between D. radiodurans and E. coli.- 9.7 Gene expression in the deinococci.- 9.7.1 The DNA repair genes mtcA, mtcB, uvsC, uvsD and uvsC.- 9.7.2 The heterologous DNA repair gene deny of bacteriophage T4.- 9.7.3 The HPI gene.- 9.7.4 The leuB gene.- 9.7.5 The trp and asp genes.- 9.8 Prospects in molecular biology.- 9.9 Biotechnology of the deinococci.- 9.9.1 Radiation exposure measure.- 9.9.2 Restriction endonucleases.- 9.9.3 Z-DNA-binding protein.- 9.9.4 DNA repair enzymes.- 9.9.5 Membrane-bound exoenzymes.- 9.9.6 DNA polymerase.- 9.9.7 Manganese.- 9.10 Prospects for biotechnology.- References.- 10 Obligate anaerobes and their biotechnological potential.- 10.1 Introduction.- 10.2 The industrial exploitation of anaerobic fermentations.- 10.2.1 The acetone/butanol/ethanol fermentation.- 10.2.2 Methane generation.- 10.2.3 Other fermentations.- 10.2.4 Anaerobic mixed culture fermentations.- 10.3 Anaerobic disposal of organic wastes.- 10.3.1 Landfilling of wastes.- 10.3.2 Anaerobic digesters.- 10.3.3 Xenobiotic breakdown.- 10.4 Anaerobic biotransformations.- 10.4.1 Fermentation manipulation.- 10.4.2 Stereospecific, reductive biotransformations.- 10.5 Anaerobic enzymes as industrial products.- 10.6 Molecular genetics of anaerobic bacteria.- 10.6.1 Host—vector system development.- 10.6.2 Gene cloning.- 10.6.3 Recombinant manipulation of anaerobes.- 10.6.4 Gene probes for the detection of anaerobes.- References.- Species index.
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