Silicon Biomineralization

Organisms: Diatoms.- Living Inside a Glass Box-Silica in Diatoms.- 1 Introduction.- 2 Silica in Protozoa, Sponges and Higher Plants.- 2.1 Phaeodaria.- 2.2 Choanoflagellates.- 2.3 Silicoflagellates.- 2.4 Sponges.- 2.5 Plants.- 3 Living in a Glass Box-the Diatoms.- 4 Biosilicification in Diatoms.- 5 Conclusion.- References.- Components and Control of Silicification in Diatoms.- 1 Introduction.- 2 Features of Diatom Cell Walls and Terminology.- 3 Transport of Silicic Acid into the Diatom Cell.- 4 Intracellular Silicic Acid Transport.- 5 Micromorphogenesis vs.Macromorphogenesis.- 5.1 Micromorphogenesis-the Nanostructure of Diatom Biosilica.- 5.2 Control of Micromorphogenesis.- 6 Macromorphogenesis-the Formation of Large-Scale Silicified Structures in the Diatom Cell Wall.- 7 The Silica Deposition Vesicle-the “Black Box” in the Process of Silicification.- 8 Conclusions and Future Prospects.- References.- The Phylogeny of the Diatoms.- 1 Introduction.- 2 Approaches to Reconstruct Phylogenies.- 3 The Diatom Silica Frustule.- 3.1 Morphology of the Silica Frustule.- 3.2 Taxonomy Based on Characteristics of the Silica Frustule.- 3.3 The Phylogeny Inferred from Nuclear SSU rDNA Sequences.- 3.4 Phylogenetic Relevance of Taxonomy and Frustule Characters.- 3.4.1 The Radial Centrics.- 3.4.2 The Bipolar Centrics.- 3.4.3 The Bipolar Centric Toxarium.- 3.4.4 The Araphid Pennates.- 3.4.5 The Position of Pseudohimantidium.- 3.4.6 The Raphid Pennates.- 4 Phylogenetic Signal in Diatom Chloroplast Structure.- 5 Phylogenetic Signal in the Life Cycle and Auxospore Ontogeny.- 5.1 Gamete Formation.- 5.2 Auxospore Development.- 6 The Phylogenetic Position of the Diatoms Within Heterokonta.- 6.1 The Ancestry of the Diatoms.- 6.2 Origin of Pigmented Heterokontophyta and the End Permian Mass Extinction.- 6.3 Origin of the Silica Cell Wall Within Heterokonta.- 7 Historical Ecology.- 8 Palaeontology and Phylogeny.- 9 Conclusions.- References.- Silicon-a Central Metabolite for Diatom Growth and Morphogenesis.- 1 Introduction.- 2 Silicon Uptake and Transport: Regulation and Influencing Factors.- 2.1 Uptake, Transport and Soluble Pools.- 2.2 Energy Requirement.- 2.3 Factors Affecting the Uptake and Transport Processes.- 3 Link Between Silicon Metabolism, Growth and Cell Division.- 3.1 Coupling Between Silicon Metabolism and Cell Growth.- 3.2 Cell-Cycle Regulation.- 4 Diatom Morphogenesis.- 4.1 Overview of the Morphogenesis Process.- 4.2 Differentiation Programs Involving Silicon Morphogenesis.- 5 Morphological Plasticity and Variation.- 5.1 Size Reduction and Polymorphism.- 5.2 Impact of Growth Conditions and Environment.- 5.2.1 Light, Major Nutrients and Temperature.- 5.2.2 Salinity and Osmotic Stress.- 5.2.3 Trace Elements and Pollutants.- 6 Regulatory Mechanisms in Silicon Metabolism and Morphogenesis.- References.- Organisms: Higher Plants.- Functions of Silicon in Higher Plants.- 1 Introduction.- 2 Beneficial Effects of Silicon in Different Plant Species.- 2.1 Si-Accumulating Plants Versus Si Nonaccumulating Plants.- 2.2 Accumulation Process of Si in Si-Accumulating Plants.- 2.3 Effect of Si on the Growth of Si-Accumulating Plants.- 2.4 Effect of Si on the Growth of Si Nonaccumulating Plants.- 3 Functions of Si in Higher Plants.- 3.1 Stimulation of Photosynthesis.- 3.2 Alleviation of Physical Stress.- 3.2.1 Radiation Damage.- 3.2.2 Water Stress.- 3.2.3 Climatic Stress.- 3.3 Improvement of Resistance to Chemical Stress.- 3.3.1 Nutrient Imbalance Stress.- 3.3.1.1 Phosphorus Deficiency and Excess 13.- 3.3.1.2 N Excess 13.- 3.3.2 Metal Toxicity Stress.- 3.3.2.1 Mn and Fe Toxicity 14.- 3.3.2.2 Na Excess 14.- 3.3.2.3 Al Toxicity 14.- 3.4 Increase in Resistance to Abiotic Stress.- 3.4.1 Disease.- 3.4.2 Pests.- 4 Conclusion.- References.- Silicon in Plants.- 1 Introduction.- 2 Silicon in Monocots.- 2.1 SiO2 Deposits in Monocots.- 2.2 Silicic Acid in Monocots.- 3 Si in Dicots.- 4 Si in Cell Walls.- 5 Formation of SiO2 Deposits in Plants.- 6 Uptake and Long-Distance Transport.- References.- Organisms: Sponges.- Silica Deposition in Demosponges.- 1 Introduction.- 2 The Cells Involved.- 3 The Axial Filament.- 4 Extracellular Versus Intracellular Silica Deposition: the Role of Membranes.- 5 The Process of Silica Polymerization.- 6 Environmental Factors Modulating Silica Deposition.- 7 The Future.- References.- Molecular Mechanism of Spicule Formation in the Demosponge Suberites domuncula: Silicatein-Collagen-Myotrophin.- 1 Introduction.- 2 Sponges.- 3 Spiculogenesis.- 3.1 The Model Test System: Primmorphs.- 3.2 Effect of Silicon on the Spicule Formation.- 3.3 Silicon-Responsive Genes.- 3.3.1 Silicatein.- 3.3.2 Collagen.- 3.3.3 Myotrophin.- 3.4 Effect of Silicon on Silicon-Responsive Genes.- 3.5 Inhibition of Biosilica Formation by Germanium.- 3.6 Proposed Pathway for Spicule Formation.- 4 Expression of Silicatein in Primmorphs and in Sponge Tissue.- 5 Biosilica Formation.- 5.1 Silicatein cDNA Expression.- 5.2 Silicatein Enzyme Assay.- 6 Effect of Iron.- 6.1 Effect of Iron on the Expression of Ferritin, Septin and Scavenger Receptor in Primmorphs.- 7 Conclusion.- References.- Biotechnology.- Biotechnological Advances in Biosilicification.- 1 Introduction.- 2 Silicon Transport in Diatoms.- 3 Proteins Closely Associated with the Silica Wall of Diatoms.- 4 Polycationic Peptides and Polyamines Accelerate Silica Condensation.- 5 Employing Silica-Condensing Peptides to Fabricate Nanostructured Devices.- 6 Polycondensation-Catalyzing, Structure-Directing Catalytic Proteins from Sponge Biosilica.- 7 Structure-Directing Polycondensation-Catalyzing Diblock Copolypeptides.- 8 Gene Expression During Sponge Development.- 9 The Biological Precursor for Silica Synthesis.- 10 Recognition of Inorganic Compounds Using Phage Display.- 11 Future Prospects.- References.- Silicase, an Enzyme Which Degrades Biogenous Amorphous Silica: Contribution to the Metabolism of Silica Deposition in the Demosponge Suberites domuncula.- 1 Introduction.- 2 Siliceous Spicule Turnover.- 3 Screening for Silica Degrading Enzymes.- 3.1 The Model Test System: Primmorphs.- 3.2 ¡°Differential Display¡± of Transcripts.- 3.3 Cloning of the Gene Encoding the Silicase.- 3.3.1 Silicase.- 3.3.2 Phylogenetic Analysis of Silicase.- 4 Cloning of a Marker Gene of the Intermediary Metabolism.- 5 Preparation of Recombinant Silicase.- 6 Enzymatic Activities of Recombinant Silicase.- 6.1 Carbonic Anhydrase Activity.- 6.2 Silicase Activity.- 7 Expression of Silicase in Response to Silicon.- 8 Proposed Mechanism of Action of Silicase.- 9 Conclusion.- References.- Studies of Biosilicas; Structural Aspects, Chemical Principles, Model Studies and the Future.- 1 Terminology.- 2 Introduction.- 3 Structural Chemistry of Biosilicas.- 4 Organic Matrix-Controlled Silica Production in Biological Organisms.- 5 The Chemistry of Silica Formation.- 5.1 Silica Chemistry in Aqueous Solution.- 5.1.1 Effects of pH and M+ Ion Identity on Speciation in Aqueous Solution.- 5.2 Silica Chemistry in Non-Aqueous Solution.- 6 Solution Additives and Model Precipitation Reactions.- 6.1 Rationale for Use of Model Precipitation Reactions; Experimental Approaches.- 6.2 Studies of the Effect of Biosilica Extracts on the In Vitro Formation of Silica.- 6.3 Biomimetic Studies of Silica Precipitation.- 7 Other Areas of Interest.- 7.1 Transport.- 7.2 The Significance of Hypervalency in Biological Silicon Chemistry.- 8 Future Directions.- 8.1 Molecular Engineering in Diatoms.- 8.2 Isolation and Identification: Labelling.- 8.3 Theoretical Studies.- 9 Conclusions.- References.- Silicon Biomineralisation: Towards Mimicking Biogenic Silica Formation in Diatoms.- 1 Introduction.- 2 Biochemical and Physico-Chemical Characteristics of Diatomaceous Silica.- 2.1 Organic Composition.- 2.2 Chemical Aspects.- 2.2.1 Principles of Silica Synthesis.- 2.2.2 Silica Synthesis in Diatoms.- 2.3 Nanoscale Structure.- 2.3.1 Specific Surface Area.- 2.3.2 Coordination of Molecules of Biogenic Silica.- 2.3.3 X-Ray Diffraction and Wide-Angle X-Ray Scattering.- 2.3.4 Small-Angle X-Ray Scattering.- 3 In Situ Silica Synthesis.- 3.1 The Application of Templates.- 3.2 Synthesis of PEG-Templated Silicas.- 4 A New Concept: Mesophases in Structure-Directing Processes in Diatom Silica Biomineralization.- 5 Conclusions and Future Perspectives.- References.