Christine Helen Foyer and Hanma Zhang are based at the Institute of Integrative and Comparative Biology at the Faculty of Biological Sciences, University of Leeds, UK.

• Contributors. Preface.1 Nitrogen Assimilation and its Relevance to Crop Improvement (Peter J. Lea and Ben J. Miflin).1.1 Introduction.1.2 The assimilation of ammonia.1.3 Crop improvement through manipulating genes for nitrogen metabolism.1.4 Conclusions.Acknowledgements.References.2 Transcriptional Profiling Approaches for Studying Nitrogen.Use Efficiency (Malcolm J. Hawkesford and Jonathan R. Howarth).2.1 N-responsive genes.2.2 Nitrogen and crop production.2.3 Targeting NUtE processes in crop plants.2.4 Validating candidate genes by correlating gene expression with complex traits.2.5 Prospects.Acknowledgements.References.3 Energetics of Nitrogen Acquisition (Arnold J. Bloom).3.1 Availability of nitrogen in the environment.3.2 Curiosities.3.3 Mineral nitrogen.3.4 Plant growth and development.3.5 Future of plant nitrogen.References.4 Transport Systems for NO−3 and NH+4 (Mathilde Orsel and Anthony J. Miller).4.1 Nitrogen forms available to plants.4.2 Nitrogen transport steps and mechanisms.4.3 Arabidopsis as a model.4.4 Ammonium transporters.4.5 Nitrate transporters.4.6 Plastid transport.4.7 Conclusions and future.Acknowledgements.References.5 Nitric Oxide Synthase-Like Activities in Plants (Hideo Yamasaki, Ryuuichi D. Itoh, Jos´ee N. Bouchard, Ata Allah Dghim, Khurshida K. Hossain, Sushma Gurung and Michael F. Cohen).5.1 Introduction.5.2 Lifetime of nitric oxide.5.3 An overview of NO-dependent signalling systems.5.4 Mammalian-type NOS – ghost enzymes in plants.5.5 Comparative NO-related signalling.5.6 Algal nitric oxide synthesis – an echo from water.5.7 Nitric oxide synthase in plant-associated bacteria: its occurrence and functions.5.8 Prospects for NO-dependent signal transduction systems in plants.5.9 Concluding remarks.Acknowledgements.References.6 Nitrate Reductase and Nitric Oxide (Werner M. Kaiser, Elisabeth Planchet and Stefan R¨umer).6.1 Introduction.6.2 Structure, basic functions and regulation of NR.6.3 NR-dependent NO formation in vivo, measured as NO emission.6.4 NO production by NR in vitro.6.5 Physiological effects of NR-derived NO.6.6 Conclusions and open questions.Acknowledgements.References .7 Nitric Oxide Signalling in Plants: Cross-Talk With Ca2+,Protein Kinases and Reactive Oxygen Species (J´eremy Astier, Ang´elique Besson-Bard, Izabela Wawer, Claire Parent, Sumaira Rasul, Sylvain Jeandroz, James Dat and David Wendehenne).7.1 Basic concepts of NO signalling in animals.7.2 NO signalling in plants.7.3 Interplays between NO and ROS.7.4 Conclusion.Acknowledgements.References.8 Theanine: Its Occurrence and Metabolism in Tea (Ning Li and Jacquie de Silva).8.1 Introduction.8.2 Physiological benefits of theanine.8.3 Chemical properties and characteristics of theanine in tea.8.4 Role of theanine in tea.8.5 Metabolism of theanine in tea.8.6 Theanine synthase.8.7 Theanine hydrolase.8.8 The site of synthesis and transport of theanine in tea.8.9 Other enzymes capable of synthesizing theanine.8.10 Nitrogen uptake and transport.8.11 Nitrate transporters.8.12 Ammonium transporters.8.13 Nitrogen assimilation by GS (glutamine synthetase) – GOGAT (glutamate synthase).8.14 Biochemical properties of glutamine synthetase in plants.8.15 Gene families of glutamine synthetase.8.16 Regulation of plant glutamine synthetase.8.17 Glutamate synthase (GOGAT) in plants.8.18 Glutamate dehydrogenase in plants.8.19 Regulation of theanine – genotypic factors .8.20 Regulation of theanine – agronomic factors.8.21 Summary.Acknowledgements.References.9 Legume Nitrogen Fixation and Soil Abiotic Stress: From Physiology to Genomics and Beyond (Alex J. Valentine, Vagner A. Benedito and Yun Kang).9.1 Introduction.9.2 Legume nitrogen fixation under drought stress.9.3 Soil acidity.9.4 Phosphate deficiency.9.5 Legume biology is taking off.9.6 Beyond genomics: prospects for legume genetic breeding .References.10 Metabolomics Approaches to Advance Understanding of Nitrogen Assimilation and Carbon–Nitrogen Interactions (Aaron Fait, Agata Sienkiewicz-Porzucek and Alisdair R. Fernie).10.1 Introduction.10.2 Methods for analysing the plant metabolome.10.3 Uptake and assimilation of nitrate and ammonium.10.4 Cross-talk between N and secondary metabolism .10.5 Summary.References.11 Morphological Adaptations of Arabidopsis Roots to Nitrogen Supply (Hanma Zhang and David J. Pilbeam).11.1 Introduction.11.2 N-related morphological adaptations in Arabidopsis roots.11.3 The developmental context of N-related morphological adaptations in Arabidopsis roots.11.4 Mechanisms of N-related morphological adaptations in Arabidopsis roots.11.5 Role of NO3− transporters in N-related morphological adaptations.11.6 Biological significance of the localized stimulatory effect.11.7 Concluding remarks.References.12 Mitochondrial Redox State, Nitrogen Metabolism and Signalling (Christine H. Foyer).12.1 Introduction.12.2 The Nicotiana sylvestris mitochondrial cytoplasmic male sterile II mutant.12.3 Metabolite profiling in CMSII leaves reveals an N-rich phenotype.12.4 Mitochondrial redox cycling is a key player in determining the rate of nitrate assimilation.12.5 Regulation of pyridine nucleotide metabolism in CMSII leaves.12.6 CMSII is an N-sensing/signalling mutant.12.7 Regulation of gibberellin metabolism and signalling in the CMSII mutant.12.8 Concluding remarks.References.13 The Utilization of Nitrogen by Plants: A Whole Plant Perspective (David J. Pilbeam).13.1 Introduction.13.2 Nitrogen and plant growth.13.3 Nitrogen, biomass partitioning and yield.13.4 Partitioning of nitrogen into metabolites.13.5 Acquisition of nitrogen by plants.13.6 Plants, nitrogen and environment.13.7 Conclusions.References.Index.

Christine Helen Foyer and Hanma Zhang are based at the Institute of Integrative and Comparative Biology at the Faculty of Biological Sciences, University of Leeds, UK.

• Contributors. Preface.1 Nitrogen Assimilation and its Relevance to Crop Improvement (Peter J. Lea and Ben J. Miflin).1.1 Introduction.1.2 The assimilation of ammonia.1.3 Crop improvement through manipulating genes for nitrogen metabolism.1.4 Conclusions.Acknowledgements.References.2 Transcriptional Profiling Approaches for Studying Nitrogen.Use Efficiency (Malcolm J. Hawkesford and Jonathan R. Howarth).2.1 N-responsive genes.2.2 Nitrogen and crop production.2.3 Targeting NUtE processes in crop plants.2.4 Validating candidate genes by correlating gene expression with complex traits.2.5 Prospects.Acknowledgements.References.3 Energetics of Nitrogen Acquisition (Arnold J. Bloom).3.1 Availability of nitrogen in the environment.3.2 Curiosities.3.3 Mineral nitrogen.3.4 Plant growth and development.3.5 Future of plant nitrogen.References.4 Transport Systems for NO−3 and NH+4 (Mathilde Orsel and Anthony J. Miller).4.1 Nitrogen forms available to plants.4.2 Nitrogen transport steps and mechanisms.4.3 Arabidopsis as a model.4.4 Ammonium transporters.4.5 Nitrate transporters.4.6 Plastid transport.4.7 Conclusions and future.Acknowledgements.References.5 Nitric Oxide Synthase-Like Activities in Plants (Hideo Yamasaki, Ryuuichi D. Itoh, Jos´ee N. Bouchard, Ata Allah Dghim, Khurshida K. Hossain, Sushma Gurung and Michael F. Cohen).5.1 Introduction.5.2 Lifetime of nitric oxide.5.3 An overview of NO-dependent signalling systems.5.4 Mammalian-type NOS – ghost enzymes in plants.5.5 Comparative NO-related signalling.5.6 Algal nitric oxide synthesis – an echo from water.5.7 Nitric oxide synthase in plant-associated bacteria: its occurrence and functions.5.8 Prospects for NO-dependent signal transduction systems in plants.5.9 Concluding remarks.Acknowledgements.References.6 Nitrate Reductase and Nitric Oxide (Werner M. Kaiser, Elisabeth Planchet and Stefan R¨umer).6.1 Introduction.6.2 Structure, basic functions and regulation of NR.6.3 NR-dependent NO formation in vivo, measured as NO emission.6.4 NO production by NR in vitro.6.5 Physiological effects of NR-derived NO.6.6 Conclusions and open questions.Acknowledgements.References .7 Nitric Oxide Signalling in Plants: Cross-Talk With Ca2+,Protein Kinases and Reactive Oxygen Species (J´eremy Astier, Ang´elique Besson-Bard, Izabela Wawer, Claire Parent, Sumaira Rasul, Sylvain Jeandroz, James Dat and David Wendehenne).7.1 Basic concepts of NO signalling in animals.7.2 NO signalling in plants.7.3 Interplays between NO and ROS.7.4 Conclusion.Acknowledgements.References.8 Theanine: Its Occurrence and Metabolism in Tea (Ning Li and Jacquie de Silva).8.1 Introduction.8.2 Physiological benefits of theanine.8.3 Chemical properties and characteristics of theanine in tea.8.4 Role of theanine in tea.8.5 Metabolism of theanine in tea.8.6 Theanine synthase.8.7 Theanine hydrolase.8.8 The site of synthesis and transport of theanine in tea.8.9 Other enzymes capable of synthesizing theanine.8.10 Nitrogen uptake and transport.8.11 Nitrate transporters.8.12 Ammonium transporters.8.13 Nitrogen assimilation by GS (glutamine synthetase) – GOGAT (glutamate synthase).8.14 Biochemical properties of glutamine synthetase in plants.8.15 Gene families of glutamine synthetase.8.16 Regulation of plant glutamine synthetase.8.17 Glutamate synthase (GOGAT) in plants.8.18 Glutamate dehydrogenase in plants.8.19 Regulation of theanine – genotypic factors .8.20 Regulation of theanine – agronomic factors.8.21 Summary.Acknowledgements.References.9 Legume Nitrogen Fixation and Soil Abiotic Stress: From Physiology to Genomics and Beyond (Alex J. Valentine, Vagner A. Benedito and Yun Kang).9.1 Introduction.9.2 Legume nitrogen fixation under drought stress.9.3 Soil acidity.9.4 Phosphate deficiency.9.5 Legume biology is taking off.9.6 Beyond genomics: prospects for legume genetic breeding .References.10 Metabolomics Approaches to Advance Understanding of Nitrogen Assimilation and Carbon–Nitrogen Interactions (Aaron Fait, Agata Sienkiewicz-Porzucek and Alisdair R. Fernie).10.1 Introduction.10.2 Methods for analysing the plant metabolome.10.3 Uptake and assimilation of nitrate and ammonium.10.4 Cross-talk between N and secondary metabolism .10.5 Summary.References.11 Morphological Adaptations of Arabidopsis Roots to Nitrogen Supply (Hanma Zhang and David J. Pilbeam).11.1 Introduction.11.2 N-related morphological adaptations in Arabidopsis roots.11.3 The developmental context of N-related morphological adaptations in Arabidopsis roots.11.4 Mechanisms of N-related morphological adaptations in Arabidopsis roots.11.5 Role of NO3− transporters in N-related morphological adaptations.11.6 Biological significance of the localized stimulatory effect.11.7 Concluding remarks.References.12 Mitochondrial Redox State, Nitrogen Metabolism and Signalling (Christine H. Foyer).12.1 Introduction.12.2 The Nicotiana sylvestris mitochondrial cytoplasmic male sterile II mutant.12.3 Metabolite profiling in CMSII leaves reveals an N-rich phenotype.12.4 Mitochondrial redox cycling is a key player in determining the rate of nitrate assimilation.12.5 Regulation of pyridine nucleotide metabolism in CMSII leaves.12.6 CMSII is an N-sensing/signalling mutant.12.7 Regulation of gibberellin metabolism and signalling in the CMSII mutant.12.8 Concluding remarks.References.13 The Utilization of Nitrogen by Plants: A Whole Plant Perspective (David J. Pilbeam).13.1 Introduction.13.2 Nitrogen and plant growth.13.3 Nitrogen, biomass partitioning and yield.13.4 Partitioning of nitrogen into metabolites.13.5 Acquisition of nitrogen by plants.13.6 Plants, nitrogen and environment.13.7 Conclusions.References.Index.

Christine Helen Foyer and Hanma Zhang are based at the Institute of Integrative and Comparative Biology at the Faculty of Biological Sciences, University of Leeds, UK.

• Contributors. Preface.1 Nitrogen Assimilation and its Relevance to Crop Improvement (Peter J. Lea and Ben J. Miflin).1.1 Introduction.1.2 The assimilation of ammonia.1.3 Crop improvement through manipulating genes for nitrogen metabolism.1.4 Conclusions.Acknowledgements.References.2 Transcriptional Profiling Approaches for Studying Nitrogen.Use Efficiency (Malcolm J. Hawkesford and Jonathan R. Howarth).2.1 N-responsive genes.2.2 Nitrogen and crop production.2.3 Targeting NUtE processes in crop plants.2.4 Validating candidate genes by correlating gene expression with complex traits.2.5 Prospects.Acknowledgements.References.3 Energetics of Nitrogen Acquisition (Arnold J. Bloom).3.1 Availability of nitrogen in the environment.3.2 Curiosities.3.3 Mineral nitrogen.3.4 Plant growth and development.3.5 Future of plant nitrogen.References.4 Transport Systems for NO−3 and NH+4 (Mathilde Orsel and Anthony J. Miller).4.1 Nitrogen forms available to plants.4.2 Nitrogen transport steps and mechanisms.4.3 Arabidopsis as a model.4.4 Ammonium transporters.4.5 Nitrate transporters.4.6 Plastid transport.4.7 Conclusions and future.Acknowledgements.References.5 Nitric Oxide Synthase-Like Activities in Plants (Hideo Yamasaki, Ryuuichi D. Itoh, Jos´ee N. Bouchard, Ata Allah Dghim, Khurshida K. Hossain, Sushma Gurung and Michael F. Cohen).5.1 Introduction.5.2 Lifetime of nitric oxide.5.3 An overview of NO-dependent signalling systems.5.4 Mammalian-type NOS – ghost enzymes in plants.5.5 Comparative NO-related signalling.5.6 Algal nitric oxide synthesis – an echo from water.5.7 Nitric oxide synthase in plant-associated bacteria: its occurrence and functions.5.8 Prospects for NO-dependent signal transduction systems in plants.5.9 Concluding remarks.Acknowledgements.References.6 Nitrate Reductase and Nitric Oxide (Werner M. Kaiser, Elisabeth Planchet and Stefan R¨umer).6.1 Introduction.6.2 Structure, basic functions and regulation of NR.6.3 NR-dependent NO formation in vivo, measured as NO emission.6.4 NO production by NR in vitro.6.5 Physiological effects of NR-derived NO.6.6 Conclusions and open questions.Acknowledgements.References .7 Nitric Oxide Signalling in Plants: Cross-Talk With Ca2+,Protein Kinases and Reactive Oxygen Species (J´eremy Astier, Ang´elique Besson-Bard, Izabela Wawer, Claire Parent, Sumaira Rasul, Sylvain Jeandroz, James Dat and David Wendehenne).7.1 Basic concepts of NO signalling in animals.7.2 NO signalling in plants.7.3 Interplays between NO and ROS.7.4 Conclusion.Acknowledgements.References.8 Theanine: Its Occurrence and Metabolism in Tea (Ning Li and Jacquie de Silva).8.1 Introduction.8.2 Physiological benefits of theanine.8.3 Chemical properties and characteristics of theanine in tea.8.4 Role of theanine in tea.8.5 Metabolism of theanine in tea.8.6 Theanine synthase.8.7 Theanine hydrolase.8.8 The site of synthesis and transport of theanine in tea.8.9 Other enzymes capable of synthesizing theanine.8.10 Nitrogen uptake and transport.8.11 Nitrate transporters.8.12 Ammonium transporters.8.13 Nitrogen assimilation by GS (glutamine synthetase) – GOGAT (glutamate synthase).8.14 Biochemical properties of glutamine synthetase in plants.8.15 Gene families of glutamine synthetase.8.16 Regulation of plant glutamine synthetase.8.17 Glutamate synthase (GOGAT) in plants.8.18 Glutamate dehydrogenase in plants.8.19 Regulation of theanine – genotypic factors .8.20 Regulation of theanine – agronomic factors.8.21 Summary.Acknowledgements.References.9 Legume Nitrogen Fixation and Soil Abiotic Stress: From Physiology to Genomics and Beyond (Alex J. Valentine, Vagner A. Benedito and Yun Kang).9.1 Introduction.9.2 Legume nitrogen fixation under drought stress.9.3 Soil acidity.9.4 Phosphate deficiency.9.5 Legume biology is taking off.9.6 Beyond genomics: prospects for legume genetic breeding .References.10 Metabolomics Approaches to Advance Understanding of Nitrogen Assimilation and Carbon–Nitrogen Interactions (Aaron Fait, Agata Sienkiewicz-Porzucek and Alisdair R. Fernie).10.1 Introduction.10.2 Methods for analysing the plant metabolome.10.3 Uptake and assimilation of nitrate and ammonium.10.4 Cross-talk between N and secondary metabolism .10.5 Summary.References.11 Morphological Adaptations of Arabidopsis Roots to Nitrogen Supply (Hanma Zhang and David J. Pilbeam).11.1 Introduction.11.2 N-related morphological adaptations in Arabidopsis roots.11.3 The developmental context of N-related morphological adaptations in Arabidopsis roots.11.4 Mechanisms of N-related morphological adaptations in Arabidopsis roots.11.5 Role of NO3− transporters in N-related morphological adaptations.11.6 Biological significance of the localized stimulatory effect.11.7 Concluding remarks.References.12 Mitochondrial Redox State, Nitrogen Metabolism and Signalling (Christine H. Foyer).12.1 Introduction.12.2 The Nicotiana sylvestris mitochondrial cytoplasmic male sterile II mutant.12.3 Metabolite profiling in CMSII leaves reveals an N-rich phenotype.12.4 Mitochondrial redox cycling is a key player in determining the rate of nitrate assimilation.12.5 Regulation of pyridine nucleotide metabolism in CMSII leaves.12.6 CMSII is an N-sensing/signalling mutant.12.7 Regulation of gibberellin metabolism and signalling in the CMSII mutant.12.8 Concluding remarks.References.13 The Utilization of Nitrogen by Plants: A Whole Plant Perspective (David J. Pilbeam).13.1 Introduction.13.2 Nitrogen and plant growth.13.3 Nitrogen, biomass partitioning and yield.13.4 Partitioning of nitrogen into metabolites.13.5 Acquisition of nitrogen by plants.13.6 Plants, nitrogen and environment.13.7 Conclusions.References.Index.