Biomineralization: progress in biology, molecular biology and application

Biomineralization Second, Completely Revised and Extended Edition......Page 4
Foreword......Page 10
Contents......Page 12
Preface......Page 20
List of Contributors......Page 22
Abbreviations......Page 26
1.1.1 A Phage Display Peptide Library in “Regular Panning” for Mineral Binding and Synthesizing Peptides......Page 28
1.1.2 A Phage Display Peptide Library in “PCR Panning” for Mineral Binding and Synthesizing Peptides......Page 33
1.2.1 Pre-biotic Vesicles for Protection and Mobility......Page 39
1.2.2 How do Pores Originate?......Page 40
References......Page 41
Magnetite (Fe(3)O(4)) and Greigite (Fe(3)S(4))......Page 42
2.1 Introduction......Page 44
2.3 Ecology of Magnetotactic Bacteria......Page 45
2.4 Magnetite Magnetosomes......Page 48
2.5 Greigite Magnetosomes......Page 52
2.6 Arrangement of Magnetosomes in Cells......Page 54
2.7 Role of Magnetosomes and Magnetosome Chains in Magnetotaxis......Page 56
2.8 Chemistry of Magnetosome Formation......Page 57
2.9 Other Intracellular Iron Oxides and Sulfides in Bacteria......Page 59
2.10 Magnetic Iron Oxides and Sulfides in Microorganisms other than Bacteria......Page 60
2.11.1 Magnetosomes as Biomarkers for Life on Ancient Mars......Page 62
2.11.2 The Biogenic Hypothesis......Page 65
2.11.4 Iron Isotopic Fractionation......Page 66
References......Page 67
3.2 The rRNA Approach to Microbial Ecology and Evolution......Page 72
3.4 The Genus Magnetospirillum Encompassing Culturable Magnetotactic Bacteria......Page 74
3.5 Phylogenetic Diversity and In Situ Identification of Uncultured Magnetotactic Cocci from Lake Chiemsee......Page 76
3.6 The Magnetotactic Bacteria are Polyphyletic with Respect to their 16S rRNA......Page 77
3.7 “Magnetobacterium bavaricum”......Page 78
3.8 Further Diversity of Magnetotactic Bacteria......Page 80
3.9 A Current View of the Phylogeny of Magnetotactic Bacteria......Page 83
References......Page 86
4.2 The Biomineralization of Magnetite in MTB......Page 88
4.3 The MM is a Unique Structure in MTB......Page 89
4.4 Biochemical Analysis of the MM in M. gryphiswaldense......Page 91
4.5.2 Cation Diffusion Facilitator (CDF) Proteins......Page 93
4.5.3 HtrA-like Serine Proteases......Page 94
4.5.4 MTB-specific Protein Families......Page 95
4.6 Genetic Organization of Magnetosome Genes......Page 96
4.7 Conclusions and Outlook......Page 98
References......Page 99
5.1 Introduction......Page 102
5.2.1 Localization and Purification of Iron Reductase from M. magnetotacticum......Page 104
5.2.2 Characterization of M. magnetotacticum Ferric Iron Reductase......Page 105
5.2.3 Function of Ferric Iron Reductase in M. magnetotacticum......Page 106
5.3 Ferrous Iron Oxidation in M. magnetotacticum......Page 107
5.3.3 Enzymatic Properties and Function of M. magnetotacticum Cytochrome cd(1)......Page 109
5.4 Nitrate Reductase of M. magnetotacticum MS-1......Page 111
5.5 Structure and Function of the 22 kDa Protein Localized in the Magnetosome Membrane......Page 112
5.6 Proposed Mechanism of Magnetite Synthesis in M. magnetotacticum......Page 113
References......Page 116
6.2.1 Pure Cultivation of Magnetic Bacteria......Page 118
6.2.3 Mass Cultivation of Magnetic Bacteria......Page 121
6.3 Iron Uptake in M. magneticum AMB-1......Page 123
6.4.1 Iron Transporter MagA......Page 124
6.5.1 Magnetosome-specific GTPase Mms16......Page 125
6.5.2 Tightly Bound Protein to Magnetite Crystal, Mms6......Page 126
6.6 Hypothesis of a Molecular Mechanism of Magnetosome Formation......Page 127
6.7.1 Magnetic Carriers for Immobilization of Molecules......Page 128
6.7.3 Expression of Foreign Protein Displayed on BMP......Page 129
6.7.4 Fully Automated Immunoassay using Protein A–BMPs......Page 130
References......Page 131
7.2.1 Behavioral Evidence of Geomagnetic Field Sensitivity in Animals......Page 134
7.2.2 A Biochemical Compass Mechanism......Page 136
7.2.3 The Magnetite Hypothesis......Page 137
7.3 The Case for a Magnetoreceptor in Homing Pigeons......Page 138
7.3.1 A New Methodological Approach to an Old Problem......Page 139
7.3.3 Likely Mechanisms to Transduce a Magnetic Stimulus into a Nervous Signal......Page 141
7.4 Discussion and Open Questions......Page 142
References......Page 144
8.1 Introduction......Page 146
8.2 General Functional Properties of Dps-like Ferritins......Page 147
8.3 General Structural Properties of Dps-like Ferritins......Page 149
8.4 Structural Aspects of a Dps-like Protein from a Halophilic Archaeon......Page 150
8.4.1 Iron Access Route into DpsA......Page 151
8.4.3 The Nucleation Sites and Nanocluster Formation......Page 154
8.5 Biomineralization in 24-meric Ferritins......Page 156
8.6 Ferrihydrite Formation in Ferritin and Ferritin-like Dps Proteins – A Masterplan for Biomineralization?......Page 157
References......Page 159
Silica-hydrated SiO(2)......Page 162
9.1 Introduction......Page 164
9.2 The Diatom Cell Wall......Page 165
9.3.1 The SDV......Page 166
9.3.2 Silicic Acid Accumulation......Page 168
9.3.4 Silica Chemistry......Page 169
9.4 Diatom Biosilica-associated Organic Components......Page 171
9.4.1 Chemical Structures of Silaffins and LCPA......Page 172
9.4.2 Silica Formation Activity of natSil-1A......Page 177
9.4.3 Silica Formation by LCPA......Page 179
9.5 Model for LCPA-mediated Morphogenesis of Biosilica Nanopatterns......Page 180
9.6 Silaffin-mediated Silica Morphogenesis......Page 181
Acknowledgments......Page 183
References......Page 184
10.1 Introduction......Page 186
10.3 The Solution Chemistry of Silicon......Page 187
10.4 Characterization of Diatom Silicic Acid Transport......Page 189
10.5 Molecular Characterization of the Silicic Acid Transport System......Page 190
10.6 Intracellular Silicon Pools......Page 193
10.7 The Relationship of Intracellular Pools and Incorporation to Uptake......Page 195
10.8 Intracellular Transport of Silicon......Page 197
10.9 Transport into the Silica Deposition Vesicle......Page 199
10.10 Summary......Page 200
References......Page 201
11.2 General Features of the Diatom “Glass House”......Page 204
11.3 The Chemistry of Biosilica Formation......Page 205
11.3.1 Parameters Affecting Silicon and Silicification......Page 206
11.3.2 Hypothetical Effects of Chelating Agents on Silica Deposition......Page 209
11.4 Silica Uptake by Diatoms......Page 211
11.5 Nanostructure of Diatom Biosilica......Page 212
11.6 Development of Diatom Biosilica within a Confined Space – Silica Deposition Vesicles (SDVs)......Page 215
11.7 Transport of Silica to the SDV......Page 217
11.9 Conclusions......Page 219
References......Page 220
Calciumcarbonates......Page 222
12.1 Introduction......Page 224
12.2.1 Coccolith Structure......Page 226
12.2.2.1 Ion Accumulation......Page 227
12.2.2.2 Calcite Nucleation......Page 231
12.2.2.3 Crystal Growth......Page 232
12.3.2 Emiliania......Page 235
12.4 Holococcolith-bearing Morphotypes......Page 236
12.5 Coccolithophore Calcification and the Ocean Carbon Cycle......Page 238
12.6 Future Prospects......Page 239
References......Page 240
13.1 Introduction......Page 244
13.3 The V-ATPase Enzyme Complex and Immunolocalization......Page 245
13.4 Proton Transport......Page 246
13.5 Conditions for Expression of Subunit c......Page 249
13.7 Carbonic Anhydrase......Page 252
13.8 Is there a Connection between Calcification and Stress?......Page 253
References......Page 254
14.2 Otoliths and Otoconia......Page 256
14.3 Characterization of Otolith Development in Wild-type Zebrafish......Page 258
14.4 Zebrafish Mutants with Defects in Otolith Formation......Page 261
14.5 Zebrafish Genes Having a Direct Role in Otolith Formation......Page 262
14.6 Proteins Reported to be Associated with Otoliths or Otoconia......Page 266
14.7 Conclusions......Page 267
References......Page 268
Calciumphosphates......Page 270
15.1 A Short History of Calcification Inhibition......Page 272
15.2 Osteogenesis and Bone Mineralization versus Calcification......Page 274
15.4 Regulation of Calcification......Page 277
15.5 α(2)-HS Glycoprotein/Fetuin-A is a Systemic Inhibitor of Unwanted Calcification......Page 284
15.6 How does Inhibition of Calcification Work?......Page 287
15.7 What Happens to the CPPs?......Page 288
References......Page 290
16.2 Basic Odontogenesis......Page 296
16.3 Dentinogenesis......Page 298
16.5 Methods and Results......Page 302
Acknowledgments......Page 307
References......Page 308
17.2 Skeleton Development and Patterning in Vertebrates......Page 310
17.3 Zebrafish as a Model for Studying Skeletal Development......Page 311
17.4 Methods for Visualizing Bones in Zebrafish......Page 312
17.5 Bone Development in Zebrafish Embryos......Page 313
17.5.1 Development of the Head Skeleton......Page 314
17.5.1.1 Jaw and Branchial Arch Mutants in Zebrafish......Page 315
17.5.1.2 Molecular Characterization of Jaw and Branchial Arch Mutants......Page 316
17.5.1.4 Hox Genes in Anterior–Posterior Patterning of the Head Skeleton......Page 317
17.5.2.1 Development of the Vertebral Skeleton......Page 318
17.5.2.3 Development of Neural Arches, Haemal Arches and Spines......Page 319
17.5.2.4 Molecular Regulation of Axial Skeleton Formation and Patterning......Page 320
17.5.3.1 Development of Median Fins......Page 322
17.5.3.2 Development of Paired Fins......Page 323
17.5.3.3 Molecular Regulation of Fin Formation......Page 324
17.6.2 Use of the Transgenic Approach to Analyze BMP Function in Bone Development......Page 325
17.6.3 Zebrafish as a Model for Bone Deformity induced by Teratogenic Chemicals......Page 326
References......Page 327
New Methods......Page 332
18.2 Infrared (IR) Spectroscopy......Page 334
18.3 Scanning Probe Microscopy......Page 335
18.4 Synchrotron Radiation Sources......Page 336
18.5 Diffraction Methods......Page 338
18.6 X-ray Absorption Spectroscopy (EXAFS)......Page 342
18.7.1 Development of the Shells in Embryos of Biomphalaria glabrata......Page 345
18.7.2 Intermediate Storage of ACC in Porcellio scaber......Page 347
18.8 X-ray Microtomography (μ-CT)......Page 348
18.9 Micromechanical Experiments......Page 349
18.10 Solid-state Nuclear Magnetic Resonance (NMR) Spectroscopy......Page 350
18.11 Conclusions......Page 351
References......Page 352
Index......Page 354