Molecular Biology of Plant Pathways

- Metabolic Organization in Plants
» Abstract & Keywords
» Introduction
» Plant Metabolic Networks and their Organization
» Tools for Analyzing Network Structure and Performance
    » Constraints-Based Network Analysis
    » Metabolic flux analysis
    » Kinetic modeling
    » Metabolic control analysis
» Integration of Plant Metabolism
    » Relationship between enzyme properties and network fluxes
    » Limitations on metabolic compensation within a network
    » Impact of physiological conditions on network performance
    » Network adjustments through alternative pathways
    » Propagation of metabolic perturbations through networks
    » Enzyme-specific responses within networks
    » Impact of metabolic change on network structure
» Summary
» Acknowledgements
» References
- Enzyme Engineering
» Abstract & Keywords
» Introduction
» Theoretical Considerations
    » Enzyme architecture is conserved
    » Genomic analysis suggests most enzymes evolve from
preexisting enzymes
    » Evolution of a new enzymatic activity in nature
    » The natural evolution process initially produces
poor enzymes
    » Sequence space and fitness landscapes
» Practical Considerations for Engineering Enzymes
    » Identifying appropriate starting enzyme(s)
    » Ways of introducing variability into genes
    » Choice of expression system
    » Identifying improved variants
    » Recombination and/or introduction of
subsequent mutations
    » Structure-based rational design
» Opportunities for Plant Improvement Through Engineered
Enzymes and Proteins
    » Challenges for engineering plant enzymes and pathways
» Summary
» Acknowledgements
» References
- Genetic Engineering of Amino Acid Metabolism in Plants
» Abstract & Keywords
» Introduction
» Glutamine, Glutamate, Aspartate, and Asparagine are Central Regulators of Nitrogen Assimilation, Metabolism, and Transport
    » GS: A highly regulated, multifunctional gene family
    » Role of the ferredoxin- and NADH-dependent GOGAT
isozymes in plant glutamate biosynthesis
    » Glutamate dehydrogenase: An enzyme with controversial
functions in plants
    » The network of amide amino acids metabolism is regulated in concert by developmental, physiological, environmental,
metabolic, and stress-derived signals
» The Aspartate Family Pathway that is Responsible for Synthesis of the Essential Amino Acids Lysine, Threonine, Methionine, and Isoleucine
    » The aspartate family pathway is regulated by several feedback inhibition loops
    » Metabolic fluxes of the aspartate family pathway are regulated by developmental, physiological, and
environmental signals
    » Metabolic interactions between AAAM and the aspartate family pathway
    » Metabolism of the aspartate family amino acids in
developing seeds: A balance between synthesis and
» Regulation of Methionine Biosynthesis
    » Regulatory role of CGS in methionine biosynthesis
    » Interrelationships between threonine and methionine biosynthesis
» Engineering Amino Acid Metabolism to Improve the Nutritional Quality of Plants for Nonruminants and Ruminants
» Future Prospects
» Summary
» Acknowledgements
» References
- Engineering Photosynthetic Pathways
» Abstract & Keywords
» Introduction
» Identification of Limiting Steps in the PCR Cycle
    » Analysis of limiting steps in photosynthesis
    » Flux control analysis
» Engineering CO2-Fixation Enzymes
    » RuBisCO
    » C4-Ization of C3 Plants
» Engineering Post-RuBisCO Reactions
    » RuBP regeneration
    » Engineering carbon flow from chloroplasts to sink organs
» Summary
» Acknowledgements
» References
- Genetic Engineering of Seed Storage Proteins
» Abstract & Keywords
» Introduction
    » The nature of seeds
    » Metabolites stored in seeds and their uses
    » Characterization of seed storage proteins
    » Challenges and limitations for seed protein modification
» Storage Protein Modification for the Improvement of Seed
Protein Quality
»   » Increasing methionine content
    » Increasing lysine content
» Use of Seed Storage Proteins for Protein Quality Improvements
in Nonseed Crops
» Modification of Grain Biophysical Properties
» Transgenic Modifications that Enhance the Utility of Seed
Storage Proteins
    » Managing allergenic proteins
    » Managing seed antinutritional characteristics
» Summary and Future Prospects
» Acknowledgements
» References
- Biochemistry and Molecular Biology of Cellulose Biosynthesis in Plants
» Abstract & Keywords
» Introduction
» The Many Forms of Cellulose
» Biochemistry of Cellulose Biosynthesis in Plants
    » UDP-glucose is the immediate precursor for
cellulose synthesis
    » In vitro synthesis of cellulose from plant extracts
    » Purification and characterization of cellulose
synthase activity
» Molecular Biology of Cellulose Biosynthesis in Plants
    » Identification of genes encoding cellulose synthases in plants
    » Mutant analysis allowed identification of genes for
cellulose synthases and other proteins required
for cellulose biosynthesis
    » The cellulose synthase genes
    » The cellulose synthase protein
» Mechanism of Cellulose Synthesis
    » Role of primer and/or intermediates during
cellulose synthesis?
    » Addition of glucose residues to the growing glucan
chain end
» Prospects for Genetic Engineering of Cellulose Biosynthesis
in Plants
    » Manipulation of cellulose biosynthesis in plants
    » Influence of cellulose alterations in plants
» Summary
» Acknowledgements
» References
- Metabolic Engineering of the Content and Fatty Acid Composition of Vegetable Oils
» Abstract & Keywords
» Introduction
» TAG Synthesis
    » Precursors for fatty acid synthesis
    » Fatty acid synthesis
    » Phosphatidic acid assembly
    » Glycerolipids and fatty acid modification
    » TAG synthesis and oil deposition
» Control of TAG Composition
    » Metabolic engineering of high oleic acid vegetable oils
    » Metabolic engineering of high and low saturated fatty acid vegetable oils
    » Metabolic engineering of high and low
polyunsaturated vegetable oils
    » Variant fatty acid desaturases for metabolic engineering of vegetable oil composition
    » Metabolic engineering of vegetable oils with short and medium-chain fatty acids
    » Metabolic engineering of vegetable oils with very
long-chain fatty acids (VLCFAs)
    » Metabolic engineering of nonplant pathways
» Summary
    » Alteration of seed oil content
    » Alteration of the fatty acid composition of vegetable oils
» Acknowledgements
» References
- Pathways for the Synthesis of Polyesters in Plants
» Abstract & Keywords
» Introduction
» Cutin and Suberin
    » Functional and ultrastructural characteristics
    » Composition of cutin and suberin
    » Biosynthesis of cutin and suberin
    » Future perspectives
» Polyhydroxyalkanoate
    » PHA as a bacterial polyester
    » Polyhydroxybutyrate
    » Poly(3-hydroxybutyrate-co-3-hydroxyvalerate)
    » Medium-chain-length polyhydroxyalkanaote
    » Future perspectives
» References
- Plant Sterol Methyltransferases
» Abstract & Keywords
» Introduction
» Pathways of Phytosterol Biosynthesis
» Phytosterolomics
» Enzymology and Evolution of the SMT
» Bioengineering Strategies for Generating Plants with Modified Sterol Compositions
» Acknowledgement
» References
- Engineering Plant Alkaloid Biosynthetic Pathways
» Abstract & Keywords
» Introduction
» Monoterpenoid Indole Alkaloids
    » Monoterpenoid indole alkaloid biosynthesis
    » Cell-specific expression of monoterpenoid indole
alkaloid biosynthetic genes
    » Genetic engineering of monoterpenoid indole
alkaloid biosynthetic pathways
» Tetrahydrobenzylisoquinoline Alkaloids
    » Tetrahydrobenzylisoquinoline alkaloid biosynthesis
    » Cell-specific expression of tetrahydrobenzylisoquinoline
alkaloid biosynthetic genes
    » Genetic engineering of tetrahydrobenzylisoquinoline
alkaloid biosynthetic pathways
» Tropane Alkaloids
»   » Tropane alkaloid biosynthesis
    » Cell-specific expression of tropane alkaloid biosynthetic genes
    » Genetic engineering of tropane alkaloid biosynthetic pathways
» Summary
» Acknowledgements
» References
- Engineering Formation of Medicinal Compounds in Cell Cultures
» Abstract & Keywords
» Introduction
» Biochemistry and Cell Biology of Secondary Metabolites
    » Isoquinoline alkaloid biosynthesis
    » Terpenoid indole alkaloid biosynthesis
    » Tropane alkaloid and nicotine biosynthesis
» Cell Culture and Metabolite Production
    » Establishment of high-metabolite-producing lines
    » Organ differentiation and secondary plant products
    » Genetic instability of productivity
» Beyond the Obstacles: Molecular Biological Approaches to
Improve Productivity of Secondary Metabolites in Plant Cells
»   » Overcoming rate-limiting processes in the pathway
    » Transcriptional regulation and overall activation
    » Qualitative control of metabolites and the isolation of desired biosynthetic genes
    » Accumulation and storage
» Future Perspectives
» Summary
» Acknowledgements
» References
- Genetic Engineering for Salinity Stress Tolerance
» Abstract & Keywords
» Salinity Stress Engineering
» The Context of Salinity Stress
» Ion Homeostasis
    » Ion transport
    » Control of ion homeostasis
» Strategies to Improve Salt Tolerance by Modulating Ion Homeostasis
» Strategies to Improve Salt Tolerance by Modulating Metabolic Adjustments
    » Osmotic adjustments and controlling factors
    » Engineering stress response control determinants
    » How to analyze transgenic lines resulting from (salinity)
stress engineering
» Plant Signal Transduction for Adaptation to Salinity
    » The SOS signal pathway controls adaptation to hypersalinity
    » What do we know about stress sensors in plants?
    » SOS independent pathways and protein kinase systems
» ABA is a Major Mediator of Plant Stress Response Signaling
» Summary
» Acknowledgements
» References
- Metabolic Engineering of Plant Allyl/Propenyl Phenol and Lignin Pathways
» Abstract & Keywords
» Introduction
    » The challenge for humanity: Renewable, sustainable
sources of bioenergy/ biofuels, intermediate chemicals, and specialty chemical bioproducts
    » Lignified biomass utilization: The lignin challenge
» Lignin Formation and Manipulation
    » Biosynthesis of monolignols
    » The challenge of lignin manipulation: Plant growth/
development versus stem structural integrity
    » New opportunities and approaches for renewable sources of bioenergy, biofuels, and bioproducts?
» Current Sources/Markets for Specialty Allyl/Propenyl Phenols
» Biosynthesis of Allyl and Propenyl Phenols and Related
Phenylpropanoid Moieties
» Potential for Allyl/Propenyl Phenols?
» Summary
» Acknowledgements
» References