Plant Cells and their Organelles

About the Editors William V. Dashek, Emeritus Professor, Mary Baldwin College, USA Dr. Dashek is the recipient of BS, MS and Ph.D. degree from Marquette University where he was a National Institute of Health pre-doctoral trainee. He was a post-doctorate fellow at the Michigan State University Plant research Laboratory. Subsequently, he began a lengthy Academic teaching and research career. Currently, Dashek is retired writing advanced textbooks. Gurbachan S. Miglani, Visiting Professor, School of Agricultural Biotechnology, Punjab Agricultural University, India Dr. Miglani obtained B.Sc. (Agri. & A.H.) and M.Sc. (Genetics) from Punjab Agricultural University (PAU), Ludhiana, Punjab, India and Ph.D. from Howard University, Washington, D.C. During his 35-year teaching stint at PAU he taught general and specialized courses in genetics. Even after retirement Miglani is still teaching molecular genetics and biotechnology at PAU. In addition to research and review papers, popular science articles, laboratory manuals he has published a dozen books and presently he is writing his next book.

Contributors ix

Preface xi

Acknowledgments xii

1 An introduction to cells and their organelles 1
William V. Dashek

Cells 1

Cell organelles – an introduction 6

Ion channels 10

Proton pumps 14

Water channels 14

Carriers 15

Cell death 17

References 18

Further reading 24

2 Isolation and characterization of subcellular organelles from plant cells 25
Milee Agarwal, P. Desai, and Harish Padh

Isolation of subcellular organelles 26

Identification and characterization of isolated organelles 33

Summary 39

References 39

Further reading 41

3 Endoplasmic reticulum 42
William V. Dashek

Structure 42

Chemical composition 42

Biogenesis 45

Functions 45

Posttranslational events 49

Inhibitors 53

In vitro protein synthesis 54

Other functions 54

References 54

Further reading 60

4 The Golgi apparatus 61
D. Davis, T.E. Wilkop, and Georgia Drakakaki

The Golgi apparatus 61

Plant Golgi introduction 66

Structure and organization 69

Golgi‐mediated vesicular trafficking 71

Plant Golgi‐dependent cellular processes 74

Imaging and visualization 76

Isolation and analysis 78

Golgi genetics and genomics 81

Significance 84

Acknowledgment 85

References 85

Further reading 87

5 Microbodies 88
Robert Donaldson

Introducing peroxisomes 88

Leaf peroxisomes 89

Peroxisomes in oil seeds and pollen 91

References 107

Further reading 109

6 Microtubules, intermediate filaments, and actin filaments 110
William V. Dashek

Microtubules 110

Intermediate filaments 113

Actin filaments (microfilaments) 116

References 119

Further reading 124

7 The mitochondrion 125
Ray J. Rose, Terence W.‐Y. Tiew, and William V. Dashek

Structure and dynamics 125

The mitochondrial genome 128

Comparison of the mitochondrial genome with chloroplast and nuclear genomes 131

The mitochondrial proteome and protein import 132

Respiratory metabolite transporters 133

The electron transport chain and oxidative phosphorylation 133

The alternative electron transfer chain in plant mitochondria 139

Plant mitochondria, stress responses and programmed cell death 139

Other functions of plant mitochondria 140

References 144

Further reading 145

8 Nucleus 146
Yogesh Vikal and Dasmeet Kaur

Structural organization of the NE 147

Nuclear pores 152

The nucleolus 157

Chromatin and chromosomes 165

DNA structure 170

DNA replication 173

RNA structure, function, and synthesis 176

Nucleocytoplasmic transport, nuclear import, and nuclear export 183

The dynamics of NE biogenesis during mitosis 188

The dynamics of nuclear pore complex biogenesis 196

Cell cycle control 200

Summary 205

References 206

Further reading 207

9 Plant cell walls 209
James E. Bidlack and William V. Dashek

Introduction 209

Structure 209

Biosynthesis 216

Chemical composition 217

Biogenesis 222

Function 225

References 231

Further reading 238

10 Plastid structure and genomics 239
Gurbachan S. Miglani

Plastid structure 239

Different forms of plastids 240

Plastid stromules 248

Chlorophyll biosynthesis 248

Plastid genomics 250

Sequenced plastomes 253

Promiscuous DNA 258

Plastid genome organization 260

Plastid gene organization, expression, and regulation 265

Systems biology approach in understanding chloroplast development 269

Chloroplast genetic engineering 284

Recent trends in chloroplast research 289

Summary 293

References 294

Further reading 299

11 Photosynthesis 300
J. Kenneth Hoober

Introduction 300

Evolution of photosynthesis 301

Development of the chloroplast 310

Absorption of light energy 317

Generation of end products 324

Distribution of the photosystems in thylakoid membranes 329

Photoinhibition: damage and repair of the PS II reaction center 332

Protection of PS II by carotenoids 332

Incorporation of carbon as CO2 into carbohydrate 334

End products of carbon assimilation 346

Conclusions for the reactions of photosynthesis 348

References 348

Further reading 350

12 Vacuoles and protein bodies 351
William V. Dashek and Amy M. Clore

Vacuoles 351

PBs and other protein storage compartments 359

References 365

Further reading 370

13 Systems biology in plant cells and their organelles 371
Rajdeep Kaur Grewal, Saptarshi Sinha, and Soumen Roy

Systems biology—“omics” 371

Genomics 373

Lipidomics 378

Metabolomics 380

Proteomics 382

Transcriptomics 384

Synthetic biology 386

Acknowledgments 388

References 389

Further reading 391

Appendix A 392

Appendix B 400

Appendix C 403

Index 407