Plant Abiotic Stress Signaling

Preface
Contents
Contributors
Part I: Questions and Approaches
Chapter 1: Interplay of Methodology and Conceptualization in Plant Abiotic Stress Signaling
1 Introduction
2 The Eukaryotic Stress Signaling Framework
3 Plant Models for Abiotic Stress Signaling Studies
4 The Discovery of Abiotic Stress Sensors and Abiotic Signaling Networks in Plant Cells
5 Abiotic Stress Signaling and the Debate on Plant Sentience and Plant Intelligence
6 Implications for Plant Ecology and Agronomy and for Global Change Biology
7 Conclusion
References
Chapter 2: Complexity of Abiotic Stress Stimuli: Mimicking Hypoxic Conditions Experimentally on the Basis of Naturally Occurri...
1 Introduction
2 Naturally Occurring Hypoxic Environments
2.1 Developmental Hypoxic Niches
2.2 Pathogen-Induced Hypoxia
2.3 Soil Waterlogging and (Partial) Submergence
3 Hypoxia Treatments: What Do They Mimic?
3.1 Waterlogging and (Partial) Submergence
3.2 Gas Replacement
3.3 Vertical Versus Horizontal Growth on Solid Agar Media
3.4 Hypoxia Stress in the Dark Compared to Light
3.5 Hypoxia Treatments in Liquid Culture Systems
4 Conclusions
References
Chapter 3: Iron Availability and Homeostasis in Plants: A Review of Responses, Adaptive Mechanisms, and Signaling
1 Introduction
2 Iron from Soil to Plants: A Diversity of Chemical Entities and Bioavailability
2.1 Soil Iron Oxides
2.2 Soil Iron Concentration
2.3 Ionic, Complexed, Amorphous, and Crystallized Species
2.4 Fe Bioavailability
3 Deleterious Impacts of Iron Deficiency in Plants
3.1 Impact on Photosynthesis
3.2 Impact on Plant Respiration
3.3 Impact on Symbiotic Nitrogen Fixation
4 Iron Homeostasis: Uptake, Transport, and Distribution
5 Signaling and Regulation of Iron Homeostasis
6 Signaling Crosstalks in the Regulation of Iron Homeostasis
7 Interactions of Iron and Reactive Oxygen Species in the Dynamics of Oxidative Stress
7.1 Dynamics of Fe-Driven Oxidative Stress
7.2 Adaptive Responses to Fe-Driven Oxidative Stress
References
Part II: Signals and Signalomics
Chapter 4: Calcium Live Imaging at Multi-Scales from Cellular to Organ Level in Arabidopsis thaliana
1 Introduction
2 Materials
2.1 YC3.60 Transgenic Plants
2.2 GCamP3 Transgenic Plants
2.3 Solutions
2.4 Equipment for FRET YC3.60 Microscopic Measurement
2.5 Equipment for GCamP3 Microscopic Measurement
3 Methods
3.1 FRET YC3.60 Microscopic Measurement
3.1.1 Acquisition Settings
3.1.2 Image Processing
3.1.3 Quantification
3.2 GCamP3 Macroscopic Measurement
3.2.1 Acquisition Settings
3.2.2 Image Processing
3.2.3 Quantification
4 Notes
References
Chapter 5: Functions of NO and H2S Signal Molecules Against Plant Abiotic Stress
1 Introduction
2 Protein Posttranslational Modifications (PTMs) Mediated by NO and H2S in Higher Plants
3 NO and H2S Mediate Gene Expression Through the Modulation of Transcription Factors (TFs)
4 Function of NO and H2S Under Abiotic Stress Conditions
5 Conclusions and Future Perspectives
References
Chapter 6: Review of Lipid Biomarkers and Signals of Photooxidative Stress in Plants
1 Introduction
1.1 Photosynthesis or Photooxidation?
1.2 The Lipid Problem Under Photooxidative Stress
2 Primary Markers of Lipid Peroxidation
3 Spectrophotometric Determination of Lipid Hydroperoxides
4 End Products of Lipid Peroxidation
5 Lipid Peroxidation-Associated Luminescence
6 Imaging of Lipid Peroxidation with Specific Probes
7 Lipophilic Antioxidants
8 Adducts to Proteins and DNA
9 Conclusions
References
Chapter 7: The Plant Metabolic Changes and the Physiological and Signaling Functions in the Responses to Abiotic Stress
1 Introduction
2 Primary Metabolites
2.1 Amino Acids
2.2 Sugars and Organic Acids
2.2.1 Sugars
2.2.2 Citric Acid
3 Lipids and Wax
3.1 Lipids
3.2 Wax
4 Secondary Metabolites (SMs)
4.1 Polyphenols
4.2 Terpenoids
4.3 Alkaloids
5 Conclusion and Perspectives
References
Chapter 8: 15N-labelling of Leaves Combined with GC-MS Analysis as a Tool for Monitoring the Dynamics of Nitrogen Incorporatio...
1 Introduction
2 Materials
2.1 15N-Labeling of Leaves
2.2 Amino Acid Extraction and Purification
2.3 Gas Chromatography Coupled to Mass Spectrometry (GC/MS)
3 Methods
3.1 15N-Labeling of Leaves
3.2 Extraction of Amino Acids
3.3 Purification of Amino Acids
3.4 GC/MS Analysis for the Determination of 15N Atom (%) Enrichment of Each Amino Acid
3.5 Quantification of Amino Acids and 15N Enrichment
3.5.1 Rationale of Heavy Isotope Abundance Calculations
3.5.2 Rationale of Amino Acid Quantification
4 Notes
References
Chapter 9: Computational Metabolomics to Elucidate Molecular Signaling and Regulatory Mechanisms Associated with Biostimulant-...
1 Introduction
2 Materials
2.1 Sample Preparation
2.2 Analytical Procedure and Data Processing
3 Methods
3.1 Spectral Data Annotation and Visualization Using Molecular Networking
3.1.1 Data Conversion
3.1.2 Data Processing
3.1.3 Exporting GNPS Input Files
3.1.4 Computing Molecular Networks in the GNPS Environment
3.2 Exploration of the Substructural Diversity of the Extracted Metabolome Using MS2LDA
3.3 Exploration of the Chemical Class Diversity Using MolNetEnhancer
3.4 Metabolic Pathway Analysis
3.5 Metabolic Network Analysis
3.6 A Contextual Summary of Postulated Mechanisms Elucidated from This Study
4 Notes
References
Chapter 10: Electrical Signaling and Its Functions Under Conditions of Abiotic Stress: A Review of Methodological Approaches a...
1 Introduction
2 Methods for Measuring Electrical Signals in the Phloem
2.1 Extracellular Recording
2.2 Intracellular Recording
2.2.1 Microelectrode Technique
2.2.2 Aphid Technique
2.3 Optical Recording
3 Means of Signal Transmission
3.1 Electrical Characteristics of Sieve Tubes
4 Types of Electrical Signals
4.1 Action Potentials
4.2 Variation Potentials (Slow Wave Potentials)
5 Physiological Effects of Electrical Signals
5.1 Regulation of Leaf Movements
5.2 Assimilate Transport
5.3 Photosynthesis and Gas Exchange
5.4 Plant Water Status
6 Conclusions
References
Part III: Signaling Processes
Chapter 11: Quantitative Measurements of Biochemical and Molecular Markers of Oxidative Stress Signaling and Responses
1 Introduction
2 Materials
2.1 Reagents and Solutions
2.1.1 For Quantification of Antioxidant Buffers: Ascorbate and Glutathione
2.1.2 For Measuring Major Antioxidative Enzymes
2.1.3 For qRT-PCR Analysis of Oxidative Stress Marker Transcripts
2.2 Equipment
3 Methods
3.1 Quantification of Antioxidant Buffers: Ascorbate and Glutathione
3.1.1 Extraction
3.1.2 Neutralization
3.1.3 Treatment of Extract Aliquots to Distinguish Between Oxidized and Reduced Forms
Treatment of Aliquots for Assay of GSSG
Reduction of Dehydroascorbate (DHA) for Assay of Total Ascorbate
3.1.4 Assay Procedures
Ascorbate Assay
Total Glutathione Assay
Total Ascorbate Assay
GSSG Assay
3.1.5 Data Processing
3.2 Measuring Major Antioxidative Enzymes
3.2.1 Extraction and Sample Preparation
3.2.2 Enzyme Assays
Catalase
Ascorbate Peroxidase (APX)
Dehydroascorbate Reductase (DHAR)
Glutathione Reductase (GR)
3.2.3 Data Processing
3.3 qRT-PCR Analysis of Oxidative Stress Marker Transcripts
3.3.1 Total RNA Purification
3.3.2 cDNA Synthesis and qPCR
3.4 Validation of Approaches
4 Notes
References
Chapter 12: Fast Identification of In Vivo Protein Phosphorylation Events Using Transient Expression in Leaf Mesophyll Protopl...
1 Introduction
2 Materials
2.1 Expression Vector Construction and Purification
2.1.1 Equipment and Reagents
2.1.2 Stock Solutions and Working Solutions
2.2 Protoplast Isolation and Polyethylene Glycol (PEG)-Ca2+ Transfection
2.2.1 Equipment and Reagents
2.2.2 Stock Solutions and Working Solutions
2.3 Phos-tag SDS Polyacrylamide Gel
2.3.1 Equipment and Reagents
2.3.2 Stock Solutions and Working Solutions
3 Methods
3.1 Expression Vector Construction and Purification
3.1.1 Generating the Expression Vector
3.1.2 Plasmid Maxiprep with CsCl Density Gradient Purification
3.2 Protoplast Isolation and PEG-Ca2+ Transfection
3.2.1 Leaf Mesophyll Protoplast Isolation
3.2.2 PEG-Ca2+ Transfection
3.3 Phos-tag SDS Polyacrylamide Gel
3.3.1 Phos-tag SDS Polyacrylamide Gel Casting
3.3.2 Phos-tag Polyacrylamide Gel Run
3.3.3 Wet Blotting
3.3.4 Blocking and Antibody Incubation
4 Notes
References
Chapter 13: Analysis of Plant L-Cysteine Desulfhydrase (LCD) Isozymes by Non-denaturing Polyacrylamide Gel Electrophoresis
1 Introduction
2 Materials
2.1 Plant Extracts and Chemicals
2.2 Non-denaturing Polyacrylamide Gel Solutions
2.3 LCD Activity Staining Solution
3 Methods
3.1 Polyacrylamide Gel Electrophoresis of Plant Extracts on 8% Acrylamide Gels
3.2 L-Cysteine Desulfhydrase Activity Staining
4 Notes
References
Chapter 14: Metabolite-Based Genome-Wide Association Studies of Large-Scale Metabolome Analysis to Illustrate Alterations in t...
1 Introduction
2 Materials
2.1 Plant Material
2.2 Chemicals
2.3 Equipment
3 Methods
3.1 Experimental Design
3.1.1 Stress Treatment Strength
3.1.2 Dynamic Stress Response
3.2 Metabolite Profiling
3.2.1 Sample Harvest and Quality Control Sample Preparation
3.2.2 Sample Extraction
3.2.3 Lipid Analysis by UPLC-MS
3.2.4 Polar and Semipolar Metabolites Analysis by GC-MS
3.2.5 Polar and Semipolar Metabolites Analysis by UPLC-MS
3.2.6 Chromatogram Analysis and Metabolite Identification
3.3 Data Mining
3.3.1 Normalization (See Note 14)
3.3.2 GWAS Analysis
3.3.3 The Validation of Candidate Function and Genetic Variation Effect
4 Notes
References
Chapter 15: Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis
1 Introduction
2 Selection of Web-Based Resources for Data Analysis
2.1 Databases
2.2 Reliability of Data and Storage
2.3 Gene Expression Data Analysis and Assembly of Genes with Similar Expression
2.4 Functional Characterization by Gene Ontology and Pathways Analysis
2.5 Contribution of Gene Networks to Functional Characterization
2.6 Definition of Regulatory Networks by Promoter Analysis and Transcription Factor Characterization
2.7 Protein-Protein Interactions and Networks
3 Application of Bioinformatics Tools for the Deciphering of Abiotic Stress Signaling Pathways: Case Studies of Xenobiotic and...
3.1 Induction of Xenobiotic Detoxification Through Multiple Signaling Pathways
3.2 Characterization of a Negative Regulator of the Xenobiotic Detoxification Pathway
3.3 Plant Responses to 2,4-D Herbicide Use ROS-Dependent Signaling Pathways
3.4 Xenobiotic Disruption of Hormonal Regulations Through Stress and Low-Energy Signaling Interferences
3.5 Cadmium Tolerance Involves a Network of Hub TFs, Post-Transcriptional Modifications and Hormonal Signaling Cascades
4 Conclusions and Perspectives
References
Chapter 16: Multi-omics Data Integration in the Context of Plant Abiotic Stress Signaling
1 Introduction
2 Materials
2.1 Hardware and Software Requirements
2.2 Plant Material
2.3 Omics Data
3 Methods
4 Case Study
4.1 Without A Priori, Can We Observe on the Transcriptomics Data the Effect of Different Environmental Growth Conditions or Di...
4.1.1 Perform Principal Component Analysis
4.1.2 Outline of the Interpretation
4.2 Can We Observe a Global Effect of Temperature on the Different Ecotypes According to their Transcriptomics Profiles?
4.2.1 Perform Projection to Latent Structures-Discriminant Analysis
4.2.2 Outline of the Interpretation
4.3 How to Know the Best Candidate Genes for the Global Effect of Temperature?
4.3.1 Perform Sparse Projection to Latent Structures-Discriminant Analysis
4.3.2 Outline of the Interpretation
4.4 Can We Highlight Relationships Between Cell Wall Proteins and Transcripts in Floral Stems?
4.4.1 Perform Projection to Latent Structures
4.4.2 Outline of the Interpretation
4.5 What Are the Main Relationships Between Transcriptomics, Proteomics, Metabolomics, and Phenotypic Data in Floral Stems?
4.5.1 Perform Regularized Generalized Canonical Correlation Analysis
4.5.2 Outline of the Interpretation
4.6 Can We Determine a Multi-omics Signature to Classify Ecotypes on the Basis of Floral Stem Data?
4.6.1 Perform Multi-block Sparse Projection to Latent Structure-Discriminant Analysis
4.6.2 Outline of the Interpretation
4.7 On the Proteomics Data, Can We Identify Behaviors that Do Not Depend on the Organ?
4.7.1 Without A Priori, What Are the Main Effects of Different Environmental Growth Conditions or Different Ecotypes, When Con...
4.7.2 Can We Discriminate the Five Ecotypes, When Controlling the Variations Due to the Organ?
4.7.3 Can We Determine a Proteomics Signature of the Five Ecotypes, When Controlling the Variations Due to the Organ?
5 Conclusion
6 Notes
References
Chapter 17: Protein-Protein Interactions in Abiotic Stress Signaling: An Overview of Biochemical and Biophysical Methods of Ch...
1 Introduction
2 In Vitro Analysis of In Vitro or In Vivo Interactions Between Two Proteins of Interest
3 In Vivo Analysis of In Vivo Interactions Between Two Proteins of Interest
4 Importance of FRET-Based and FCS-Based Methods for the In Vivo Identification and Characterization of Protein-Protein Intera...
5 Large-Scale Discovery of Novel Protein-Protein Interactions and Interactomes
6 Conclusions and Perspectives
References
Chapter 18: Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the R...
1 Introduction
2 Epigenetic Regulations
2.1 Histone Acetylation
2.2 Histone Methylation
2.3 DNA Methylation
2.4 RNA Methylation
2.5 Other Base Modifications in RNAs
2.6 ncRNAs
3 B-DNA and Non-B DNA Structures
4 Guanine-Quadruplexes (G4s)
4.1 Description of G4s Folding and Stacking
4.2 G4 Formation and Its Impact on Cellular Processes
4.3 Factors Driving Formation and Resolving of G4s
5 R-Loops
6 Cruciforms and Hairpins
7 Epigenetics in the Context of Plant Growth Regulation and Stress Responses
7.1 Epigenetics and Stress Responses
7.2 Epigenetics and Plant Growth and Development
8 Selection of Methods for Studying Epigenetic Regulations and Non-B DNA Structures in Plants
8.1 Characterization of Histone Modifications
8.2 Characterization of the DNA Methylation Status
8.3 Analysis of ncRNAs
8.4 Characterization of Non-B DNAs
8.5 Characterization of G4 Structures
9 Conclusion and Future Perspectives
References
Part IV: Systemic and Ecosystemic Signaling
Chapter 19: Laser Microdissection: A High-Precision Approach to Isolate Specific Cell Types from Any Plant Species for Downstr...
1 Introduction
2 Materials
2.1 Materials and Equipment (See Note 1)
2.2 Reagents and Solutions (See Note 2)
3 Methods
3.1 Preparation of the Citrus Fruit Sample
3.2 Preparation of Sections Using the Anti-Roll Glass Plate Method
3.3 Slide Fixation and Dehydration
3.4 Laser Microdissection
4 Notes
References
Chapter 20: An Experimental Rhizobox System for the Integrative Analysis of Root Development and Abiotic Stress Responses Unde...
1 Introduction
2 Materials
2.1 Seeds
2.2 Equipment
2.3 Plant Cultivation Substrates
2.4 Solutions
2.5 Assembly of the Rhizobox System
3 Methods
3.1 Seed Sowing and Cultivation of Arabidopsis Seedlings
3.2 Seed Sowing and Cultivation of Pea Seedlings
3.3 Application of Water-Deficit Conditions
3.4 Non-destructive Observation of Root Development in the Rhizobox
3.5 Sample Collection
4 Notes
References
Chapter 21: Live Whole-Plant Detection of Rapidly Accumulating Reactive Oxygen Species Following Applied Stress in Arabidopsis...
1 Introduction
2 Materials
3 Methods
3.1 Whole-plant ROS Imaging of Arabidopsis thaliana
3.2 Image and Data Acquisition Using Living Image 4.7.2 Software
4 Notes
References
Chapter 22: Analysis of Small Non-coding RNAs as Signaling Intermediates of Environmentally Integrated Responses to Abiotic St...
1 Introduction
2 Materials
2.1 Plant Cultivation, Rhizosphere and Soil Sampling
2.2 Isolation of miRNAs from Rhizosphere and Control Soil
2.3 RNA Quality Control
2.4 NGS Library Preparation
2.5 NGS Library Purification
2.6 NGS Library Quality Control
2.7 NGS Library Sequencing
2.8 Bioinformatics Tools
2.9 Bioinformatics Databases
3 Methods
3.1 Plant Culture
3.2 Rhizosphere and Bulk Soil Sampling
3.3 RNA Isolation
3.4 Analysis of RNA Integrity Assayed by Agarose Gel Electrophoresis
3.5 RNA Quantification by NanoDrop Spectrophotometer ND-1000
3.6 NGS Library Preparation
3.6.1 Ligation of the 3′ SR Adapter to the 3′OH of the RNA
3.6.2 Hybridization of the Reverse Transcription Primer
3.6.3 Ligation of the 5′ SR Adapter
3.6.4 Reverse Transcription
3.6.5 PCR Amplification
3.6.6 Purification of the Library and Illumina Sequencing
3.7 NGS miRNA Bioinformatics Analysis
3.7.1 Raw Reads Processing, miRNA Identification, and Abundance Estimation
3.7.2 miRNA Target Identification
3.7.3 Code Availability
3.7.4 Data Availability
4 Notes
References
Chapter 23: Perspectives in Plant Abiotic Stress Signaling
1 Introduction
2 Deciphering the Complexity of Multiple Abiotic Stress Signaling and Signaling Interferences
3 Cell-Specific Processes and Cell-Cell Interactions Under Abiotic Stress
4 In Vivo and Real-Time Processes
5 Mathematical Modeling
6 Mechanisms of Stress Training and Stress Memory
7 Abiotic Stress Signaling in the Field and In Natura
8 Conclusion
References
Index