Elsevier S & T

Bioengineering and Molecular Biology of Plant Pathways

Lewis, Norman

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Table of contents
  • Contentsvii
  • Contributorsxi
  • Introduction to the Series and Acknowledgementsxv
  • Preface to Volume 1xvii
  • Prologuexxi
  • Chapter 1: Metabolic Organization in Plants: A Challenge for the Metabolic Engineer1
  • 1. Introduction2
  • 2. Plant Metabolic Networks and Their Organization3
  • 3. Tools for Analyzing Network Structure and Performance7
  • 3.1. Constraints-based network analysis8
  • 3.2. Metabolic flux analysis10
  • 3.3. Kinetic modeling12
  • 3.4. Metabolic control analysis13
  • 4. Integration of Plant Metabolism15
  • 4.1. Relationship between enzyme properties and network fluxes15
  • 4.2. Limitations on metabolic compensation within a network15
  • 4.3. Impact of physiological conditions on network performance16
  • 4.4. Network adjustments through alternative pathways17
  • 4.5. Propagation of metabolic perturbations through networks18
  • 4.6. Enzyme-specific responses within networks20
  • 4.7. Impact of metabolic change on network structure21
  • 5. Summary22
  • Acknowledgements23
  • References23
  • Chapter 2: Enzyme Engineering29
  • 1. Introduction30
  • 2. Theoretical Considerations31
  • 2.1. Enzyme architecture is conserved31
  • 2.2. Genomic analysis suggests most enzymes evolve from preexisting enzymes31
  • 2.3. Evolution of a new enzymatic activity in nature32
  • 2.4. The natural evolution process initially produces poor enzymes34
  • 2.5. Sequence space and fitness landscapes34
  • 3. Practical Considerations for Engineering Enzymes35
  • 3.1. Identifying appropriate starting enzyme(s)36
  • 3.2. Ways of introducing variability into genes37
  • 3.3. Choice of expression system37
  • 3.4. Identifying improved variants38
  • 3.5. Recombination and/or introduction of subsequent mutations40
  • 3.6. Structure-based rational design41
  • 4. Opportunities for Plant Improvement Through Engineered Enzymes and Proteins42
  • 4.1. Challenges for engineering plant enzymes and pathways43
  • 5. Summary44
  • Acknowledgements44
  • References44
  • Chapter 3: Genetic Engineering of Amino Acid Metabolism in Plants49
  • 1. Introduction51
  • 2. Glutamine, Glutamate, Aspartate, and Asparagine are Central Regulators of Nitrogen Assimilation,52
  • 2.1. GS: A highly regulated, multifunctional gene family54
  • 2.2. Role of the ferredoxin- and NADH-dependent GOGAT isozymes in plant glutamate biosynthesis56
  • 2.3. Glutamate dehydrogenase: An enzyme with controversial functions in plants58
  • 2.4. The network of amide amino acids metabolism is regulated in concert by developmental, physiolog59
  • 3. The Aspartate Family Pathway that is Responsible for Synthesis of the Essential Amino Acids Lysin60
  • 3.1. The aspartate family pathway is regulated by several feedback inhibition loops60
  • 3.2. Metabolic fluxes of the aspartate family pathway are regulated by developmental, physiological,62
  • 3.3. Metabolic interactions between AAAM and the aspartate family pathway63
  • 3.4. Metabolism of the aspartate family amino acids in developing seeds: A balance between synthesis64
  • 4. Regulation of Methionine Biosynthesis66
  • 4.1. Regulatory role of CGS in methionine biosynthesis67
  • 4.2. Interrelationships between threonine and methionine biosynthesis68
  • 5. Engineering Amino Acid Metabolism to Improve the Nutritional Quality of Plants for Nonruminants a69
  • 5.1. Improving lysine levels in crops: A comprehensive approach70
  • 5.2. Improving methionine levels in plant seeds: A source-sink interaction71
  • 5.3. Improving the nutritional quality of hay for ruminant feeding72
  • 6. Future Prospects73
  • 7. Summary74
  • Acknowledgements74
  • References74
  • Chapter 4: Engineering Photosynthetic Pathways81
  • 1. Introduction82
  • 2. Identification of Limiting Steps in the PCR Cycle83
  • 2.1. Analysis of limiting steps in photosynthesis83
  • 2.2. Flux control analysis83
  • 3. Engineering CO2-Fixation Enzymes85
  • 3.1. RuBisCO85
  • 3.2. C4-ization of C3 plants94
  • 4. Engineering Post-RuBisCO Reactions95
  • 4.1. RuBP regeneration95
  • 4.2. Engineering carbon flow from chloroplasts to sink organs97
  • 5. Summary97
  • Acknowledgements98
  • References99
  • Chapter 5: Genetic Engineering of Seed Storage Proteins107
  • 1. Introduction108
  • 1.1. The nature of seeds108
  • 1.2. Metabolites stored in seeds and their uses108
  • 1.3. Characterization of seed storage proteins109
  • 1.4. Challenges and limitations for seed protein modification112
  • 2. Storage Protein Modification for the Improvement of Seed Protein Quality113
  • 2.1. Increasing methionine content113
  • 2.2. Increasing lysine content117
  • 3. Use of Seed Storage Proteins for Protein Quality Improvements in Nonseed Crops119
  • 4. Modification of Grain Biophysical Properties120
  • 5. Transgenic Modifications that Enhance the Utility of Seed Storage Proteins122
  • 5.1. Managing allergenic proteins122
  • 5.2. Managing seed antinutritional characteristics124
  • 6. Summary and Future Prospects124
  • Acknowledgements127
  • References127
  • Chapter 6: Biochemistry and Molecular Biology of Cellulose Biosynthesis in Plants: Prospects for Gen135
  • 1. Introduction136
  • 2. The Many Forms of Cellulose„A Brief Introduction to the Structure and Different Crystalline For137
  • 3. Biochemistry of Cellulose Biosynthesis in Plants139
  • 3.1. UDP-glucose is the immediate precursor for cellulose synthesis139
  • 3.2. In vitro synthesis of cellulose from plant extracts140
  • 3.3. Purification and characterization of cellulose synthase activity143
  • 4. Molecular Biology of Cellulose Biosynthesis in Plants144
  • 4.1. Identification of genes encoding cellulose synthases in plants144
  • 4.2. Mutant analysis allowed identification of genes for cellulose synthases and other proteins requ145
  • 4.3. The cellulose synthase genes149
  • 4.4. The cellulose synthase protein150
  • 5. Mechanism of Cellulose Synthesis151
  • 5.1. Role of primer and/or intermediates during cellulose synthesis?151
  • 5.2. Addition of glucose residues to the growing glucan chain end151
  • 6. Prospects for Genetic Engineering of Cellulose Biosynthesis in Plants152
  • 6.1. Manipulation of cellulose biosynthesis in plants152
  • 6.2. Influence of cellulose alterations in plants154
  • 7. Summary154
  • Acknowledgements155
  • References155
  • Chapter 7: Metabolic Engineering of the Content and Fatty Acid Composition of Vegetable Oils161
  • 1. Introduction163
  • 2. TAG Synthesis167
  • 2.1. Precursors for fatty acid synthesis167
  • 2.2. Fatty acid synthesis169
  • 2.3. Phosphatidic acid assembly171
  • 2.4. Glycerolipids and fatty acid modification171
  • 2.5. TAG synthesis and oil deposition174
  • 3. Control of TAG Composition175
  • 3.1. Metabolic engineering of high oleic acid vegetable oils175
  • 3.2. Metabolic engineering of high and low saturated fatty acid vegetable oils176
  • 3.3. Metabolic engineering of high and low polyunsaturated vegetable oils178
  • 3.4. Variant fatty acid desaturases for metabolic engineering of vegetable oil composition178
  • 3.5. Metabolic engineering of vegetable oils with short and medium-chain fatty acids185
  • 3.6. Metabolic engineering of vegetable oils with very long-chain fatty acids (VLCFAs)186
  • 3.7. Metabolic engineering of nonplant pathways187
  • 4. Summary189
  • 4.1. Alteration of seed oil content189
  • 4.2. Alteration of the fatty acid composition of vegetable oils190
  • Acknowledgements192
  • References192
  • Chapter 8: Pathways for the Synthesis of Polyesters in Plants: Cutin, Suberin, and Polyhydroxyalkano201
  • 1. Introduction202
  • 2. Cutin and Suberin203
  • 2.1. Functional and ultrastructural characteristics203
  • 2.2. Composition of cutin and suberin204
  • 2.3. Biosynthesis of cutin and suberin207
  • 2.4. Future perspectives212
  • 3. Polyhydroxyalkanoate213
  • 3.1. PHA as a bacterial polyester215
  • 3.2. Polyhydroxybutyrate216
  • 3.3. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate)223
  • 3.4. Medium-chain-length polyhydroxyalkanaote225
  • 3.5. Future perspectives231
  • References232
  • Chapter 9: Plant Sterol Methyltransferases: Phytosterolomic Analysis, Enzymology, and Bioengineering241
  • 1. Introduction242
  • 2. Pathways of Phytosterol Biosynthesis244
  • 3. Phytosterolomics251
  • 4. Enzymology and Evolution of the SMT258
  • 5. Bioengineering Strategies for Generating Plants with Modified Sterol Compositions268
  • Acknowledgement276
  • References276
  • Chapter 10: Engineering Plant Alkaloid Biosynthetic Pathways: Progress and Prospects283
  • 1. Introduction284
  • 2. Monoterpenoid Indole Alkaloids286
  • 2.1. Monoterpenoid indole alkaloid biosynthesis286
  • 2.2. Cell-specific expression of monoterpenoid indole alkaloid biosynthetic genes288
  • 2.3. Genetic engineering of monoterpenoid indole alkaloid biosynthetic pathways290
  • 3. Tetrahydrobenzylisoquinoline Alkaloids292
  • 3.1. Tetrahydrobenzylisoquinoline alkaloid biosynthesis292
  • 3.2. Cell-specific expression of tetrahydrobenzylisoquinoline alkaloid biosynthetic genes296
  • 3.3. Genetic engineering of tetrahydrobenzylisoquinoline alkaloid biosynthetic pathways298
  • 4. Tropane Alkaloids299
  • 4.1. Tropane alkaloid biosynthesis300
  • 4.2. Cell-specific expression of tropane alkaloid biosynthetic genes302
  • 4.3. Genetic engineering of tropane alkaloid biosynthetic pathways302
  • 5. Summary304
  • Acknowledgements305
  • References305
  • Chapter 11: Engineering Formation of Medicinal.Compounds in Cell Cultures311
  • 1. Introduction312
  • 2. Biochemistry and Cell Biology of Secondary Metabolites314
  • 2.1. Isoquinoline alkaloid biosynthesis316
  • 2.2. Terpenoid indole alkaloid biosynthesis320
  • 2.3. Tropane alkaloid and nicotine biosynthesis323
  • 3. Cell Culture and Metabolite Production325
  • 3.1. Establishment of high-metabolite-producing lines327
  • 3.2. Organ differentiation and secondary plant products328
  • 3.3. Genetic instability of productivity330
  • 4. Beyond the Obstacles: Molecular Biological Approaches to Improve Productivity of Secondary Metabo331
  • 4.1. Overcoming rate-limiting processes in the pathway332
  • 4.2. Transcriptional regulation and overall activation333
  • 4.3. Qualitative control of metabolites and the isolation of desired biosynthetic genes334
  • 4.4. Accumulation and storage337
  • 5. Future Perspectives337
  • 6. Summary338
  • Acknowledgements338
  • References338
  • Chapter 12: Genetic Engineering for Salinity Stress Tolerance347
  • 1. Salinity Stress Engineering348
  • 2. The Context of Salinity Stress349
  • 3. Ion Homeostasis353
  • 3.1. Ion transport354
  • 3.2. Control of ion homeostasis356
  • 4. Strategies to Improve Salt Tolerance by Modulating Ion Homeostasis358
  • 5. Strategies to Improve Salt Tolerance by Modulating Metabolic Adjustments359
  • 5.1. Osmotic adjustments and controlling factors364
  • 5.2. Engineering stress response control determinants366
  • 5.3. How to analyze transgenic lines resulting from (salinity) stress engineering366
  • 6. Plant Signal Transduction for Adaptation to Salinity369
  • 6.1. The SOS signal pathway controls adaptation to hypersalinity369
  • 6.2. What do we know about stress sensors in plants?370
  • 6.3. SOS independent pathways and protein kinase systems370
  • 7. ABA is a Major Mediator of Plant Stress Response Signaling371
  • 8. Summary373
  • Acknowledgements374
  • References374
  • Chapter 13: Metabolic Engineering of Plant Allyl/Propenyl Phenol and Lignin Pathways: Future Potenti385
  • 1. Introduction387
  • 1.1. The challenge for humanity: Renewable, sustainable sources of bioenergy/biofuels, intermediate387
  • 1.2. Lignified biomass utilization: The lignin challenge388
  • 2. Lignin Formation and Manipulation389
  • 2.1. Biosynthesis of monolignols391
  • 2.2. The challenge of lignin manipulation: Plant growth/development versus stem structural integrity398
  • 2.3. New opportunities and approaches for renewable sources of bioenergy, biofuels, and bioproducts?402
  • 3. Current Sources/Markets for Specialty Allyl/Propenyl Phenols404
  • 4. Biosynthesis of Allyl and Propenyl Phenols and Related Phenylpropanoid Moieties406
  • 5. Potential for Allyl/Propenyl Phenols?415
  • 6. Summary421
  • Acknowledgements421
  • References421
  • Author Index429
  • Subject Index445
Book details
  • Vendor Elsevier S & T
  • SKU 9780080449722
  • ISBN-13 9780080556963
  • Author Lewis, Norman
  • Category Science
  • Subject Biotechnology

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The increased knowledge about the structure of genomes in a number of species, about the complexity of transcriptomes, and the rapid growth in knowledge about mutant phenotypes have set off the large scale use of transgenes to answer basic biological questions, and to generate new crops and novel products. This volume includes twelve chapters, which to variable degrees describe the use of transgenic plants to explore possibilities and approaches for the modification of plant metabolism, adaptation or development. The interests of the authors range from tool development, to basic biochemical know-how about the engineering of enzymes, to exploring avenues for the modification of complex multigenic pathways, and include several examples for the engineering of specific pathways in different organs and developmental stages.

* Prologue by Paul K. Stumpf and Eric E. Conn
* Incorporates new concepts and insights in plant biochemistry and biology
* Provides a conceptual framework regarding the challenges faced in engineering pathways
* Discusses potential in engineering of metabolic end-products that are of vast economical importance, including genetic engineering of cellulose, seed storage proteins, and edible and industrial oils