Red Algae in the Genomic Age (Cellular Origin, Life in Extreme Habitats and Astrobiology)

978-90-481-3795-4_Chapter_1......Page 1
1. Introduction......Page 2
2. The Evolution and Spread of Chloroplasts in Eukaryotes......Page 4
3.1.1. Involvement of FtsZ Proteins in Chloroplast Division......Page 5
3.1.2. Other Chloroplast Division Proteins of Cyanobacterial Origin......Page 6
3.1.3. Possible Division Factors of Cyanobacterial Origin......Page 7
3.2.1. Paralogous Evolution of FtsZ Proteins......Page 8
3.2.2. The PD Ring......Page 9
3.2.3. Dynamin-Related Proteins......Page 10
3.2.4. PDV1 and PDV2......Page 11
4.1. ORGANIZATION AND DYNAMICS OF THE DIVISION MACHINERY......Page 12
4.2. CONSERVATION OF AND DIFFERENCES IN THE DIVISION MACHINERY AMONG SEVERAL DIFFERENT LINEAGES......Page 13
5. Summary......Page 15
6. References......Page 16
978-90-481-3795-4_Chapter_2......Page 22
1.1. ORIGIN OF THE RED ALGAL PLASTID AND ITS RELATIONSHIP TO OTHER PLANTAE......Page 24
1.2. RED ALGAL FOSSILS AND LINEAGE DIVERGENCE TIMES......Page 26
2. Classification of the Rhodophyta......Page 27
3.1. CLASS CYANIDIOPHYCEAE......Page 29
3.2. CLASS BANGIOPHYCEAE......Page 31
3.4 CLASS COMPSOPOGONOPHYCEAE......Page 32
3.5. CLASS PORPHYRIDIOPHYCEAE......Page 33
3.6. CLASS RHODELLOPHYCEAE......Page 34
4. Summary......Page 35
6. References......Page 36
978-90-481-3795-4_Chapter_3......Page 40
1. Invasive and Alien Red Seaweeds in the Mediterranean......Page 42
3. Galaxaura rugosa in the Haifa Bay: Invasion?......Page 46
4. Summary......Page 51
6. References......Page 52
978-90-481-3795-4_Chapter_4......Page 56
1.2. REPRODUCTION AND LIFE CYCLE......Page 57
2.1. DESICCATION......Page 58
2.2. PHOTOACCLIMATION AND PHOTOINHIBITION......Page 59
2.4. TEMPERATURE......Page 61
4. Economic Aspects of Porphyra......Page 62
4.1. CULTIVATION......Page 63
5. Porphyra in Globally Changing Environments......Page 65
7. References......Page 66
978-90-481-3795-4_Chapter_5......Page 70
1. Introduction......Page 71
2.1. ECOLOGICAL ISOLATION......Page 74
2.2. TEMPORAL ISOLATION......Page 76
2.3. BIOCHEMICAL ISOLATION......Page 77
3. Postzygotic Isolating Mechanism......Page 78
3.1. INVIABLE OR STERILE F1 GAMETOPHYTES......Page 79
3.2. ABORTIVE CYSTOCARPS OR INVIABLE F1 SPOROPHYTES......Page 80
3.3. PSEUDOCYSTOCARPS......Page 81
4. Relationships Between Reproductive Affinities, Geographic Distance, and Genetic Diversity......Page 89
5. Perspective......Page 91
5.2. APOMIXIS......Page 92
5.4 GENETIC BASIS OF ADAPTATION......Page 93
7. References......Page 94
978-90-481-3795-4_Chapter_6......Page 102
1.1. GENUS PULVINASTER (WEST ET AL., 2007A, b). TYPE SPECIES: PULVINUS VENETUS......Page 103
3. Order Acrochaetiales (Feldmann, 1953). Type Family: Family Acrochaetiaceae (Fritsch)......Page 104
4.2. GENUS RHODODRAPARNALDIA (SHEATH ET AL., 1994). TYPE SPECIES: RHODODRAPARNALDIA OREGONICA (SHEATH ET AL., 1994)......Page 105
5.1.1.2. Section Batrachospermum. Type Species: Batrachospermum gelatinosum (Linnaeus) (De Candolle, 1801)......Page 106
5.1.2. Genus Sirodotia (Kylin, 1912). Synonym: Section Sirodotia (Kylin) Necchi and Entwisle. Type Species: Sirodotia suecic......Page 107
5.2.1. Genus Psilosiphon (Entwisle, 1989): Type Species: Psilosiphon scoparium (Entwisle)......Page 108
5.3.4. Genus Balliopsis (Saunders and Necchi. 2002). Type Species: Balliopsis prieurii (Saunders and Necchi)......Page 109
7.1.1. Genus Hildenbrandia (Nardo, 1834). Type Species: Hildenbrandia rubra (Sommerfelt) (Meneghini)......Page 110
8.2.1. Genus Bostrychia (Montagne). Type Species: Bostrychia scorpioides (Hudson) (Montagne)......Page 111
10. References......Page 112
978-90-481-3795-4_Chapter_7......Page 116
PORPHYRA: COMPLEX LIFE HISTORIES IN A HARSH ENVIRONMENT:......Page 117
1. Introduction......Page 118
3. Asexual Reproduction......Page 120
4. Genome Evolution......Page 121
5. Associations with Other Organisms......Page 123
6. Cytoskeletons, Cell Division, and Flagellar Genes......Page 124
7. Photosynthesis, and Light Absorbing Molecules......Page 125
8. Carbohydrates: Storage and Cell Wall Composition......Page 127
9. Circadian and Circannual Rhythms......Page 128
11. Future Approaches and Challenges......Page 129
13. References......Page 130
978-90-481-3795-4_Chapter_8......Page 135
1. Introduction......Page 137
2. Polyglucosans, Glycogen, Starch, and Floridean Starch......Page 139
3. Discovery of Laforin in Protists......Page 140
4. Biochemical Properties and Subcellular Localization of C. merolae Laforin......Page 142
5. Laforin’s Evolutionary Lineage......Page 143
6. Lack of Malin......Page 145
7. Insights from Green Algae/Land Plants......Page 146
8. The Role of Phosphorylation in Starch Metabolism......Page 147
9. Cyanidioschyzon merolae as a Model Organism to Study Lafora Disease......Page 149
10. References......Page 150
978-90-481-3795-4_Chapter_9......Page 156
2. Plastid Genome of Red Algae and Green Plants......Page 157
3. Plastid RNA Polymerase......Page 159
3.2. PEP SIGMA FACTORS......Page 160
3.3. NEP (Nuclear-Encoded Plastid RNA Polymerase)......Page 161
4.1. TRANSCRIPTION FACTORS IN RED ALGAE......Page 163
4.2. TRANSCRIPTION FACTORS IN GREEN PLANTS......Page 164
5.1. PLASTID TRANSCRIPTIONAL REGULATION IN RED ALGAE......Page 165
5.2. PLASTID TRANSCRIPTIONAL REGULATION IN GREEN PLANTS......Page 166
6. Transcription Regulation of Nuclear Genes by Plastid-Derived Signals......Page 167
7. Summary and Conclusion......Page 168
8. References......Page 169
978-90-481-3795-4_Chapter_10......Page 175
2. Origin and Evolution of Plastids......Page 176
2.1. PRIMARY ENDOSYMBIOSIS......Page 177
2.2. SECONDARY AND TERTIARY ENDOSYMBIOSIS......Page 178
3. The Genomic “Footprint” of Endosymbiosis: How Big and How Important?......Page 179
3.2. EUKARYOTE–EUKARYOTE GENE TRANSFERS AND REPLACEMENTS......Page 180
4. Deep Algal Phylogenomics: Problems and Promise in Light of EGT and EGR......Page 182
6. References......Page 184
978-90-481-3795-4_Chapter_11......Page 188
2. Biotechnology of Production of Valuable Chemicals from Red Microalgae......Page 189
3.1. EXPRESSED SEQUENCE TAGS (ESTs) OF RED MICROALGAE......Page 192
ADP-Ribosylation-Factor- and ADP-Ribosylation-Factor-Like Proteins......Page 194
3.2.1.1. Flavohemoprotein/Flavohemoglobin......Page 195
3.3.1. Similarity Between Porphyridium sp. and Dixoniella grisea......Page 196
3.3.2. Similarity of Porphyridium sp. and Dixoniella grisea unigenes to Various Proteomes......Page 197
4.1. PERSPECTIVES: ACHIEVEMENTS AND DIFFICULTIES......Page 199
4.1.1. Chloroplast and Nuclear Gene Transformation......Page 200
4.1.2. Red Microalgae as Cell Factories: Difficulties and Potential......Page 201
6. References......Page 202
978-90-481-3795-4_Chapter_12......Page 208
1. Introduction......Page 209
2. Nuclear Genomes of Red Algae......Page 211
3. Chloroplast Genomes of Red Algae......Page 212
4. Mitochondrial Genomes of Red Algae......Page 214
5. Conclusions......Page 216
7. References......Page 217
978-90-481-3795-4_Chapter_13......Page 221
1. Introduction......Page 223
2.3. GENOMICS......Page 227
3.1. TAXONOMY AND SYSTEMATICS......Page 228
3.3. GENOMICS......Page 229
4.1. TAXONOMY AND SYSTEMATICS......Page 230
4.3. GENOMICS......Page 231
5.1. TAXONOMY AND SYSTEMATICS......Page 232
6.1. TAXONOMY AND SYSTEMATICS......Page 233
7.1. TAXONOMY AND SYSTEMATICS......Page 234
8. Summary......Page 235
9. References......Page 236
978-90-481-3795-4_Chapter_14......Page 240
2. Phylogeny of Red Algal Plastids......Page 242
2.1. EVIDENCE FOR A SINGLE PRIMARY ENDOSYMBIOTIC EVENT GIVING RISE TO ALL PLASTIDS......Page 243
2.2. WHAT WAS LOST IN THE RED ALGAL PLASTID LINEAGE AND WHEN DID IT SPLIT OFF?......Page 244
3. The Biosynthesis of Red Algae Pigments......Page 245
4. Localization and Regulation of Phycobiliprotein Production......Page 248
5. Summary......Page 249
7. References......Page 250
978-90-481-3795-4_Chapter_15......Page 253
1. Introduction......Page 254
2. Fate of Genes from the Cyanobacterial Plastid Precursor in Red Algae......Page 255
3. Plastid Functions in Red Algae Using Cyanobacterial and Noncyanobacterial Genes......Page 256
4. Mitochondria Functions......Page 260
7. C4 Photosynthesis in Red Algae?......Page 261
8. Conclusions......Page 262
11. References......Page 263
978-90-481-3795-4_Chapter_16......Page 268
1. Introduction......Page 269
2. The Significance of Intron Distributions for Gene Prediction......Page 270
3.1. MODELS AND PROGRAMS......Page 272
3.2. TRAINING OF PARAMETERS......Page 274
3.2.2. Cross-Species Training......Page 275
4. Extrinsic Approaches to Gene Finding......Page 276
4.1. USING CDNA ALIGNMENTS......Page 277
4.2. USING PROTEIN HOMOLOGY......Page 279
5. Discussion......Page 280
6. References......Page 281
978-90-481-3795-4_Chapter_17......Page 283
1. Introduction......Page 285
2.1. STATUS OF TISSUE AND CALLUS CULTURE IN RED ALGAE......Page 287
2.2. TRENDS IN PROTOPLAST RESEARCH OF RED ALGAE......Page 292
3. Molecular Biotechnology of Red Algae......Page 302
3.1. STATUS OF GENETIC ENGINEERING......Page 303
3.3. DEVELOPMENTS IN MOLECULAR GENETIC MARKERS......Page 304
3.4. GENOMIC ORGANIZATION OF RED SEAWEED......Page 306
4. Conclusions......Page 307
6. References......Page 308
978-90-481-3795-4_Chapter_18......Page 318
1. Introduction......Page 319
2. Origins and Evolution......Page 320
3. Habitats......Page 321
4. Cave Cyanidium......Page 322
6. Taxonomy and Phylogeny......Page 323
8. Biochemistry and Physiology......Page 324
11. References......Page 325
978-90-481-3795-4_Chapter_19......Page 329
2. Aspects of Cyanidiales Ecology......Page 331
3. Biodiversity......Page 335
4. Biogeographical Considerations......Page 337
5. Evolution of the Cyanidiales......Page 339
8. References......Page 340
978-90-481-3795-4_Chapter_20......Page 344
2. Mechanisms of Acido-tolerance in Cyanidium caldarium......Page 346
2.1. ACTIVE H+ EFFLUX AGAINST THE STEEP pH GRADIENT ACROSS THE PLASMA MEMBRANE......Page 347
2.2. MEASUREMENT OF INTRACELLULAR pH IN CYANIDIUM CELLS BY 31P-NMR......Page 348
2.3. CHARACTERIZATION OF PLASMA MEMBRANE H+-ATPase IN CYANIDIUM CELLS......Page 349
2.4. MECHANISMS OF ACIDO-TOLERANCE IN CYANIDIUM CELLS......Page 350
3.1. PHOTOSYSTEM II......Page 351
3.2. PHOTOSYSTEM I......Page 354
4. References......Page 357
978-90-481-3795-4_Chapter_21......Page 361
1. Introduction......Page 362
2. Regulation of NADP-Dependent Glyceraldehyde 3-Phosphate Dehydrogenase (NADP-GAPDH) and Phosphoribulokinase (PRK)......Page 363
3. Regulation of Chloroplast Fructose 1,6-bisphosphatase (FBPase)......Page 365
4. Regulation of Glucose 6-Phosphate Dehydrogenase (G6PDH)......Page 366
5.2. RUBISCO ACTIVASE (RCA)......Page 367
6.1. THIOREDOXIN REDUCTASES (FTR AND NTR)......Page 368
6.2. THIOREDOXINS (TRX)......Page 369
6.3. FERREDOXIN (Fd) AND FERREDOXIN-NADP REDUCTASE (FNR)......Page 370
8. Summary......Page 372
10. References......Page 374
978-90-481-3795-4_Chapter_22......Page 377
1.2. HISTORY OF CYANIDIALES......Page 378
2.1. ECOLOGY......Page 379
2.2. MORPHOLOGY......Page 381
3. Taxonomy and Molecular Phylogeny of Cyanidiales......Page 382
4. Mechanisms of Dispersal and Establishment of New Population......Page 384
5.1. CYANIDIOSCHYZON GENOME......Page 386
5.3.3. Tolerance to Heavy Metal......Page 387
5.3.5. Adaptation to Osmotic Stress......Page 388
7. References......Page 389
978-90-481-3795-4_Chapter_23......Page 394
1. Introduction......Page 396
2. Chilean Cave Cyanidium......Page 397
3. Cave Description......Page 398
4. Atacama Cave Cyanidium Molecular Characterization......Page 400
6. References......Page 404
978-90-481-3795-4_Chapter_24......Page 407
1. Introduction......Page 408
2. A High Biochemical Diversity of Low Molecular Weight Carbohydrates......Page 409
4. Biosynthesis of Low Molecular Weight Carbohydrates......Page 412
5. Function of Low Molecular Weight Carbohydrates......Page 414
8. References......Page 417
978-90-481-3795-4_Chapter_25......Page 420
1. Introduction......Page 421
2. Defenses Against Fouling Organisms and Pathogens......Page 422
4. The Oxidative Burst......Page 425
5. Oxidative Burst-Associated Halogenation......Page 427
6. Oxylipin Signals......Page 429
7. Defenses Against Herbivores......Page 431
8. Integrating Gene-Regulated Responses into Studies of Red Algal Defenses......Page 432
10. References......Page 434
Summary, Final Comments and Conclusions......Page 440
1. References......Page 442