Biochemical Pathways and Environmental Responses in Plants: Part B

1st Edition - January 27, 2023

Editor: Joseph Jez

Hardback ISBN:

9 7 8 - 0 - 4 4 3 - 1 8 5 8 4 - 7

eBook ISBN:

9 7 8 - 0 - 4 4 3 - 1 8 5 8 5 - 4

Biochemical Pathways and Environmental Responses in Plants, Part B, Volume 682 in the Methods in Enzymology series, highlights advances in the field with this new volume… Read more

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Biochemical Pathways and Environmental Responses in Plants, Part B, Volume 682 in the Methods in Enzymology series, highlights advances in the field with this new volume presenting chapters on MIE 681/682: Biochemical pathways and environmental responses in plants, Structure, function, and engineering of plant polyketide synthases, A sensitive LC-MS/MS assay for enzymatic characterization of methylthioalkylmalate synthase involved in glucosinolate side-chain elongation, Assaying formate-tetrahydrofolate ligase with monoglutamylated and polyglutamylated substrates using a fluorescence-HPLC based assay, An Approach to Nearest Neighbor Analysis of Pigmented Protein Complexes by Using Chemical Crosslinking in Combination with Mass Spectrometry, Biochemical characterization of plant aromatic aminotransferases, and much more.

Other chapters focus on Functional Analysis of Phosphoethanolamine N-methyltransferase (PMT) in Plants and Parasites, A structure-guided computational screening approach for predicting plant enzyme-metabolite interactions, Plant metacaspase: an example of microcrystal structure determination and analysis, Biocatalytic system for comparative assessment of functional association of cytochrome P450 monooxygenases with their redox partners, Dirigent Protein Family Function and Structure, and more.

Cover
Title page
Table of Contents
Copyright
Contributors
Preface
Section I: Protein
Chapter One: Systems and strategies for plant protein expression
Abstract
1: Introduction
2: Transit peptide prediction
3: Cloning NAXD and NAXE expression vectors
4: Optimizing expression
5: Purification and storage of recombinant enzymes
6: Troubleshooting and additional considerations for plant protein expression
7: Conclusions
Acknowledgments
References
Chapter Two: Biochemical characterization of plant aromatic aminotransferases
Abstract
1: Introduction
2: Heterologous production of Aro AT proteins
3: Conducting Aro AT catalyzed enzymatic reactions
4: Detection methods for Aro AT product formation or substrate consumption
Acknowledgments
References
Chapter Three: Assaying plant formate-tetrahydrofolate ligase with monoglutamylated and polyglutamylated substrates using a fluorescence-HPLC based method
Abstract
1: Introduction
2: Methods
3: Summary
Acknowledgment
References
Further reading
Chapter Four: Functional analysis of phosphoethanolamine N-methyltransferase in plants and parasites: Essential S-adenosylmethionine-dependent methyltransferase in choline and phospholipid metabolism
Abstract
1: Introduction
2: Genomic and structural analysis of PMTs
3: Cloning, expression, and purification of PMTs
4: In vitro functional analysis of PMTs
5: Conclusion
Acknowledgments
References
Chapter Five: An approach to nearest neighbor analysis of pigment-protein complexes using chemical cross-linking in combination with mass spectrometry
Abstract
1: Introduction
2: Protein sample preparation
3: Mass spectrometry sample preparation
4: LC-MS/MS instrumentation
5: Identification of chemically cross-linked peptides
6: Network analysis of cross-linked sites
7: Conclusion and perspectives
References
Chapter Six: Structural characterization of protein–DNA complexes using small angle X-ray scattering (SAXS) with contrast variation
Abstract
1: Introduction
2: Sample preparation for SAXS contrast variation
3: SAXS data collection and analysis
4: Summary of procedures
5: Expected outcomes
6: Conclusion
7: Optimization and troubleshooting
References
Chapter Seven: A fast and cost-effective procedure for reliable measurement of trypsin inhibitor activity in soy and soy products
Abstract
1: Introduction
2: Development of a simplified trypsin inhibitor assay
3: Calculation of trypsin inhibitor activity
4: Immunoblot analysis of soybean lines with contrasting trypsin inhibitor content
5: Measurement of KTi activity in soybean lines with contrasting trypsin inhibitor content
6: Comparison of the 10 mL, 5 mL and the simplified 1 mL assay procedures
7: Measurement of trypsin inhibitor activity of hexane defatted SBM samples
8: Measurement of trypsin inhibitor activity of select commercial SBM samples
9: Measurement of TI activity using a microtiter plate
10: Conclusions
Acknowledgments
References
Section II: Metabolite
Chapter Eight: Strategies to study the metabolic origins of specialized plant metabolites: The specialized 1,4-naphthoquinones
Abstract
1: Introduction
2: Strategies to study the metabolic origins of specialized metabolites
3: Conclusions and future directions
Acknowledgments
References
Chapter Nine: A liquid chromatography-mass spectrometry-based metabolomics strategy to explore plant metabolic diversity
Abstract
1: Introduction
2: Sample harvesting and homogenization
3: Metabolite extraction
4: Data acquisition
5: Data analysis
Acknowledgments
References
Chapter Ten: Quantification of plant cardenolides by HPLC, measurement of Na+/K+-ATPase inhibition activity, and characterization of target enzymes
Abstract
1: Introduction
2: Rationale
3: Plant sample preparation
4: HPLC analysis of cardenolide abundance
5: Assays of Na+/K+-ATPase inhibition by plant extracts
6: Inhibition of Na+/K+-ATPase from insect nervous tissue
Acknowledgments
References
Chapter Eleven: Ex vivo metabolomics—A hypothesis-free approach to identify native substrate(s) and product(s) of orphan enzymes
Abstract
1: Introduction
2: Materials
3: Methods
4: Notes
Acknowledgments
References
Chapter Twelve: Metabolite fingerprinting: A powerful metabolomics approach for marker identification and functional gene annotation
Abstract
1: Introduction
2: Materials
3: Methods
4: Notes
Acknowledgments
References
Section III: Environment
Chapter Thirteen: Controlled environments for cannabis cultivation to support “omics” research studies and production
Abstract
1: Introduction
2: Equipment and other resources
3: Reagents
4: Supplies
5: Preparing growing areas
6: Preparing mother plants
7: Obtaining clones and initial aeroponic propagation
8: Hardening clones prior to greenhouse growth
9: Vegetative growth period in the greenhouse
10: Early flowering period in the greenhouse
11: Late flowering period in the greenhouse
12: Flower harvest
13: Conclusions and additional comments
References
Chapter Fourteen: Standard operating procedures for the comprehensive and reliable analysis of cannabis terpenes
Abstract
1: Introduction
2: Equipment
3: Equipment, accessories and consumables
4: Equipment, supplies, and reagents for sample processing
5: Sample processing for headspace analysis without tissue homogenization
6: Sample processing for headspace analysis with tissue homogenization
7: Sample processing for solvent extraction with tissue homogenization
8: Autosampler settings for headspace analysis
9: Autosampler settings for headspace SPME analysis
10: Autosampler settings for liquid sample injection
11: GC settings for separating terpenes over an HP5-MS column
12: GC settings for separating terpenes over a DB-WAX column
13: GC settings for separating terpene enantiomers over a Cyclodex-B column
14: Settings for GC–MSD data acquisition
15: Settings for FID data acquisition
16: Generating calibration curves with authentic standards
17: Setting up an automated data analysis method
18: Application Example 1: Impact of different sample processing methods on terpene profiles
19: Application Example 2: Using comprehensive terpene analyses to address common peak mis-annotations
20: Conclusions and outlook
References
Chapter Fifteen: Isolation of novel chemical components and their plant target proteins under selenium stress
Abstract
1: Introduction
2: Chemical screening under selenate stress conditions
3: Characterizing the selected candidate chemicals
4: Identification of chemical-binding target proteins in plants
5: Characterization of the interaction between selected chemical compounds and target proteins
6: Summary
Acknowledgments
References
Chapter Sixteen: Imaging systemic calcium response and its molecular dissection using virus-induced gene silencing
Abstract
1: Introduction
2: Before you begin
3: Materials and equipment
4: Cloning with VIGS vectors, the tobacco rattle virus
5: Agroinfiltration into N. benthamiana and A. thaliana and silencing confirmation
6: GCaMP imaging
7: GCaMP analysis
8: Summary and conclusions
Acknowledgments
References
Chapter Seventeen: Analysis of plant flooding response
Abstract
1: Introduction
2: Partial and full submergence with plants grown in pots
3: Partial and full submergence in petri dishes
4: Waterlogging in pots
5: Measurement of growth-related parameters from leaves
6: Measurement of chlorophyll and carotenoid from leaves
7: Measurement of anthocyanin from leaves
8: Measurement of malondialdehyde from leaves
9: Measurement of molecular markers for flooding stress
10: Summary and conclusions
Acknowledgments
References