Plant MicroRNAs and Stress Response 1st Edition by Deepu Pandita, Anu Pandita ISBN 1032344504 9781032344492

1 MicroRNA-induced Silencing Complex Assembly and MicroRNA Turnover

1 Introduction

2 miRNA Biogenesis

2.1 Canonical Pathway

2.2 Non-canonical Pathway

2.3 sno-derived miRNAs

2.4 miRNA from tRNA

2.5 shRNA

2.6 siRNA

2.7 Regulation of Biogenesis

3 RISC Assembly

3.1 RISC Loading

3.2 Unwinding of siRNA

4 Translational Repression and Target Degradation

4.1 miRNA Turnover

5 miRNA Editing

6 Conclusion

References

2 MicroRNAs in Plants and Animals: Converging and Diverging Insights

1 Introduction

2 miRNA Biogenesis

2.1 Biogenesis of miRNA in Plants

2.2 Biogenesis of miRNA in Animals

3 Target Recognition

3.1 Target Recognition in Plants

3.2 Target Recognition in Animals

4 Mechanism of miRNA Action

4.1 miRNA-mediated Decay of MRNA in Animals

4.2 miRNA-mediated Decay of MRNA in Plants

4.3 miRNA-mediated Repression of Translation in Animals

4.4 miRNA-mediated Repression of Translation in Plants

5 Regulation of miRNA Biogenesis in Plants

5.1 Regulation of miRNA Transcription

5.2 Regulation of the miRNA Core Processing Machinery

5.3 Regulation of miRNA Biogenesis by Structure of Pri-miRNA and RNA Splicing

5.4 Control of Pri-miRNA Stability

6 Regulation of miRNA Biogenesis in Animals

6.1 Transcriptional Control

6.2 Regulation of the Microprocessor

6.3 Regulation of miRNA Stability

7 Evolution of miRNA in Plants and Animals

7.1 Origin of MIR Genes in Plants

7.2 miRNA Divergence in Plants

7.3 miRNA and Target Gene Co-evolution in Plant

7.4 Origin of MIR Genes in Animals

8 Conservation of Expression Pattern in Animal miRNAs

9 Functions of miRNA in Animals

10 Functions of miRNA in Plants

References

3 Regulatory Roles of Plant MicroRNAs

1 Introduction

2 Role in Plant Regulation

2.1 Gene Expression Regulation

2.2 Regulation by miRNAs in Abiotic Stresses

2.3 Role of miRNAs in Biotic Stresses

3 Conclusion

References

4 MicroRNA-mediated Regulation of Plant Growth and Development

1 Introduction

2 Seed Development, Embryogenesis and Germination

2.1 Leaf Development

2.2 Apical Meristem, Shoot and Vascular Development

2.3 Root Development

2.4 Reproductive Phase and Flowering

Fruit Development

3 Conclusion

References

5 Silencing of Stress-regulated miRNAs in Plants

1 Introduction

2 Types of miRNAs

2.1 miRNA-mediated Stress Regulation in Crop Plants

2.2 Biogenesis

2.3 Modulation and Regulation

3 Silencing of Biotic Stress-regulated miRNAs in Plants

4 Silencing of Abiotic Stress-regulated miRNAs in Plants

5 Summary and Future Concerns

References

6 MicroRNA-mediated Regulation of Heat Stress Response

1 Introduction

2 Heat Stress in Plants

3 Heat Responsive Transcriptional Regulation

3.1 Clarification of MicroRNAs Concept and Types of MicroRNAs

3.2 Overview of Plant miRNAs Responses to Heat Stress

3.3 Heat Shock and Heat Stress Memory

3.4 miRNAs and Phytohormone Responses to Heat Stress

3.5 The Role of miRNAs in Flowering time and Reproduction: A Critical Stage for Heat Stress

3.6 Heat Stress Cross Talk: miRNAs Responsive to Combined Stresses

3.7 Implications for Crop Improvement

Conclusion and Perspectives

References

7 MicroRNA-mediated Regulation of Drought Stress Response

1 Introduction

2 Global Warming Concerns and Drought Stress

3 Key Players in Plant Drought Tolerance Scenario

4 MicroRNAs, Tiny Molecules with Macro Impacts

5 Resources and Approaches Towards miRNAS Discovery

6 Regulation of Drought Stress

6.1 miRNAs Involved in ABA Response

6.2 miRNAs Modulate Auxin Signalling

6.3 miRNAs and Ethylene Signalling and Senescence during Drought

6.4 miRNAs Regulate Water Relations and Osmotic Adjustment

6.5 miRNAs Mediate Photosynthesis and Respiration under Water Stress

6.6 miRNAs Regulate Growth and Development under Drought Stress

6.7 miRNAs and Antioxidant Defence System

7 Conclusion

References

8 MicroRNA-mediated Regulation of UV Radiation Stress Response

1 Introduction

2 Conserved miRNAs in Plants

3 Non-conserved miRNAs in Plants

4 UV-B Responsive miRNAS

5 Plant MicroRNA Regulation under UV-B Stress Response

5.1 UV-B Responsive miRNAs in in vitro-grown Plantlets

5.2 UV-B Response in Greenhouse and Fields

6 Plant MicroRNAs: Biogenesis, Homeostasis and Degradation

7 Specific Effects of UV-B Radiation on Plants

7.1 Different Types of UV Induces DNA Damage

7.2 DNA Repair Possibilities in Plants

7.3 UV Radiation-induced DNA Damage and Plant Cell Response

7.4 The Role of miRNA in the DNA Repair Process

7.5 Light-relevant cis-elements in the Promoters of miRNA genes

7.6 Different UV-responsive Expression Pathways Involved miRNAs in Plants

7.7 Regulatory Role of MicroRNAs in Response to Ultraviolet Radiation Stress Tolerance of Plants

8 Conclusion and Future Prospects

References

9 MicroRNA-mediated Regulation of Salinity Stress

1 Introduction

2 Ion Imbalance

3 Osmotic Homeostasis

4 Hormone Signalling

5 Antioxidant Response

6 Regulation of Plant Growth

7 Conclusion

References

10 MicroRNA-mediated Regulation of Cold and Chilling Stress Response

1 Introduction

2 Key Players Involved in Cold and Chilling Tolerance

2.1 MicroRNAs-mediated Regulation of Cold Stress

2.2 Regulation Mechanisms of MicroRNAs in Cold Stress

3 Conclusion

References

11 MicroRNA-mediated Regulation of Heavy Metal Stress in Plants

1 Introduction

2 MicroRNA-mediated Regulation of Mercury Toxicity in Plants

3 MicroRNA-mediated Regulation of Arsenic Toxicity in Plants

4 MicroRNA-mediated Regulation of Cadmium Toxicity in Plants

5 MicroRNA-mediated Regulation of Aluminium Toxicity in Plants

6 MicroRNA-mediated Regulation of Manganese Toxicity in Plants

7 MicroRNA-mediated Regulation of Other Metal Toxicity in Plants

8 Conclusion and Future Perspectives

Acknowledgements

References

12 MicroRNA-mediated Regulation of Osmotic and Oxidative Stress

1 Introduction

2 MicroRNAs in Plants

3 Genesis and Mechanistic Action of Bio-miRNAs

4 Role of miRNAs in Plant Stress Response

4.1 Abiotic Stress and mi-RNAs

4.2 Biotic Stress and mi-RNAs

4.3 Phytohormone Stress and mi-RNAs

4.4 Mechanical Stress and mi-RNAs

5 Osmotic and Oxidative Stress and its Regulation by miRNAs

6 Conclusion

Acknowledgements

References

13 MicroRNA-mediated Regulation of Herbicide Resistance

1 Introduction

2 Plant MicroRNAs Biogenesis: An Overview

2.1 Formation and Mechanism of Working of miRNAs

2.2 Biogenesis and Mechanisms of siRNA

3 The Roles of miRNA in Plant Abiotic or Biotic Responses

3.1 Stress Responses

3.2 Drought Stress

3.3 Salt Stress

3.4 Cold Stress

3.5 Heat Stress

3.6 UV-B Radiation

3.7 Heavy Metal Stress

3.8 Nutrition Deprivation

3.9 Bacteria

3.10 Fungi

3.11 Virus

3.12 Insect

3.13 Nematode

4 Herbicide Tolerance in Plants

5 MicroRNA-mediated Herbicide Resistance

5.1 RNA Interference (RNAi) Technology

5.2 Advances in Weed Management

5.3 Improvised Gene Functions for Resistance against Herbicides

6 Conclusion

References

14 MicroRNA-mediated Regulation of Plant Viral Disease Development

1 Introduction

2 MicroRNAs in Plants

2.1 Origins and Biogenesis

3 MiRNA and Plant Disease Regulation

3.1 miRNA as Key Player in Plant Antiviral Immunity

3.2 Application of Plant miRNAs against Virus Infections

4 Signalling in Antiviral Defences related to miRNAS

5 miRNA-based Molecular Marker in Disease Resistance

6 Conclusion and Future Perspective

References

15 Crosstalk of MicroRNAs with Phytohormone Signalling Pathways

1 Introduction

2 miRNAS and Plant Hormones in Response to Stress

2.1 microRNA Responses during Biotic Stress

2.2 MicroRNAs Responses during Abiotic Stress

3 Most Studied miRNAs Regulating Phytohormones in Plants

3.1 miR159

3.2 miR160 and miR167

3.3 miR156 and miR172

3.4 miR164 and miR319

3.5 miR390

3.6 miR393

3.7 miR396

4 Conclusion

References

16 Role of MicroRNAs in Plant-Microbe Interactions

1 Introduction

2 Role of MicroRNAs in Plant Microbe Interactions

2.1 Bacteria

2.2 Aphids

2.3 Viral Infection

2.4 Fungal Infection

2.5 Symbiotic Interactions

3 Conclusion

References

17 Micro-RNA: A Versatile Tool as Molecular Markers in Plants

1 Introduction

2 Markers in Crop Improvement

2.1 Conventional Markers

2.2 Molecular Markers

3 Non-coding RNAs as Markers in Plants

4 Development of miRNA-based Markers

5 Applications of miRNA Markers in Crop Management

6 MicroRNAs as Markers for Plant Stress

6.1 Drought Stress

6.2 Submergence/Flooding/Waterlogging Stress

6.3 Salinity Stress

6.4 Heat Stress

6.5 Biotic Stress

7 Future Perspectives

8 Conclusion

References

18 MicroRNAs and other Non-coding RNAs in Plant Epigenetics

1 Introduction

2 DNA (Cytosine) Methylation

3 Histone Modifications

4 miRNAs Regulate Plant Epigenetics

3.1 DNA Methylation Regulated by Conventional miRNAs in Arabidopsis

3.2 DNA (cytosine) Methylation in Moss

3.3 siRNAs-derived from miRNA Loci Methylate DNA

3.4 DNA (Cytosine) Methylation by lmiRNAs

3.5 TAS/PHAS Loci-derived siRNAs that are miRNA-triggered also Methylate DNA

4 miRNA Trigger easiRNA Biogenesis to Inhibit RDR2-Dependent RdDM

5 miRNAs Directly Regulate Methylation Players

6 Role of siRNAs in Plant Epigenetics

6.1 siRNAs and DNA Methylation

6.2 De Novo DNA Methylation of Cytosines Begins with the Biosynthesis of siRNAs

6.3 Production of Scaffold RNAs

6.4 Recruitment of siRNA Silencing Machinery on Target Sites

6.5 siRNAs Induce Histone Modifications

6.6 Architecture of siRNAs in the Methylation and Chromatin Modifications

6.7 siRNAs and Paramutation

6.8 Epigenetic Modifications Modulated by siRNAs

7 Long Non-coding RNAs Regulate Epigenetic Programming in Plants

7.1 Long Non-coding RNAs are the Progenitors of RdDM Silencing Pathway

7.2 Role of lncRNA in FLC Repression Mediated by Polycomb in Vernalisation

7.3 lncRNAs Assume a Significant Role in Enlistment of Polycomb Restraint Complex 1 (PRC1)

7.4 LncRNAs are Precursors to Abiotic Stress Responses

7.5 LncRNA in Crop Plants

7.6 Other lncRNA Classes in Plant Physiology

References

19 MicroRNA-based Plant Genetic Engineering for Crop Improvement

1 Introduction

2 What are MicroRNAs (miRNAs)?

2.1 Origin of miRNA

2.2 Properties of miRNA

2.3 Localisation of MicroRNA

2.4 Impact of miRNA on Plant Structure and Growth

3 miRNA’S Role in Development of Shoots, Vascular Tissues and Roots

4 miRNA Regulation in Plant Engineering

4.1 Effective Techniques

5 RNA Interference Function in Crop Enhancement

5.1 Improvement in Crop Yield

5.2 Fruit Enhancement

References

20 The miRNA-encoded Peptides

1 Introduction

2 Biogenesis of miRNAs and miPEPS

3 miPEPs: The New Technology for Functional Genomics

4 Screening of Hidden Peptides

5 Integration and Uptake of miPEPs in Plants

6 Regulatory Activities of Primary miRNA-derived Peptides

7 Regulation of Root Growth and Yield Trait in Crops through miRNA

8 Agronomic Significance of miPEPs

9 Conclusion and Future Perspectives

References

21 Plant MicroRNAs: Physiological Significance in Plants and Animals

1 Introduction

2 Physiological Role of miRNAs in Plants

2.1 miRNAs in Embryogensis

2.2 miRNAs in Leaf Development

2.3 miRNAs in Flowering

2.4 miRNAs in Root Development

2.5 miRNAs in Seed Germination

3 miRNAs are Differentially Expressed during Physiological Stress

4 miRNAs Levels Change with Nutrient Deficiency

5 Plant-derived miRNAs Regulate Gene Expression in Animals

References

Index