Title Page -- Copyright Page -- Contents -- List of contributors -- Preface -- Section A Physiology of plant respiration and involvement of alternative oxidase -- Chapter 1 Integrating classical and alternative respiratory pathways -- Introduction -- Alternative oxidase (AOX) -- NADPH dehydogenases linked to AOX -- Uncoupling proteins (UCPs) -- Electron transfer flavoprotein (ETF) -- Deploying electron dissipatory mechanisms whilst maintaining ATP production under stress situations -- Conclusions -- References -- Chapter 2 Non-coupled pathways of plant mitochondrial electron transport and the maintenance of photorespiratory flux -- Introduction: Carbon fluxes through plant mitochondria in the light -- Activation of glycine oxidation by malate -- Oscillations of respiratory and photorespiratory fluxes -- NADH and NADPH dehydrogenases in the mitochondrial membranes -- Increase of the mitochondrial capacity in the light via engagement of rotenone-insensitive dehydrogenases -- Physiological role of alternative oxidase -- Equilibration of adenylates in the intermembrane space of mitochondria -- Bicarbonate pool and refixation of photorespiratory carbon -- Malate and citrate valves -- Conclusion -- References -- Chapter 3 Taxonomic distribution of alternative oxidase in plants -- What is alternative oxidase? -- Historical investigations of AOX in plants -- Taxonomic distribution of alternative oxidase in all domains of life -- Taxonomic distribution of alternative oxidase in plants -- Chlorophyte algae -- Streptophyte algae -- Land plants -- Recent functional hypotheses based on studies of AOX in multiple plants -- Where should efforts be focused next? -- References -- Chapter 4 Alternative pathways and phosphate and nitrogen nutrition -- Introduction -- Phosphate limitation -- Nitrogen nutrition and respiratory pathways -- Summary -- References.

Chapter 5 Structural elucidation of the alternative oxidase reveals insights into the catalytic cycle and regulation of activity -- Introduction -- Function and species spread of alternative oxidase -- Structure of the trypanosomal alternative oxidase -- Models of the alternative oxidase -- Modelling the structure of plant alternative oxidase -- Summary -- References -- Chapter 6 The role of alternative respiratory proteins in nitric oxide metabolism by plant mitochondria -- Introduction -- Targets of NO in mitochondria -- Mitochondrial NO degradation -- NO degradation by external NAD(P)H dehydrogenases -- Involvement of AOX in NO signalling and homeostasis -- Oxidative pathways for NO synthesis -- Reductive pathways for NO synthesis -- Summary -- Acknowledgments -- References -- Chapter 7 Control of mitochondrial metabolism through functional and spatial integration of mitochondria -- Introduction -- Functional and spatial integration: scope of the review -- Mitochondria: origins and functions -- Functional integration of mitochondria in plant cellular metabolism -- Concluding remarks -- References -- Chapter 8 Modes of electron transport chain function during stress: Does alternative oxidase respiration aid in balancing cellular energy metabolism during drought stress and recovery? -- Introduction -- Imbalances in energy metabolism -- Strategies to combat energy imbalances in the chloroplast electron transport chain -- Strategies to combat energy imbalances in the mitochondrial electron transport chain -- Plant respiration and alternative oxidase during drought stress -- Conclusions -- Acknowledgements -- Abbreviations -- References -- Chapter 9 Regulation of cytochrome and alternative pathways under light and osmotic stress -- Introduction -- AOX characteristics: distribution, abundance and activity -- Structure and regulation of AOX activity.

Cytochrome and alternative respiratory pathways under stress conditions with special reference to light and osmotic stress -- Other physiological roles of AOX -- References -- Chapter 10 Alternative respiratory pathway in ripening fruits -- Introduction -- Ethylene triggers normal and alternative respirations during fruit ripening -- ARP in climacteric fruit -- ARP in fruits undergoing non-climacteric ripening -- Conclusion -- References -- Chapter 11 Respiratory pathways in bulky tissues and storage organs -- Introduction -- The gene encoding potato alternative oxidase and its tissue-specific expression in potato tuber -- Development of alternative respiration pathway capacity of potato tuber slices during the aging process -- Alternative oxidase in aged potato tuber slices is a protein synthesized de novo during the aging process -- The relationship between endogenous ethylene and the development of the alternative respiration pathway capacity of potato tuber slices during the aging process -- Alternative respiration pathway capacity can be induced by hydrogen peroxide and salicylic acid in aging potato tuber slices -- Activation of alternative oxidase by pyruvate in mitochondria of aged potato tuber slices -- Comparison of the estimated alternative respiration pathway activities of aging potato tuber slices by hydroxamate-inhibition method and oxygen-isotope-fractionation method -- Conclusions -- Acknowledgements -- References -- Section B From AOX diversity to functional marker development -- Introduction -- Chapter 12 Exploring AOX gene diversity -- Chapter 12.1 Natural AOX gene diversity -- Variability at family pattern and plant genome organization -- Gene structure variability -- Variability at sequence level -- Polymorphisms in protein coding sequences -- Polymorphisms located in intronic sequences.

Polymorphisms in untranslated regions (UTRs) -- Conclusions and implications for future studies on FM development -- Chapter 12.2 AOX gene diversity in Arabidopsis ecotypes -- AOX gene polymorphisms -- Conclusions -- Chapter 12.3 Artificial intelligence for the detection of AOX functional markers -- Short review of current methodologies and improved tools -- Development of AOX centric tools -- Natural language processing for alignment to reference sequence and variant detection -- Towards a complete analyses pipeline -- Conclusions -- Chapter 12.4 Evolution of AOX genes across kingdoms and the challenge of classification -- Determining which organisms harbour AOX genes -- Classifying AOX genes -- Using sequence data to answer questions about AOX -- Conclusions - Addressing the challenges -- Chapter 13 Towards exploitation of AOX gene diversity in plant breeding -- Chapter 13.1 Functional marker development from AOX genes requires deep phenotyping and individualized diagnosis -- Conclusion -- Chapter 13.2 AOX gene diversity can affect DNA methylation and genome organization relevant for functional marker development -- DNA sequence interacts with DNA methylation -- DNA sequence interacts with genome rearrangements -- Conclusions and implications for FM development strategies -- Chapter 13.3 Gene technology applied for AOX functionality studies -- Novel functions of AOX revealed through transgenic technology -- Role of AOX during abiotic stress in different transgenic host systems -- Role of AOX during biotic stress response -- Limitations of transgenic technology -- Role of regulatory elements on AOX gene expression -- Future focus -- Concluding remarks -- Chapter 14 AOX goes risk: A way to application -- Chapter 14.1 AOX diversity studies stimulate novel tool development for phenotyping: calorespirometry -- Why calorespirometry?.

First results confirm the genotype discriminatory power of calorespirometry -- Perspectives -- Chapter 14.2 AOX gene diversity in arbuscular mycorrhizal fungi (AMF) products: a special challenge -- A link between plants and fungi: the mycorrhiza -- Some clues on the role of AOX in AMF -- Plants and AMF symbiosis upon stress -- Functional marker development in mycorrhiza - a genetic challenge -- Perspectives -- Chapter 14.3 Can AOX gene diversity mark herbal tea quality? A proposal -- AOX involvement -- Mycorrhizal symbiosis -- Future prospects -- Chapter 14.4 AOX in parasitic nematodes: a matter of lifestyle? -- Perspectives -- Chapter 14.5 Bacterial AOX: a provocative lack of interest! -- Perspectives -- General conclusion -- Acknowledgements -- References -- Section C Protocols -- Chapter 15 Technical protocol for mitochondria isolation for different studies -- Introduction -- General aspects of plant mitochondria isolation -- Specific protocol for isolation of sunflower mitochondria as a basic protocol -- Conclusions -- Acknowledgements -- References -- Chapter 16 Simultaneous isolation of root and leaf mitochondria from Arabidopsis -- Introduction -- Materials -- Method -- Discussion -- Acknowledgements -- Notes -- References -- Index -- Supplemental Images -- EULA.